A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Ribonucleic acid that makes up the genetic material of viruses.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Viruses whose genetic material is RNA.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
The processes of RNA tertiary structure formation.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
A family of proteins that promote unwinding of RNA during splicing and translation.
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
RNA present in neoplastic tissue.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Established cell cultures that have the potential to propagate indefinitely.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The rate dynamics in chemical or physical systems.
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Viruses parasitic on plants higher than bacteria.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Deoxyribonucleic acid that makes up the genetic material of viruses.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.
The functional hereditary units of VIRUSES.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.
The sum of the weight of all the atoms in a molecule.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.
A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.
Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Viruses which produce a mottled appearance of the leaves of plants.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).
The relationships of groups of organisms as reflected by their genetic makeup.
A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.
Proteins prepared by recombinant DNA technology.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A cell line derived from cultured tumor cells.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Proteins found in any species of bacterium.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.
A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.
Use for nucleic acid precursors in general or for which there is no specific heading.
The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
Deletion of sequences of nucleic acids from the genetic material of an individual.
A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.
Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
Proteins obtained from ESCHERICHIA COLI.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Elements of limited time intervals, contributing to particular results or situations.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.
A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

Ribozymes, genomics and therapeutics. (1/2154)

Genome-sequencing projects are proceeding at a rapid pace and determining the function of open reading frames is the next great challenge. Ribozymes with site-specific cleaving activity could aid greatly in this process. High-throughput screening methods to identify optimal target sites for ribozyme cleavage will provide tools for functional genomics as well as therapeutic reagents.  (+info)

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (2/2154)

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.  (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (3/2154)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.  (+info)

High level inhibition of HIV replication with combination RNA decoys expressed from an HIV-Tat inducible vector. (4/2154)

Intracellular immunization, an antiviral gene therapy approach based on the introduction of DNA into cells to stably express molecules for the inhibition of viral gene expression and replication, has been suggested for inhibition of HIV infection. Since the Tat and Rev proteins play a critical role in HIV regulation, RNA decoys and ribozymes of these sequences have potential as therapeutic molecular inhibitors. In the present study, we have generated several anti-HIV molecules; a tat-ribozyme, RRE, RWZ6 and TAR decoys and combinations of decoys, and tested them for inhibition of HIV-1 replication in vitro. We used T cell specific CD2 gene elements and regulatory the HIV inducible promoter to direct high level expression and a 3' UTR sequence for mRNA stabilization. We show that HIV replication was most strongly inhibited with the combination TAR + RRE decoy when compared with the single decoys or the tat-ribozyme. We also show that the Tat-inducible HIV promoter directs a higher level of steady-state transcription of decoys and inhibitors and that higher levels of expression directly relate to increased levels of inhibition of HIV infection. Furthermore, a stabilization of the 3' end of TAR + RRE inhibitor transcripts using a beta-globin 3' UTR sequence leads to an additional 15-fold increase in steady-state RNA levels. This cassette when used to express the best combination decoy inhibitor TAR + RRE, yields high level HIV inhibition for greater than 3 weeks. Taken together, both optimization for high level expression of molecular inhibitors and use of combinations of inhibitors suggest better therapeutic application in limiting the spread of HIV.  (+info)

Rpp14 and Rpp29, two protein subunits of human ribonuclease P. (5/2154)

In HeLa cells, the tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. Five of these proteins (hPop1p, Rpp20, Rpp30, Rpp38, and Rpp40) have been partially characterized. Here we report on the cDNA cloning and immunobiochemical analysis of Rpp14 and Rpp29. Polyclonal rabbit antibodies raised against recombinant Rpp14 and Rpp29 recognize their corresponding antigens in HeLa cells and precipitate catalytically active RNase P. Rpp29 shows 23% identity with Pop4p, a subunit of yeast nuclear RNase P and the ribosomal RNA processing enzyme RNase MRP. Rpp14, by contrast, exhibits no significant homology to any known yeast gene. Thus, human RNase P differs in the details of its protein composition, and perhaps in the functions of some of these proteins, from the yeast enzyme.  (+info)

Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme. (6/2154)

The 3' splice site of group I introns is defined, in part, by base pairs between the intron core and residues just upstream of the splice site, referred to as P9.0. We have studied the specificity imparted by P9.0 using the well-characterized L-21 Scal ribozyme from Tetrahymena by adding residues to the 5' end of the guanosine (G) that functions as a nucleophile in the oligonucleotide cleavage reaction: CCCUCUA5 (S) + NNG <--> CCCUCU + NNGA5. UCG, predicted to form two base pairs in P9.0, reacts with a (kcat/KM) value approximately 10-fold greater than G, consistent with previous results. Altering the bases that form P9.0 in both the trinucleotide G analog and the ribozyme affects the specificity in the manner predicted for base-pairing. Strikingly, oligonucleotides incapable of forming P9.0 react approximately 10-fold more slowly than G, for which the mispaired residues are simply absent. The observed specificity is consistent with a model in which the P9.0 site is sterically restricted such that an energetic penalty, not present for G, must be overcome by G analogs with 5' extensions. Shortening S to include only one residue 3' of the cleavage site (CCCUCUA) eliminates this penalty and uniformly enhances the reactions of matched and mismatched oligonucleotides relative to guanosine. These results suggest that the 3' portion of S occupies the P9.0 site, sterically interfering with binding of G analogs with 5' extensions. Similar steric effects may more generally allow structured RNAs to avoid formation of incorrect contacts, thereby helping to avoid kinetic traps during folding and enhancing cooperative formation of the correct structure.  (+info)

The influence of junction conformation on RNA cleavage by the hairpin ribozyme in its natural junction form. (7/2154)

In the natural form of the hairpin ribozyme the two loop-carrying duplexes that comprise the majority of essential bases for activity form two adjacent helical arms of a four-way RNA junction. In the present work we have manipulated the sequence around the junction in a way known to perturb the global folding properties. We find that replacement of the junction by a different sequence that has the same conformational properties as the natural sequence gives closely similar reaction rate and Arrhenius activation energy for the substrate cleavage reaction. By comparison, rotation of the natural sequence in order to alter the three-dimensional folding of the ribozyme leads to a tenfold reduction in the kinetics of cleavage. Replacement with the U1 four-way junction that is resistant to rotation into the antiparallel structure required to allow interaction between the loops also gives a tenfold reduction in cleavage rate. The results indicate that the conformation of the junction has a major influence on the catalytic activity of the ribozyme. The results are all consistent with a role for the junction in the provision of a framework by which the loops are presented for interaction in order to create the active form of the ribozyme.  (+info)

Mutational analysis of the antigenomic trans-acting delta ribozyme: the alterations of the middle nucleotides located on the P1 stem. (8/2154)

Our previous report on delta ribozyme cleavage using a trans -acting antigenomic delta ribozyme and a collection of short substrates showed that the middle nucleotides of the P1 stem, the substrate binding site, are essential for the cleavage activity. Here we have further investigated the effect of alterations in the P1 stem on the kinetic and thermodynamic parameters of delta ribozyme cleavage using various ribozyme variants carrying single base mutations at putative positions reported. The kinetic and thermodynamic values obtained in mutational studies of the two middle nucleotides of the P1 stem suggest that the binding and active sites of the delta ribozyme are uniquely formed. Firstly, the substrate and the ribozyme are engaged in the formation of a helix, known as the P1 stem, which may contain a weak hydrogen bond(s) or a bulge. Secondly, a tertiary interaction involving the base moieties in the middle of the P1 stem likely plays a role in defining the chemical environment. As a con-sequence, the active site might form simultaneously or subsequently to the binding site during later steps of the pathway.  (+info)

TY - JOUR. T1 - Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. AU - Soukup, Garrett. AU - Breaker, Ronald R.. PY - 1999/7/15. Y1 - 1999/7/15. N2 - Background: Ribozymes can function as allosteric enzymes that undergo a conformational change upon ligand binding to a site other than the active site. Although allosteric ribozymes are not known to exist in nature, nucleic acids appear to be well suited to display such advanced forms of kinetic control. Current research explores the mechanisms of allosteric ribozymes as well as the strategies and methods that can be used to create new controllable enzymes. Results: In this study, we exploit the modular nature of certain functional RNAs to engineer allosteric ribozymes that are activated by flavin mononucleotide (FMN) or theophylline. By joining an FMN- or theophylline-binding domain to a hammerhead ribozyme by different stem II elements, we have identified a minimal connective bridge comprised of a G·U ...
A hammerhead ribozyme was demonstrated to be a metalloenzyme. By controlling the metal-binding ability of the hammerhead ribozyme in the presence or absence of a specific sequence of interest, we engineered an allosterically controllable ribozyme, designated the maxizyme. Hybrid ribozymes were then constructed by coupling the site-specific cleavage activity of a hammerhead ribozyme with the unwinding activity of an endogenous RNA helicase. This leads to extremely efficient cleavage of target mRNA, not only in vitro, but also in vivo, and eliminates one of the major problems arising in the application of ribozymes for cleavage of mRNA in vivo: that many target sites on the RNA were previously inaccessible to cleavage owing to secondary and/or tertiary structure formation. Since hybrid ribozymes can efficiently attack target sites within mRNA, libraries were made of hybrid ribozymes with randomized binding arms, which were then introduced into cells. This procedure made it possible to readily ...
View Notes - Lecture8 from BIOC 100A at UCSC. 25 26 The hammerhead ribozyme (plant virus) Martick & Scott, Cell 2006 27 Group I intron ribozyme Golden et al, and cech Science (1998) 28 Acid-Base
Ribozyme-Catalyzed Transcription of an Active Ribozyme Aniela Wochner, James Attwater, Alan Coulson, and Philipp Holliger* Science 8 April 2011: Vol. 332 no. 6026 pp. 209-212 doi: 10.1126/science.1200752 For molecular biology lovers! Michael Yarus offer a very nice presentation of the paper: Climbing in 190 Dimensions doi: 10.1126/science.1205379A critical event in the origin of life is…
Despite great progress in the treatment of AIDS, the Human Immunodeficiency Virus type I (HIV-1) remains one of the major concerns as a human pathogen. One of the therapeutic strategies against viral infections is the application of catalytic ribonucleic acids (ribozymes) that can significantly reduce expression of a target gene by site-specific hydrolysis of its mRNA. In this paper we report a study on the activity of several variants of hammerhead ribozymes targeting a conserved region within mRNA encoding HIV-1 envelope glycoprotein gp41. Based on the data from in vitro assays and gene silencing in the cultured cells, we propose a new hammerhead ribozyme targeting the gp41-encoding sequence that can be potentially used as a therapeutic agent in AIDS treatment. Moreover, we demonstrate that the hydrolytic activity of the ribozyme in the intracellular environment can not be inferred solely from the results of the in vitro experiments. ...
Hammerhead ribozyme, molecular model. Ribozymes are RNA (ribonucleic acid) molecules that catalyse certain biochemical reactions. Until their discovery in the 1980s, it was thought only proteins had this ability. Most ribozymes catalyse their own cleavage, or that of other RNAs, but some also have roles within ribosomes, the location of protein synthesis. - Stock Image F009/6228
The discovery that RNA can act as a biological catalyst, as well as a genetic molecule, indicated that there was a time when biological reactions were catalysed in the absence of protein-based enzymes. It also provided the platform to develop those catalytic RNA molecules, called ribozymes, as trans -acting tools for RNA manipulation. Viral diseases or diseases due to genetic lesions could be targeted therapeutically through ribozymes, provided that the sequence of the genetic information involved in the disease is known. The hammerhead ribozyme, one of the smallest ribozymes identified, is able to induce site-specific cleavage of RNA, with ribozyme and substrate being two different oligoribonucleotides with regions of complementarity. Its ability to down-regulate gene expression through RNA cleavage makes the hammerhead ribozyme a candidate for genetic therapy. This could be particularly useful for dominant genetic diseases by down-regulating the expression of mutant alleles. The group I intron
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Purpose: To investigate enzymatic performance of a proven hammerhead ribozyme (hhRz) against human rod opsin (hRHO) in a smaller supportive RNA scaffold in a mutation-independent gene silencing therapeutic strategy for autosomal dominant retinitis pigmentosa. VAI RNA of chicken embryonic lethal orphan (CELO) virus was chosen as a smaller (91 nt) scaffold for the hhRz (725 HH16) (prior human VAI scaffolds ,160 nt). Smaller chimeras allow 3D RNA algorithms for structural design and biophysical investigation of hhRz structure/function performance.. Methods: CELO-VAI scaffold, designed using RNAStructure, was PCR constructed with partially overlapping DNA primers, then directionally ligated into pNEB193-T7. hhRz cDNA or control sequence was cloned into an adapter placed at a unique CELO-VAI restriction site. Target hRHO fragment cDNA (510 nt RNA) containing the hhRz cleavage site was cloned into pBlueScript. Transcription with T7 RNA polymerase generated chimeric CELO-VAI-hhRzs and target RNA to ...
TY - JOUR. T1 - Role of Divalent Metal Ions in the Hammerhead RNA Cleavage Reaction. AU - Dahm, Sue Ann C. AU - Uhlenbeck, Olke C.. PY - 1991/10/1. Y1 - 1991/10/1. N2 - A hammerhead self-cleaving domain composed of two oligoribonucleotides was used to study the role of divalent metal ions in the cleavage reaction. Cleavage rates were measured as a function of MgCl2, MnCl2, and CaCl2 concentration in the absence or presence of spermine. In the presence of spermine, the rate vs metal ion concentration curves are broader, and lower concentrations of divalent ions are necessary for catalytic activity. This suggests that spermine can promote proper folding of the hammerhead and one or more divalent ions are required for the reaction. Six additional divalent ions were tested for their ability to support hammerhead cleavage. In the absence of spermine, rapid cleavage was observed with Co2+ while very slow cleavage occurred with Sr2+ and Ba2+. No detectable specific cleavage was observed with Cd2+, ...
We explore RNA catalysis to learn about the catalytic potential of RNA and to decipher what is fundamental to all biological catalysts through comparison with protein enzyme catalysis. These studies also define the unique properties of RNA and proteins lead to catalytic and behavioral distinctions. The fundamental properties and behaviors of RNA molecules that we uncover teach us about how the potential function of RNA early in evolution and about the function of RNA molecules in modern-day biology. This knowledge may also be applied as RNA is co-opted for medical, technological and industrial applications.. Energy from binding interactions can be used to facilitate reactions of bond substrates, a fundamental precept of enzymology posited by Jencks for protein enzymes and demonstrated in our studies of RNA enzymes.. We currently focus on the group I ribozyme, the most well-studied catalytic RNA in both structure and function. We harness previous studies, including multiple crystal structures, a ...
We explore RNA catalysis to learn about the catalytic potential of RNA and to decipher what is fundamental to all biological catalysts through comparison with protein enzyme catalysis. These studies also define the unique properties of RNA and proteins lead to catalytic and behavioral distinctions. The fundamental properties and behaviors of RNA molecules that we uncover teach us about how the potential function of RNA early in evolution and about the function of RNA molecules in modern-day biology. This knowledge may also be applied as RNA is co-opted for medical, technological and industrial applications.. Energy from binding interactions can be used to facilitate reactions of bond substrates, a fundamental precept of enzymology posited by Jencks for protein enzymes and demonstrated in our studies of RNA enzymes.. We currently focus on the group I ribozyme, the most well-studied catalytic RNA in both structure and function. We harness previous studies, including multiple crystal structures, a ...
Since the discovery of catalytic RNA molecules (ribozymes), intense research has been devoted to understand their structure and activity. Among RNA molecules, the large ribozymes, namely group I and group II introns and RNase P, are of special importance. The first two ribozymes are known for their ability to perform self-splicing while RNase P is responsible for the 5′-end maturation of tRNA in bacteria, archea, and eukaryotes. All three groups of ribozymes show a significant requirement for metal ions in order to establish the active tertiary structure that enables catalysis. The primary role of both monovalent and divalent metal ions is to screen the negative charge associated with the phosphate sugar backbone, but the metal ions also play an active role in catalysis. Biochemical and biophysical investigations, supported by recent findings from X-ray crystal structures, allow clarifying and rationalizing both the structural and catalytic roles of metal ions in large ribozymes. In ...
RNA enzymes or ribozymes can act as endoribonucleases, catalyzing the cleavage of RNA molecules with a sequence specificity of cleavage greater than that of known ribonucleases and approaching that of the DNA restriction endonucleases, thus serving as RNA sequence specific endoribonucleases. An example is a shortened form of the self-splicing ribonsomal RNA intervening sequence of Tetrahymena (L-19 IVS RNA). Site-specific mutagenesis of the enzyme active site of the L-19 IVS RNA alters the substrate sequence specificity in a predictable manner, allowing a set of sequence-specific endoribonucleases to be synthesized. Varying conditions allow the ribozyme to act as a polymerase (nucleotidyltransferase), a dephosphorylase (acid phosphatase or phosphotransferase) or a sequence-specific endoribonuclease.
View Cell Theory from BIOLOGY MCB2010 at Broward College. • Genetic material -> catalyst (RNA catalyst not regulated. Protein catalyst can be regulated.) • Metabolism (get energy -> grow
3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA.
服部良一,児嶋長次郎,リジン残基13Cメチル化NMR法による相互作用解析と構造変化の検出,生物物理 56, 288-289 (2016). DOI: 10.2142/biophys.56.288 田中好幸,DNA分子を利用した水銀除染法及び機能性核酸構造解析法の開発研究,The ANNALS of Intelligent Cosmos Academic Foundation 14, 9-12 (2010). Yoshiyuki Tanaka and Akira Ono, Structural Studies on MercuryII-mediated T-T Base-pair with NMR Spectroscopy (Chapter 16), In Nick Hadjiliadis and Einar Sletten Eds., Metal Complexes - DNA Interactions, John Wiley & Sons, West Sussex, UK (2009). DOI: 10.1002/9781444312089 Ikumi kawahara, Kaichiro Haruta, Chojiro Kojima, and Yoshiyuki Tanaka, NMR studies of HAC1 mRNA, Nucleic Acids Symposium Series 53, 269-270 (2009). Hisaaki Tateoka, Ikumi Kawahara, Satomi Hasegawa, Kaichiro Haruta, Yoshinori Kondo, Chojiro Kojima, and Yoshiyuki Tanaka, Preparations of hammerhead ribozymes for investigations of their cleavable sequences, Nucleic Acids ...
2MTJ: Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.
Researchers: Andrew Babiskin, Travis Bayer, Chase Beisel, Stephanie Culler, Katie Galloway, Kevin Hoff, Maung Nyan Win We are exploring the design strategies for constructing molecular switches that act in vivo as both biosensors and ligand-controlled regulators of gene expression in bacteria, yeast, and mammalian cell culture. Much of our effort is focused on the design of nucleic acid-based molecular sensors, although the design of some protein-based sensors is being explored as well. In the area of trans-acting molecular switches, we are exploring the design of sensors that act through diverse gene regulation mechanisms such as the RNA interference (RNAi) pathway, ribozyme-based cleavage, and the antisense pathway. In the area of cis-acting molecular switches, we are exploring the design of sensors that act through regulatory mechanisms such as alternative splicing, RNase III cleavage, ribozyme-based cleavage, and internal ribosome entry site (IRES) activity. In order to effectively monitor ...
The hammerhead ribozyme is a small RNA motif that catalyzes the cleavage and ligation of RNA. The well-studied minimal hammerhead… Expand ...
The second extended Meyer quote youve dug up is just awful. In addition to the whole protein-dominated ribosome, Meyer claims that 1) peptidyl transferase ribozymes are made of ribosomal RNA and 2) that these ribozymes are quite limited because they require another catalyst. (1) is wrong - the Zhang and Cech papers he cites _evolved_ ribozymes from random sequence, they are not free-standing ribosomal RNA. With (2) its hard to tell what Meyer was even thinking: my best guess is that the other catalyst hes referring to is magnesium, which is the only thing that could be considered another catalyst mentioned in the Zhang and Cech paper. If so, thats absurd - first, they dont even show that magnesium is playing a catalytic role, it may just be required for ribozyme folding (as it is for proper folding and function of the protein dominated ribosome); second, even if it is a cofactor involved directly in catalysis, that is incredibly common, not a weakness of the ribozyme. Many enzymes, ...
Enzyme. Enzymes ( /ˈɛnzaɪmz/) are large biological molecules responsible for the thousands of chemical interconversions that sustain life. They are highly selective catalysts, greatly accelerating both the rate and specificity of metabolic reactions, from the digestion of food to the synthesis of DNA. Most enzymes are proteins, although some catalytic RNA molecules have been identified. Enzymes adopt a specific three-dimensional structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ion) cofactors to assist in catalysis.. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that ...
In this paper we outline therapeutic uses of ribonucleic enzymes (ribozymes) and small interfering RNA (siRNA). The discovery of ribozymes is described and the structure of hammerhead ribozymes and their mechanism of catalysis is explained. Application of ribozymes as antiviral agents for the treatment of cancer as well as viral infections is described. The article also describes the history and discovery of siRNA and explains the mechanism of its use as an antiviral agent. Ongoing clinical trials for si RNA-mediated therapeutical approaches are listed. ...
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate. . ...
As ribozymes picked up these abiotic peptides, the pool of these useful short peptides started to dwindle. There wouldnt be enough, so there will be a competitive situation, which would reward those ribozymes that could string up amino acids by themselves, says Lupas. If your ribozyme-based organism develops the ability to ligate amino acids, it will have an advantage over others because it doesnt have to scavenge for the peptides. This would lead to selection of peptides that have desirable functions. Once those functions were in place, the peptide could grow larger and more complex and begin to adopt folds and cavities.. Lupas thinks that function had to precede structure, because producing a complex structure is an incredibly hard job. After 3.5 billion years of evolution, nature still has a substantial folding problem, he states. He points out that, under normal circumstances, about one-third of a modern cells resources is devoted to protein quality control and turnover. Were not ...
The broad goals of this proposal are to provide a molecular-level understanding of how RNA enzymes (ribozymes) catalyze chemical reactions. We are studying a se...
J.Mol.Biol. 2000; 297:309-319 PDF supplementary information. Expanding the structural and functional diversity of RNA: analog uridine triphosphates as candidates for in vitro selection of nucleic acids. Vaish NK, Fraley AW, Szostak JW, McLaughlin LW. Nucleic Acids Res. 2000 Sep 1;28(17):3316-22. PDF. Ribozyme-catalyzed tRNA aminoacylation. Lee N, Bessho Y, Wei K, Szostak JW, Suga H. Nat Struct Biol. 2000 Jan;7(1):28-33. PDF Optimized synthesis of RNA-protein fusions for in vitro protein selection. Liu R, Barrick JE, Szostak JW, Roberts RW. Methods Enzymol. 2000;318:268-93. 1999. In vitro Selection of functional nucleic acids. Wilson DW, Szostak JW. Ann. Rev. Biochem., 1999; 68:611-648. PDF 1998. In vitro selection and directed evolution. Szostak JW. 1998 Harvey Lecture Series. 1997-98;93:95-118. Review. Isolation and characterization of fluorophore-binding RNA aptamers. Holeman LA, Robinson SL, Szostak JW and Wilson C. Folding & Design, 1998; 3:423-431. Isolation of a fluorophore-specific DNA ...
The problem of the start of biological evolution in the ancient RNA world is considered. It is postulated that the appearance of catalytic RNAs - ribozymes - via spontaneous cis- and trans-rearrangeme
The VS ribozyme is one of the nucleolytic ribozymes, that catalyse the breakage of the phosphodiester bond at a particular site by a transesterification reaction in which the 2?-oxygen carries out a nucleophilic attack on the 3?-phosphorus. The reaction o
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Ribozymes are ideal model systems for the vast number of non-protein coding RNAs found in all domains of life, since they have an easily detectable biological f...
IMPACT™ is a novel protein purification system using the inducible self-cleavage activity of a protein splicing element to separate the target protein and tag.
W rzs występują zaburzenia nabytej odpowiedzi immunologicznej przejawiające się autoreaktywnością limfocytów, gromadzeniem komórek pamięci, nadczynnością limfocytów B, preferencyjnym różnicowaniem limfocytów Th17 i upośledzeniem czynnościowym limfocytów Treg. W warunkach prawidłowych odpowiedź nabyta rozwija się w szpiku i obwodowych narządach limfatycznych (węzły chłonne, śledziona). Natomiast w przypadku rzs również w ekotopowej tkance limfatycznej. W rzs odpowiedź nabyta jest inicjowana przez czynniki genetyczne i środowiskowe. Głównym genetycznym czynnikiem ryzyka rozwoju rzs są geny kodujące cząsteczki HLA-DR ze „wspólnym epitopem (DRSE+). Spośród wielu środowiskowych czynników ryzyka rozwoju rzs najlepiej udokumentowany jest wpływ palenia tytoniu, zwłaszcza u pacjentów, którzy w haplotypie mają cząsteczki HLA-DR zawierające „wspólny epitop i wytwarzają przeciwciała swoiste dla cytrulinowanych peptydów. Najnowsze doniesienia ...
Researchers at University of Texas have identify the process through which the double stranded RNA is remodeled inside cells in both their normal and disease states.
Hammann and Westhof conclude that a combination of improved sequence searching algorithms and more functional screening assays is required to help identify novel classes of ribozymes. One approach they did not mention is sequence comparisons between different species. I may be biased by my work in the field of gene promoter evolution, but I would expect that comparing the sequences of known ribozymes in different species would yield some interesting insights into the general patterns of ribozyme conservation throughout evolution. Novel ribozymes could then conceivably be identified by screening genomes for regions of unknown function that display similar patterns of sequence conservation. ...
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Two modular elements (P5abc and ΔP5) in the Tetrahymena group I ribozyme can be separated physically to generate a two-piece ribozyme derivative consisting of a separately prepared P5abc (P5 RNA) and the rest of the intron (ΔP5 RNA). Molecular recognition in the interface assembling P5 RNA and ΔP5 R …
For the development of specific and effective basic genetic materials to inhibit replication of hepatitis C virus (HCV), HCV genome-targeting trans-splicing aptazyme, which activity is allosterically regulated by a specific ligand, was developed. The aptazyme was designed to be comprised of sequence of RNA aptamer to the ligand, communication module sequence which can transfer structural transition for inducing ribozyme activity upon binding the ligand to the aptamer, and trans-splicing ribozyme targeting +199 nt of HCV IRES. Especially, when the aptamer and the communication module was inserted at both P6 and P8 catalytic domain of the specific ribozyme, allosteric activity of the aptazyme was the most induced. The aptazyme was shown to induce activity of trans-splicing reaction specifically and efficiently only in the presence of the specific ligand, but neither in the absence of any ligand nor in the presence of control ligand. This aptazyme can be used as a specific and effective genetic ...
Large complex RNAs, like the Tetrahymena ribozyme, tend to have complex kinetic folding pathways with multiple intermediates. Are these intermediates required for folding, or are they the result of kinetic traps? One way to discriminate between these possibilities is to vary folding conditions such as temperature or ion concentration or to make mutations that may destabilize the folding intermediates and to see how these changes affect folding rates. In the present study, the effects of [Mg2+] and temperature on the rates of P3-P7 formation (kP3-P7) and folding to the catalytically active structure (koverall) were compared for the wild-type Tetrahymena ribozyme and the A183U mutant ribozyme. Reducing the [Mg2+] leads to an increase in the value of koverall and reveals the presence of an additional kinetic trap on the folding pathway of both ribozymes. Interestingly, this trap is stabilized by high [Mg2+]. Recent studies with the self-splicing Tetrahymena group I intron pre-RNA, from which the ...
BACKGROUND: Reverse genetics systems enable the manipulation of viral genomes and therefore serve as robust reverse genetic tools to study RNA viruses. A DNA-launched rescue system initiates the transcription of viral genomic cDNA from eukaryotic promoter in transfected cells, generating homogenous RNA transcripts in vitro and thus enhancing virus rescue efficiency. As one of the hazardous pathogens to ducklings, the current knowledge of the pathogenesis of duck astrovirus type 1 (DAstV-1) is limited. The construction of a DNA-launched rescue system can help to accelerate the study of the virus pathogenesis. However, there is no report of such a system for DAstV-1. METHODS: In this study, a DNA-launched infectious clone of DAstV-1 was constructed from a cDNA plasmid, which contains a viral cDNA sequence flanked by hammerhead ribozyme (HamRz) and a hepatitis delta virus ribozyme (HdvRz) sequence at both terminals of the viral genome. A silent nucleotide mutation creating a Bgl II site in the ORF2 ...
Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical ...
All life on Earth uses three integrated molecular systems in which genetic information contained in DNA base sequences is transmitted to ribosomes by RNA and a genetic code, then translated into the amino acid sequences of structural and catalytic proteins. Therefore, the most important point for understanding the origin of life is to determine how such systems could emerge from random processes on the early Earth. In this review, two alternatives are compared: the RNA world hypothesis and the [GADV]-protein world hypothesis. [GADV] refers to four amino acids, Gly [G], Ala [A], Asp [D] and Val [V] that are conserved in the amino acid sequences of many common proteins. Here I will argue that the origins of the three primary processes required for life to begin can be better explained by the GADV hypothesis than the RNA world hypothesis. The GADV hypothesis also incorporates a conversion process by which random polymers can evolve into proteins with ordered sequences.
Ribozymes are currently a centerpiece in the ongoing debate on the origin of life. The ability of some RNA polymerizing ribozymes to synthesize functional products without the need for a DNA template[16] (they use an RNA template instead) makes RNA an attractive candidate for hypothetical primitive biochemistry. There is a growing body of chemical, molecular biological, and geological evidence which supports this hypothesis[17][18][19][20][21][22][23]. Additionally, the recent development of a self-replicating ribozyme derived from a viral ribozyme[24][25], demonstrates that self-replicating RNAs can exist. However, the evidence remains largely circumstantial as nothing conclusive has been found thus far and, even among biochemists, the hypothesis does have its detractors[26]. This hypothesis that life originated from RNA and ribonucleoprotein based biochemistry is called the RNA world hypothesis. It is considered by many biochemists to be the most plausible current hypothesis for the origin of ...
HRP catalyzes the decomposition of hydrogen peroxide in solution causing the oxidation of a number of substrates.Enzymes accelerate, or catalyze, chemical reactions, and they are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules. Choose specific enzymes for cleaving bonds, removing genomic DNA from RNA preparations, for producing fragments of proteins, or for use in ion exchange chromatography. Enzymes are used in the chemical industry and other industrial applications when extremely specific catalysts are required.
Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules. Enzymes are principally classified and named according to the reaction they catalyse. The chemical reaction catalysed is the specific property that distinguishes one enzyme from another, and it is logical to use it as the basis for the classification and naming of enzymes. The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) classifies enzymes into families, using a four number code, on the basis of the reactions they catalyse. In this section you will find a series of brief reviews about various enzyme subfamilies, based on their functional activity in enzymology or characteristics as many drugs targets. ...
The mechanism of RNA cleavage by the hammerhead ribozyme and the sequence specific recognition of RNA by bacteriophage coat proteins will be studied by biochemical and biophysical methods. The two projects were chosen because they allow a detailed study of RNA function in a situation where the biologically relevant activity is contained with an RNA sufficiently small that variants can easily be synthesized by chemical or embryological methods. The availability of several X-ray crystal structures and quantitative assays for both systems permits the design of sophisticated experiments to refine our concepts of how RNA works. Experiments on the hammerhead will focus on obtaining additional evidence that the X-ray structure and the major solution conformation are not in a catalytically active conformation. A nucleotide analogue interference approach will be used to identify essential functional groups and attempt to identify revertants of hammerhead base mutations. Hammerhead modifications that ...
Two trajectories are possible in converting a GC base pair to an AU base pair. One of them passes through a GU base pair intermediate, the other through an AC mismatch intermediate (see figure 4; electronic supplementary material, figure S3). In our data, a ribozyme with the GU intermediate is always more active than that with the AC intermediate (from +1.4 to +22.7%; average = +10.3%). This confirms predictions of the relative effects of these two intermediates based on the geometry of base pairs [32], experimental measurements [33] and bioinformatic analysis of tRNA evolution [34]. Our data support a continuous ridge or neutral network model (see Landscapes caused by a base pair switch in Supporting Information, electronic supplementary material) of compensatory evolution in RNA secondary structure, because in our experiments, the GU intermediate shows a significant decrease in fitness only in a single instance, and in this instance the base pair switch is not compensatory but ...
Synthetic catalytic RNAs, i.e. ribozyme, including a hairpin portion, binding sites for binding to a human papilloma virus after viral base 419 and 434, respectively, and cleavage sites for cleaving the virus at the binding sites have been constructed.
488D: Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
Cells must have preceded by simpler chemical systems (protocells) that had the capacity of a spontaneous self-assembly process and the ability to confine chemical reaction networks together with a form of information. The presence of lipid molecules in the early Earth conditions is sufficient to ensure the occurrence of spontaneous self-assembly processes, not defined by genetic information, but related to their chemical amphiphilic nature. Ribozymes are plausible molecules for early life, being the first small polynucleotides made up of random oligomers or formed by non-enzymatic template copying. Compartmentalization represents a strategy for the evolution of ribozymes; the attachment of ribozymes to surfaces, such as formed by lipid micellar aggregates may be particular relevant if the surface itself catalyzes RNA polymerization.It is conceivable that the transition from pre-biotic molecular aggregates to cellular life required the coevolution of the RNA world, capable of synthesizing ...
Tumour cells can develop a lot of resistance mechanisms against cytostatic drugs. Examinations of three human tumour cell lines and their cisplatinresistant variants showed an association of elevated MRP2 expression and the occurrance of cisplatinresistance. Moreover, the cisplatinresistant cell lines were crossresistant against carboplatin. To examine further factors in context of cisplatinresistance the mutation status of p53 and the cellular glutathione content of the cell lines were determined. The MRP2-open reading frame of the cisplatinresistant ovarian carcinoma cell line A2780RCIS was used for transfection into the cisplatinsensitive cell line A2780. The transfectants showed an overexpression of MRP2 and a resistance against cisplatin and carboplatin. This could be confirmed with analysis of the cell cycle and apoptosis induction after treatment with cisplatin. Using computer aided folding analysis of MRP2 mRNA parts two possible ribozyme cleavage sites were selected. The constructed ...
The gaming focused manufacturer Razer announced the Hammerhead and Hammerhead Pro in-ear headphones, with the latter adding an omni-directional microphone with an in-line remote for phone-call control and convenient voice communication. Both in-ear headsets are machined out of aircraft-grade aluminum, include 9mm
The Hammerhead is an uncommon creature found in the frigid oceans of Barotrauma. 1 Description 2 In-game 3 Variants 4 Damage Values 5 Trivia 6 Gallery Hammerheads are medium-size shark-like creatures. They have at least two pairs of eyes, four claws, four fins, and a long tail, which is their...
4854 To gain insight into the molecular mechanisms by which human cells replicate DNA containing fork-blocking lesions, stable transfection of human fibroblasts with antisense or hammerhead ribozymes was used to eliminate expression of key replication proteins, e.g., the subunits of human Pol zeta (hRev3, hRev7) or hRev1, a protein necessary for hPol zeta-facilitated bypass. For studies of the role of these proteins, we identified transfectant cell strains expressing high levels of antisense, or lower than normal levels of mRNA, and assayed them for the cytotoxic and mutagenic effects of exposure to UV radiation or benzo(a)pyrene diol epoxide (BPDE). For studies of the role of hRev7, antibodies were available for identifying cell strains that no longer expressed this protein, or expressed it at decreased levels. Transfectants expressing high levels of antisense against hRev3 or hRev1, were found not to be significantly more sensitive to the cytotoxic effect of UV or BPDE (as measured by loss of ...
HA3459/3 Functional analysis of Hammerhead Ribozymes from plants. A personal Fellowship to Dr. Sandeep Ojha had been granted by the Fritz Thyssen Foundation. Further previous grants include a personal fellowship in the EU-Biotechnology program and the EU-Strep FOSRAK.. ...
As promised, my penultimate note will be on the epistemological indistinguishability of the Copenhagen interpretation and the many worlds hypothesis. If youve stuck with me this far, but didnt understand that last sentence... well, you know what? Im willing to say that thats entirely my fault - Im trying to write this for the layman, after all. What I mean is that, if either the Copenhagen interpretation or the many worlds hypothesis was true, we could not tell the difference between them. The reason for this is that, under the many worlds hypothesis, we can only describe the future in terms of a probabilistic idea space (this is in fact what the many worlds hypothesis says reality is like). However, in hindsight, we will see only a series of quantum events that played out probabilistically. But under the Copenhagen interpretation, we can only describe the future in terms of probabilities, and if we were to fully describe all possible futures, this would be exactly the same as the many ...
Hammerhead sharks by the hundreds swirl around Peter Klimley. This sounds like a nightmare with teeth, but for the adventurer and scientist, its just another swim with his favorite animal.. Klimley, a marine biologist at the University of California, Davis, has spent many hours in the water with these sharks-some more than four meters long. Although hammerheads have a man-eater reputation, theyve never harmed him. I once wanted to get a hammerhead on the research boat, so I lassoed it by the tail, says Klimley. I was afraid it would turn around and bite me, but it just swam faster.. As a teenager, Klimley raised tropical fish. He became interested in sharks as a college student. There was something romantic about sharks, he says. It was my dream to study sharks in the water. I believe that if you want to understand an animal, you have to enter its environment.. Scalloped hammerheads are one of the largest of the nine species of hammerheads. As a young scientist, Klimley heard about ...
A pre-cellular, virus-like stage of evolution appears to be, effectively, a logical inevitability. It is unimaginable that life started with large and complex genomes that were similar to those of archaea and bacteria, especially within the framework of the RNA world hypothesis, because large RNA genomes could not exist owing to RNA fragility. Thus, a pre-cellular stage of evolution must have involved genetic elements of virus-like size and complexity: the selfish replicons4,7. Importantly, unlike cellular life forms, viruses exploit different genome replication strategies, including those that were indispensable in the RNA world and during the transition to a DNA world, namely, RNA-dependent synthesis of RNA and DNA. The corresponding enzymes, the RNA-dependent RNA polymerases and reverse transcriptases, are bona fide VHGs that are shared by vast virus groups4. Conceivably, the diverse viral genomic strategies are relics of the primordial stage of evolution from which one strategy was ...
Consider the following addendum to the article Engineering and characterization of a superfolder green fluorescent protein from nature biotechnology. Retraction: Identification of genes that function in the TNF-α-mediated apoptotic pathway using randomized hybrid ribozyme libraries. Hiroaki Kawasaki, Reiko Onuki, Eigo Suyama & Kazunari Taira Nat. Biotechnol. 20, 376-380 (2002) Although the gene discovery technology described in this paper has been demonstrated to have practical utility by several independent researchers, the first author of the paper failed to maintain a proper data notebook to support the results presented. As this constitutes nonadherence to the ethical standards in scientific research, and in accordance with the recommendations from the National Institute of Advanced Industrial Science & Technology (AIST), R. Onuki, E. Suyami and K. Taira respectfully retract this paper. H. Kawasaki declines to associate himself with this retraction and maintains that all the data ...
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The Great Hammerhead (Sphyrna mokarran) and Scalloped Hammerhead (Sphyrna lewini) sharks are long lived, late maturing, and relatively slow growing. Great Hammerhead Sharks can live to up to 44 years and have a gestation period of 11 months producing 6-33 pups biennially. Scalloped Hammerhead Sharks can live to up to 35 years and have a gestation period of 8-12 months producing 15-31 pups biennially.. ...
As recently as the early 1980s, the generally accepted view among scientists was that enzymes were proteins. The idea of proteins having a monopole of biocatalytic capacity has been deeply rooted, and created a fundamental dogma of biochemistry. This is the very basic perspective in which we have to regard the discovery today being rewarded with the Nobel Prize for Chemistry. When Sidney Altman showed that the enzyme denoted RNaseP only needed RNA in order to function, and when Thomas Cech discovered self-catalytic splicing of a nucleic acid fragment from an immature RNA molecule, this dogma was well and truly holed below the waterline. They had shown that RNA can have catalytic capacity and can function as an enzyme. The discovery of catalytic RNA came as a great surprise and was indeed met with a certain amount of scepticism. Who could ever have suspected that scientists, as recently as in our own decade, were missing such a fundamental component in their understanding of the molecular ...
As recently as the early 1980s, the generally accepted view among scientists was that enzymes were proteins. The idea of proteins having a monopole of biocatalytic capacity has been deeply rooted, and created a fundamental dogma of biochemistry. This is the very basic perspective in which we have to regard the discovery today being rewarded with the Nobel Prize for Chemistry. When Sidney Altman showed that the enzyme denoted RNaseP only needed RNA in order to function, and when Thomas Cech discovered self-catalytic splicing of a nucleic acid fragment from an immature RNA molecule, this dogma was well and truly holed below the waterline. They had shown that RNA can have catalytic capacity and can function as an enzyme. The discovery of catalytic RNA came as a great surprise and was indeed met with a certain amount of scepticism. Who could ever have suspected that scientists, as recently as in our own decade, were missing such a fundamental component in their understanding of the molecular ...
As recently as the early 1980s, the generally accepted view among scientists was that enzymes were proteins. The idea of proteins having a monopole of biocatalytic capacity has been deeply rooted, and created a fundamental dogma of biochemistry. This is the very basic perspective in which we have to regard the discovery today being rewarded with the Nobel Prize for Chemistry. When Sidney Altman showed that the enzyme denoted RNaseP only needed RNA in order to function, and when Thomas Cech discovered self-catalytic splicing of a nucleic acid fragment from an immature RNA molecule, this dogma was well and truly holed below the waterline. They had shown that RNA can have catalytic capacity and can function as an enzyme. The discovery of catalytic RNA came as a great surprise and was indeed met with a certain amount of scepticism. Who could ever have suspected that scientists, as recently as in our own decade, were missing such a fundamental component in their understanding of the molecular ...
Scientists have been debating for decades the origin of life on earth. A number of hypotheses were proposed as to what emerged first RNA or DNA; with most scientists are in favour of the RNA World hypothesis. Assuming ...
Enzyme Genes encode Enzymes, biological molecules (usually proteins) that possess catalytic activity. Catalytic RNA and catalytic DNA molecules have also been identified. (NCI)
SOLUTION STRUCTURE OF A 22-NUCLEOTIDE HAIRPIN SIMILAR TO THE P5ABC REGION OF A GROUP I RIBOZYME WITH COBALT(III)HEXAMMINE COMPLEXED TO THE GAAA TETRALOOP. ...
Ripley s Believe It or Not! Fact Bizarre Things from Around the World. Amazing Artifacts And Attractions. Provides videos, details about exhibits, and their history.
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Scientists who sought to solve mysteries about hammerhead sharks were only left with another when one of the first adults ever tagged ended up eluding them.
Bipalium vagum, the Mollusc-eating hammerhead worm; Volusia county, Florida (08 September 2015). Learn more about this species at iNaturalist.org.
MEDAN. RZ cabang Medan untuk memperingati Hari Menanam Pohon Indonesia 2013 menggelar kegiatan menanam pohon tembakau sebanyak 300 pohon di Kelurahan Sicanang
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Hampel, A; Tritz, R (Jun 13, 1989). "RNA catalytic properties of the minimum (-)sTRSV sequence". Biochemistry. 28 (12): 4929- ... The hairpin ribozyme is an RNA motif that catalyzes RNA processing reactions essential for replication of the satellite RNA ... Hampel, A; Tritz, R (1989). "RNA catalytic properties of the minimum (-)sTRSV sequence". Biochemistry. 28 (12): 4929-4933. doi: ... The hairpin ribozyme is a small section of RNA that can act as a ribozyme. Like the hammerhead ribozyme it is found in RNA ...
In another scientific context, catalytic RNAs have been deemed Cheshire cats. This metaphor is used to describe the fading of ... Yarus, Michael (1993). "How many catalytic RNAs? Ions and the Cheshire cat conjecture". The FASEB Journal. 7 (1): 31-39. doi: ... the ribonucleotide construct, which leaves behind a smile of only the mineral components of the RNA catalyst. Similarly, the ...
The most common of these is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their ... Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three- ... This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and ... and product release steps of the catalytic cycle, consistent with catalytic resonance theory. Substrate presentation is a ...
Since Cech's and Altman's discovery, other investigators have discovered other examples of self-cleaving RNA or catalytic RNA ... RNA life would have depended on an RNA-dependent RNA polymerase ribozyme to copy functional RNA molecules, including copying ... Tang and Breaker isolated self-cleaving RNAs by in vitro selection of RNAs originating from random-sequence RNAs. Some of the ... They also participate in a variety of RNA processing reactions, including RNA splicing, viral replication, and transfer RNA ...
Steitz, T. A.; Steitz, J. A. (1993). "A general two-metal-ion mechanism for catalytic RNA". Proceedings of the National Academy ... "August Newsletter of the RNA Society" (PDF). The RNA Society. Retrieved September 13, 2018. "Caledonian Research Fund Prize ... code for sno RNAs that target the modification of other cellular RNAs during their maturation. More recently she has found new ... Her nomination for the Royal Society reads: Joan Steitz is one of the pioneers of the field of RNA biology who is world- ...
... of the DNA directed RNA polymerase III. This subunit includes the catalytic site of RNA polymerase III.[citation needed] ...
"for their discovery of catalytic properties of RNA". *^ "The Nobel Prize in Chemistry 1990". Nobelprize.org. http://nobelprize. ... for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active ...
... of catalytic RNA (ribozyme). Discovery of the function of histone acetylation. Demonstration of the roles of posttranslational ... It is at this junctional zone that several hundred fusion pores form, allowing for the mutual exchange of protein, RNA and ... Discovery of the molecular structure of telomeres, telomerase enzyme, the templating role of telomerase RNA and their roles in ... Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (November 1982). "Self-splicing RNA: autoexcision and ...
The twister ribozyme is a catalytic RNA structure capable of self-cleavage. The nucleolytic activity of this ribozyme has been ... In contrast to in vitro selection methods, which have aided in identifying several classes of catalytic RNA motifs, the twister ... The twister ribozyme generates catalytic activity by specifically orienting the to-be-cleaved P O bond for in-line nucleophilic ... RNA. 8 (3): n/a. doi:10.1002/wrna.1402. ISSN 1757-7012. PMC 5408937. PMID 27863022.. ...
doi:10.1261/rna.5181104. PMC 1370934. PMID 14970384. Liu J, Carmell MA, Rivas FV, et al. (2004). "Argonaute2 is the catalytic ... RNA. 10 (3): 387-94. doi:10.1261/rna.5181104. PMC 1370934. PMID 14970384. Mourelatos Z, Dostie J, Paushkin S, Sharma A, ... RNA. 12 (1): 163-76. doi:10.1261/rna.2150806. PMC 1370895. PMID 16301602. Maniataki E, Mourelatos Z (2006). "A human, ATP- ... Doi N, Zenno S, Ueda R, Ohki-Hamazaki H, Ui-Tei K, Saigo K (January 2003). "Short-interfering-RNA-mediated gene silencing in ...
RNA. 9 (1): 77-87. doi:10.1261/rna.2137903. PMC 1370372. PMID 12554878. Ohnishi T, Yamashita A, Kashima I, Schell T, Anders KR ... The catalytic activity of SMG6 resides in its PIN domain, which is required for the degradation of premature translation ... RNA. 14 (12): 2609-17. doi:10.1261/rna.1386208. PMC 2590965. PMID 18974281. Mega JL, Stitziel NO, Smith JG, Chasman DI, ... RNA. 14 (12): 2609-17. doi:10.1261/rna.1386208. PMC 2590965. PMID 18974281. Chakrabarti S, Bonneau F, Schüssler S, Eppinger E, ...
... molecules using a DNA methyltransferase-like catalytic mechanism". RNA. 14 (8): 1663-70. doi:10.1261/rna.970408. PMC 2491481. ... "RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage". Genes & Development. 24 (15): 1590-5. doi: ...
... sequence associated with the catalytic core. The ret gene product is responsible for processing the msd/msr portion of the RNA ... results in a DNA/RNA chimera which is composed of small single-stranded DNA linked to small single-stranded RNA. The RNA strand ... they consist of an RT encoded within a catalytic, self-splicing RNA structure. Group II intron mobility is mediated by a ... Retron msr RNA is the non-coding RNA produced by retron elements and is the immediate precursor to the synthesis of msDNA. The ...
Deoxyribozymes, also called DNAzymes or catalytic DNA, are artificial catalytic DNA molecules that were first produced in 1994 ... a variety of reactions can be catalyzed by DNAzymes including RNA/DNA cleavage, RNA/DNA ligation, amino acid phosphorylation ... Parallels and differences in catalytic strategies have been reviewed.[47] Pb2+ (lead) can replace Ca2+ (calcium) as, for ... Breaker RR, Joyce GF (December 1994). "A DNA enzyme that cleaves RNA". Chemistry & Biology. 1 (4): 223-9. doi:10.1016/1074-5521 ...
Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases. RNA methylation is ... Similarly, RNA methylation occurs in different RNA species viz. tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. ... 5-methylcytosine (5-mC) also commonly occurs in various RNA molecules. Recent data strongly suggest that m6A and 5-mC RNA ... Rana, Ajay K.; Ankri, Serge (1 January 2016). "Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases ...
2006). Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 439(7078):879-84.. ...
"Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase". RNA. 23 (2): 202 ... doi:10.1261/rna.057620.116. ISSN 1355-8382. PMC 5238795. PMID 28096445. Kabra, Ashish; Fatma, Farheen; Shahid, Salman; Pathak, ...
While nuclear PAPs contain a catalytic domain and an RNA-binding domain, GLD-2 family members have only a catalytic domain. GLD ... For RNA specificity, GLD-2 associates with an RNA-binding protein, typically a GLD-3, to form a heterodimer that acts as a ... Kwak JE, Wickens M (June 2007). "A family of poly(U) polymerases". RNA. 13 (6): 860-7. doi:10.1261/rna.514007. PMC 1869031. ... It is proposed by some studies that GLD-3 stimulates GLD-2 by recruiting it to the RNA. If so, then bringing GLD-2 to the RNA ...
According to this model, the virus-associated RNA polymerase starts firstly the synthesis of leader RNA and then the five mRNA ... P protein acts as a non-catalytic cofactor of large protein polymerase. It is binding to N and L protein. P protein has two ... Replication follows the negative stranded RNA virus replication model. Negative stranded RNA virus transcription, using ... In addition to RNA synthesis, it is thought to be involved in methyl capping and polyadenylation activity. P protein plays ...
The hachimoji DNA system produced one type of catalytic RNA (ribozyme or aptamer) in vitro. Natural DNA is a molecule carrying ... DNA and RNA are naturally composed of four nucleotide bases that form hydrogen bonds in order to pair. Hachimoji DNA uses an ... An enzyme (T7 polymerase) was adapted by the researchers to be used in vitro to transcribe hachimoji DNA into hachimoji RNA, ... Hachimoji bases have been demonstrated in both DNA and RNA analogs, using deoxyribose and ribose respectively as the backbone ...
It uses ATP dependent RNA helicase catalytic activity to regulate the translation of multiple mRNAs. Vasa unwinds the duplex ... Vasa is an RNA binding protein with an ATP-dependent RNA helicase that is a member of the DEAD box family of proteins. The vasa ... As with other Vasa related proteins, human Vasa has a N terminus rich in glycine and RGG motif repeats that function in RNA ... Vasa was found to bind RNA in a sequence specific manner. In the Drosophila embryos, Vasa binds the Uracil rich motif of the ...
Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA). tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule of ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
Since the catalytic component of telomerase is its reverse transcriptase, hTERT, and the RNA component hTERC, hTERT is an ... December 1997). "Reconstitution of human telomerase with the template RNA component hTR and the catalytic protein subunit hTRT ... The core promoter of hTERT includes 330 base pairs upstream of the translation start site (AUG since it's RNA by using the ... Lastly, iPS cells generated with DKC cells with a mutated dyskerin (DKC1) gene cannot assemble the hTERT/RNA complex and thus ...
... is a small ribozyme (catalytic RNA), which catalyzes the cleavage of a specific phosphodiester bond. It was discovered ... The targeting of these RNA motifs by lead in mRNAs and other RNAs may explain lead-mediated toxicity resulting in cell death. ... The cleavage site of leadzyme is located within a four-nucleotide long asymmetric internal loop that also consists of RNA ... However, in the second conformation, termed the 'pre-catalytic' state, the ribozyme shows two Sr2+ binding sites. G43 and G42 ...
Promote proper folding of RNA and to form the catalytic core. Since RNA itself did not contain enough variation in the ... It is one of several catalytic RNAs (ribozymes) known to occur in nature. It serves as a model system for research on the ... Similar reports confirmed and extended these observations, unveiling the hammerhead ribozyme as a ubiquitous catalytic RNA in ... In its natural state, a hammerhead RNA motif is a single strand of RNA. Although the cleavage takes place in the absence of ...
Iron-sulfur protein RNA world Miller-Urey experiment Wächtershäuser, Günter (1988-12-01). "Before enzymes and templates: theory ... It had a composite structure of a mineral base with catalytic transition metal centers (predominantly iron and nickel, but also ... In principle, this could lead to the development of complex catalytic sets capable of self-maintenance. Russell adds a ... The catalytic transition metal centers became autocatalytic by being accelerated by their organic products turned ligands. The ...
"Enhancement of replication of RNA viruses by ADAR1 via RNA editing and inhibition of RNA-activated protein kinase". Journal of ... Within the catalytic core there is an inositol hexakisphosphate (IP6), which stabilizes arginine and lysine residues. It has ... ADARs acting on RNA is one of the most common forms of RNA editing, and has both selective and non-selective activity. ADAR is ... 2018). "RNA editing in nascent RNA affects pre-mRNA splicing". Genome Res. 28 (6): 812-823. doi:10.1101/gr.231209.117. PMC ...
Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA. Nat Struct Mol Biol. 2010 Apr ... siRNAs are small RNA molecules that induce the sequence-specific degradation of other RNAs. siRNA treatment can function ... "Minimum length requirement of the alignment domain of human telomerase RNA to sustain catalytic activity in vitro". Nucleic ... Feng J, Funk WD, Wang SS, Weinrich SL, Avilion AA, Chiu CP, Adams RR, Chang E, Allsopp RC, Yu J (September 1995). "The RNA ...
Wedekind JE, Dance GS, Sowden MP, Smith HC (2003). "Messenger RNA editing in mammals: new members of the APOBEC family seeking ... "Entrez Gene: APOBEC2 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2". Human APOBEC2 genome location and ... 2001). "ARCD-1, an apobec-1-related cytidine deaminase, exerts a dominant negative effect on C to U RNA editing". Am. J. ...
Upon recruitment of the tri-snRNP, several RNA-RNA rearrangements precede the first catalytic step and further rearrangements ... Structural and catalytic roles of metal ions in RNA. Metal Ions in Life Sciences. 9. RSC Publishing. pp. 235-51. doi:10.1039/ ... and participate in several RNA-RNA and RNA-protein interactions. The canonical assembly of the spliceosome occurs anew on each ... is one example of an RNA-RNA interaction displacing a protein-RNA interaction. Upon recruitment of U2 snRNP, the branch binding ...
Nicholas C. Price, Lewis Stevens (1999). Fundamentals of Enzymology: The Cell and Molecular Biology of Catalytic Proteins ( ... RNA zavisna DNK polimeraza) Kristalografska struktura HIV reverzne transkriptaze. [1] Identifikatori Simbol RVT_1 ...
X-ray crystallography of DNA and RNA polymerases show that, other than having a Mg2+ ion at the catalytic site, they are ... Non-coding RNA or "RNA genes". These are a broad class of genes that encode RNA which is not translated into protein. The most ... RNA polymerase IV synthesizes siRNA in plants.[5]. *RNA polymerase V synthesizes RNAs involved in siRNA-directed ... RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.[4] ...
positive regulation of catalytic activity. • mitochondrial transport. • post-embryonic development. • positive regulation of ... negative regulation of transcription from RNA polymerase II promoter. • proteolysis. • regulation of synaptic plasticity. • ...
9,0 9,1 Polgar, L. (2005). The catalytic triad of serine peptidases. CMLS, Cell. Mol. Life Sci., nr 62, lk 2161-2172. link. ... mida kasutatakse DNA ja RNA eraldamiseks bioloogilisest materjalist[12][13] ja papaiin, mida kasutatakse rakkude isoleerimiseks ... 16,0 16,1 Fujinaga, M., et al., (2004) The molecular structure and catalytic mechanism of a novel carboxyl peptidase from ... A SEVENTH CATALYTIC TYPE OF PROTEOLYTIC ENZYMES. The Journal of Biological Chemistry, nr 286, lk 38321-38328. www.jbc.org ...
... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... and mutations within the VPg sequence can severely diminish RdRp catalytic activity. While the tyrosine hydroxyl of VPg can ... The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as ... Genomic RNAs of picornaviruses possess multiple RNA elements and they are required for both negative and plus strand RNA ...
Direct selection on these mutants allowed catalytic properties of B-lactamase to be identified and allowed structure-function ... evidence of the importance of Ral was provided when cortical neurons were depleted of endogenous RalA and RalB isoforms by RNA ...
catalytic activity. • transferase activity, transferring acyl groups. • 3-hydroxyacyl-CoA dehydrogenase activity. • RNA binding ... The encoded protein can also bind RNA and decreases the stability of some mRNAs. The genes of the alpha and beta subunits of ...
"for their discovery of catalytic properties of RNA"[۳۳] ۱۹۹۲ رادولف مارکوس[۱] United States "for his contributions to the ... "for their discovery of the course of the catalytic conversion of گلیکوژن"[۴۸] ... "for his discovery of آران‌ای سرکوبگر - gene silencing by double-stranded RNA"[۷۹] ...
Nicholas C. Price, Lewis Stevens (1999). Fundamentals of Enzymology: The Cell and Molecular Biology of Catalytic Proteins ( ... coli ribonuclease which removes an extra nucleotide from a biosynthetic intermediate of bacteriophage T4 proline transfer RNA ...
... as well as the sensitivity of combustion to impurities such as moisture and to the catalytic effects of container surfaces ...
Research on psoralen has historically focused on interactions with DNA and RNA (in particular, ICL formation). Psoralen, ... "Photo-Activated Psoralen Binds the ErbB2 Catalytic Kinase Domain, Blocking ErbB2 Signaling and Triggering Tumor Cell Apoptosis ... and therefore have been used extensively for the analysis of interactions and structures for both DNA and RNA.[26][27] ... "RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure". Cell. 165 (5): 1267-1279. doi:10.1016/j.cell. ...
The RNA world hypothesis is supported by the observations that ribosomes are ribozymes: the catalytic site is composed of RNA, ... Atkins JF, Gesteland RF, Cech T (2006). The RNA world: the nature of modern RNA suggests a prebiotic RNA world. Plainview, N.Y ... RNAs are known to play roles in other cellular catalytic processes, specifically in the targeting of enzymes to specific RNA ... of RNAs with molecular properties predicted for RNAs of the RNA World constitutes an additional argument supporting the RNA ...
Alternately, trans-splicing of two non-functional RNA molecules may produce a single, functional RNA. Similarly, at the protein ... For example, removing any member of the catalytic triad of many enzymes will reduce activity to levels low enough that the ... for stability or catalytic activity). This is sometimes called a double mutant cycle and involves producing and assaying the ...
효소는 5,000가지 이상의 생화학 반응 유형들을 촉매하는 것으로 알려져 있다.[5] 대부분의 효소들은 단백질이지만, 일부 효소들은 촉매 기능을 가지고 있는 RNA 분자이다. 촉매 기능을 가지고 있는 RNA를 리보자임이라고 한다 ... "The Catalytic Site Atlas". The European Bioinformatics Institute. 2007년 4월 4일에 확인함.. ... 리보자임이라고 불리는 소수의 RNA 기반 생물학적 촉매가 존재하며, 리보자임은 단독으로 또는 단백질과 복합체를 형성하여 작용할 수 있다. 리보자임들 중 가장 일반적인 것은 촉매 기능을 가진 RNA와 단백질의 복합체인 리보솜이다. ... Polgár, L. (2005년 7월 7일). "The catalytic triad of serine peptidases". 》Cellular and Molecular Life Sciences》 (영어) 62 (19-20): ...
transcription initiation from RNA polymerase II promoter. • G1/S transition of mitotic cell cycle. • negative regulation of ... It is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression. The activity of ...
regulation of catalytic activity. • Rho protein signal transduction. • regulation of actin polymerization or depolymerization. ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • phospholipase binding. • GTPase ...
Integration occurs following production of the double-stranded viral DNA by the viral RNA/DNA-dependent DNA polymerase reverse ... a catalytic core domain (RNaseH fold) a C-terminal DNA-binding domain (SH3 fold) Crystal and NMR structures of the individual ...
Briefly, ncRNAs are involved in signaling cascades with epigenetic marking enzymes such as HMTs, and/or with RNA interference( ... "Additive neuroprotective effects of a histone deacetylase inhibitor and a catalytic antioxidant in a transgenic mouse model of ... significantly increases SMN2 RNA/protein levels in spinal muscular atrophy cells". primary. Human Genetics. 120 (1): 101-10. ... non-coding RNA (ncRNA) function. Briefly, histone-mediated transcriptional control occurs by the wrapping of DNA around a ...
PrP messenger RNA contains a pseudoknot structure (prion pseudoknot), which is thought to be involved in regulation of PrP ... negative regulation of catalytic activity. • positive regulation of neuron apoptotic process. • regulation of peptidyl-tyrosine ... "Circadian regulation of prion protein messenger RNA in the rat forebrain: a widespread and synchronous rhythm". Neuroscience. ...
Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: ... They are transfer RNA (tRNA) and ribosomal RNA (rRNA).. tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ...
negative regulation of transcription from RNA polymerase II promoter. • osteoblast differentiation. • in utero embryonic ... GO:0048554 positive regulation of catalytic activity. • positive regulation of glycogen biosynthetic process. • positive ... regulation of transcription from RNA polymerase II promoter. • positive regulation of insulin receptor signaling pathway. • ...
"for their discovery of catalytic properties of RNA"[81] تھومس چیک امریکا ... "for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active ...
RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • aldo-keto reductase (NADP) ...
... a catalytic subunit of RNA polymerase II". Journal of Virology. 86 (13): 7180-91. doi:10.1128/JVI.00541-12. PMC 3416352. PMID ... It was first isolated in 1953 in Tanzania and is an RNA virus with a positive-sense single-stranded genome of about 11.6kb.[34] ... In a mouse model, viral RNA was detected specifically in joint-associated tissue for at least 16 weeks after inoculation, and ... Diagnosis is by either testing the blood for the virus's RNA or antibodies to the virus.[3] The symptoms can be mistaken for ...
The catalytic domains of all the aaRSs of a given class are found to be homologous to one another, whereas class I and class II ... Aminoacyl tRNA therefore plays an important role in RNA translation, the expression of genes to create proteins. ... In a typical scenario, an aaRS consists of a catalytic domain (where both the above reactions take place) and an anticodon ... As genetic efficiency evolved in higher organisms, 13 new domains with no obvious association with the catalytic activity of ...
RNA binding. Cellular component. • cytoplasm. • U5 snRNP. • catalytic step 2 spliceosome. • U4/U6 x U5 tri-snRNP complex. • ... Although individual snRNPs are believed to recognize specific nucleic acid sequences through RNA-RNA base pairing, the specific ...
... in the catalytic domain and a substitution (Glu102Lys) in the second EGF-like domain". British Journal of Haematology. 90 (4): ... RNA expression pattern. More reference expression data. Gene ontology. Molecular function. • calcium ion binding. • peptidase ...
Catalytic mechanismEdit. In order for the reaction to proceed, S-Adenosyl methionine (SAM) and the lysine residue of the ... RNA polymerase control by chromatin structure. *Histone methylation. ReferencesEdit. *^ a b c d Wood A (2004). " ... The catalytic domain of PRMTs consists of a SAM binding domain and substrate binding domain (about 310 amino acids in total).[5 ... Catalytic mechanismEdit. A glutamate on a nearby loop interacts with nitrogens on the target arginine residue. This interaction ...
... messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary ... Gutteridge A, Thornton JM (November 2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences. 30 (11 ... Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only ... The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site. ...
"for their discovery of catalytic properties of RNA"[88] Thomas Cech United States ... "for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active ...
Catalytic RNA. Definition. Catalytic RNA (ribonucleic acid) are RNA molecules that have enzyme activity. The classic example is ... Discovery of catalytic RNA contributed to the hypothesis of an RNA world, describing the origin of life as starting from RNA ... Catalytic RNAs are involved in a number of biological processes, including RNA processing and protein synthesis. ... Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes *Chiu-Ho ...
Mineral components of the Murchison meteorite were investigated in terms of potential catalytic effects on synthetic and ... Cech TR (1987) The chemistry of self-splicing RNA and RNA enzymes. Science 236:1532-1539PubMedCrossRefGoogle Scholar ... Catalytic effects of Murchison Material: Prebiotic Synthesis and Degradation of RNA Precursors. ... Cheng LK, Unrau PJ (2010) Closing the circle: replicating RNA with RNA. In: Deamer D, Szostak J (eds) Origins of Life. Cold ...
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic ... RNA RIBOZYME STRAND A. 16 synthetic 16-MER FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE B. 20 synthetic 20-MER, 3-END CYCLIC ... RNA LINKING C9 H13 N3 O10 P2 C ... CATALYTIC RNA ENZYME-PRODUCT COMPLEX. *DOI: 10.2210/pdb488d/pdb ...
Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA. Xunqing Jiang and Joel G. Belasco ... Within the catalytic domain of these enzymes, there presumably is a site that can interact productively with RNA 5′ ends that ... 3B ). In the case of RNase G, the increase in k cat for the monophosphorylated RNA (2.1 ± 0.1 min-1) versus the hydroxyl RNA ( ... Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA ...
Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.. Qi Y1, He X, Wang XJ, Kohany O, ... DNA methylation can be induced by double-stranded RNA through the RNA interference (RNAi) pathway, a response known as RNA- ... Single mutations in the Asp-Asp-His catalytic motif of AGO4 do not affect siRNA-binding activity but abolish its catalytic ... Here we show that AGO4 binds to small RNAs including small interfering RNAs (siRNAs) originating from transposable and ...
These catalytic RNA sequences are called ribozymes. The function of a ribozyme depends upon the primary sequence of the RNA ... Catalytic RNA and Structure *. Please ensure you have JavaScript enabled in your browser. If you leave JavaScript disabled, you ... p023/biotechnology-techniques/catalytic-rna-and-structure. You may print and distribute up to 200 copies of this document ... "Catalytic RNA and Structure" Science Buddies. Science Buddies, 28 July 2017. Web. 24 Mar. 2018 ,https://www.sciencebuddies.org/ ...
RNA-dependent RNA polymerase which is responsible for replication and transcription of virus RNA segments. The transcription of ... During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a ... Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA. Interacts (via N-terminus) with PA (via C-terminus). ... In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. ...
RNA-directed RNA polymerase catalytic subunit. Details. Name. RNA-directed RNA polymerase catalytic subunit. Synonyms. *2.7. ... Rna-directed rna polymerase activity. Specific Function. RNA-dependent RNA polymerase which is responsible for replication and ... lcl,BSEQ0010060,RNA-directed RNA polymerase catalytic subunit MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSERGRWTKNTE ... RNA-directed RNA polymerase subunit P1. Gene Name. PB1. Organism. Influenza A virus (strain A/Beijing/11/1956 H1N1). Amino acid ...
Since the discovery of catalytic RNA molecules (ribozymes), intense research has been devoted to understand their structure and ... Among RNA molecules, the large ribozymes, namely group I and group II introns and RNase P, are of special importance. The first ... allow clarifying and rationalizing both the structural and catalytic roles of metal ions in large ribozymes. In particular, the ...
Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA ... Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA ... Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA ... Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA ...
RNA-directed RNA polymerase catalytic subunit (Fragment). Influenza C virus (C/Eastern India/1202/2011) ... RNA-directed RNA polymerase catalytic subunitUniRule annotation. Automatic assertion according to rulesi ... RNA-directed RNA polymerase catalytic subunit. Influenza D virus (D/bovine/Mexico/S62/2015) ... RNA-directed RNA polymerase catalytic subunit. Influenza D virus (D/bovine/Mexico/S7/2015) ...
During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a ... In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. ... RNA-dependent RNA polymerase which is responsible for replication and transcription of virus RNA segments. The transcription of ... help/catalytic_activity target=_top>More...,/a>,/p>Catalytic activityi. Nucleoside triphosphate + RNA(n) = diphosphate + RNA ...
Environmental change exposes beneficial epistatic interactions in a catalytic RNA Message Subject (Your Name) has sent you a ... Environmental change exposes beneficial epistatic interactions in a catalytic RNA. Eric J. Hayden, Andreas Wagner ... Here, we reconstruct the fitness landscape of a catalytic RNA molecule (ribozyme), including all possible intermediates that ... 1997 Equally parsimonious pathways through an RNA sequence space are not equally likely. J. Mol. Evol. 45, 278-284. doi:10.1007 ...
2008) An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol ... Nanomechanical constraints acting on the catalytic site of cellular RNA polymerases Message Subject (Your Name) has forwarded a ... Nanomechanical constraints acting on the catalytic site of cellular RNA polymerases. Robert O.J. Weinzierl ... 2003) Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22:2234-2244. ...
Silencing Expression of the Catalytic Subunit of DNA-dependent Protein Kinase by Small Interfering RNA Sensitizes Human Cells ... Silencing Expression of the Catalytic Subunit of DNA-dependent Protein Kinase by Small Interfering RNA Sensitizes Human Cells ... Silencing Expression of the Catalytic Subunit of DNA-dependent Protein Kinase by Small Interfering RNA Sensitizes Human Cells ... Silencing Expression of the Catalytic Subunit of DNA-dependent Protein Kinase by Small Interfering RNA Sensitizes Human Cells ...
Modulation of Catalytic RNA Biological Activity by Small Molecule Effectors. Author(s): Anastassios Vourekas, Dimitra ... Abstract: Catalytic RNAs, known as ribozymes, act as true enzymes and are implicated in important biological processes, such as ... Catalytic RNAs, known as ribozymes, act as true enzymes and are implicated in important biological processes, such as protein ... Anastassios Vourekas, Dimitra Kalavrizioti, Constantinos Stathopoulos and Denis Drainas, " Modulation of Catalytic RNA ...
Functional Multimerization of Human Telomerase Requires an RNA Interaction Domain in the N Terminus of the Catalytic Subunit. ... Reconstitution of human telomerase with the template RNA component hTR and the catalytic protein subunit hTRT. Nat. Genet.17: ... Functional Multimerization of Human Telomerase Requires an RNA Interaction Domain in the N Terminus of the Catalytic Subunit ... Functional human telomerase complexes are minimally composed of the human telomerase RNA (hTR) and a catalytic subunit (human ...
... Dong, Hengjiang Uppsala ... We have studied the expression of 4.5 S RNA and Fv Il RNA, the catalytic subunit of Escherchia coli RNase P, under various ... but has little effect on the expression of M1 RNA. These data suggest that the expression of both 4.5 S RNA and M1 RNA genes ... Both RNA species increase in abundance as a function of growth rate. There are roughly 450 molecules of 4.5 S RNA and 80 ...
Ubiquitination close to the active site of RNAPII occurs in response to RNA processing events and is linked to transcriptional ... RNA-seq. RNA was extracted as previously described (Tollervey, 1987). The RNA samples were either enriched for mRNA using ... Bre5 binds RNA in vitro and in vivo.. (A) Bre5 and Ubp3 plus Bre5 bind RNA in vitro. Recombinant Bre5 and Ubp3 were expressed ... RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit. ...
A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA ... A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA ... A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA ... A non-catalytic role for inositol 1,3,4,5,6-pentakisphosphate 2-kinase in the synthesis of ribosomal RNA ...
Model RNAs and proteins are also reported here.. Reference GRCm38.p4 C57BL/6J. Genomic * NC_000075.6 Reference GRCm38.p4 C57BL/ ... Gclc glutamate-cysteine ligase, catalytic subunit [Mus musculus] Gclc glutamate-cysteine ligase, catalytic subunit [Mus ... glutamate-cysteine ligase, catalytic subunitprovided by MGI. Primary source. MGI:MGI:104990 See related. Ensembl: ... glutamate--cysteine ligase catalytic subunit. Names. GCS heavy chain. gamma GCS-HS. gamma-ECS. gamma-glutamylcysteine ...
C: RNA blotting analysis was performed with the indicated RNA samples as described in research design and methods using labeled ... RNA blot analysis.. Total RNA was isolated from adult mouse frontal brain and cerebellum using TRI Reagent (Molecular Research ... Thus, although IGRP mRNA was not detected in whole-brain tissue by RNA blot analysis using poly A+ RNA (3), it was possible ... Mouse pancreas Poly A+ RNA was purchased from BD Biosciences Clontech. Poly A+ RNA (5 μg cerebellum and frontal brain, 2 μg ...
Catalytic RNAs. Ribozymes are non-coding RNAs that can precisely position reactants and accelerate chemical reactions by ... catalytic RNAs) and the interactions between RNA and proteins at the level of atomic structure. Dr. Ferré-DAmaré is also ... New tools for RNA cell biology. Tens of thousands of non-coding RNAs have been discovered in the human transcriptome, and new ... Ferré-DAmarés second translational research focus is on the role of a catalytic RNA-glmS-in controlling the synthesis of the ...
Catalytic RNAs. - Adrian R. Ferré-DAmaré, Ph.D. Research Ribozymes are non-coding RNAs that can precisely position reactants ... RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. ... catalytic RNAs) and the interactions between RNA and proteins at the level of atomic structure. Dr. Ferré-DAmaré is also ... New tools for RNA cell biology. - Adrian R. Ferré-DAmaré, Ph.D. Research Tens of thousands of non-coding RNAs have been ...
RNA self-cleaving domain can be assembled from two RNA molecules: a large (approximately 34 nucleotide) ribozyme RNA containing ... These observations demonstrate that the secondary structure of substrate RNA can be a major determinant of hammerhead catalytic ... Four such hammerheads that contained identical catalytic core sequences but differed in the base composition of the helices ... most of the catalytically essential nucleotides and a small (approximately 13 nucleotide) substrate RNA containing the cleavage ...
Ribosomal RNA (rRNA). Main article: Ribosomal RNA. Ribosomal RNA is the catalytic component of the ribosomes, the protein ... Non-coding RNA. RNA genes (also known as non-coding RNA or small RNA) are genes that encode RNA that is not translated into a ... Transfer RNA (tRNA). Main article: Transfer RNA. Transfer RNA is a small RNA chain of about 74-95 nucleotides that transfers a ... Messenger RNA (mRNA). Main article: Messenger RNA. Messenger RNA is RNA that carries information from DNA to the ribosome sites ...
The catalytic RNA component of ribonuclease P (P RNA) is an essential enzyme required for the 5′ maturation of all tRNAs and ... RNA Polymerases.. The wild-type E. coli RNA polymerase was purchased from USB (Cleveland, OH). The mutant E. coli RNA ... To evaluate whether RNA polymerase-induced pausing influences P RNA folding, we investigated the folding of E. coli P RNA ... Expedient RNA folding must avoid the formation of undesirable structures as the nascent RNA emerges from the RNA polymerase. We ...
Chemical modifications of RNA have been attracting increasing interest because of their impact on RNA fate and function. ... provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11:1609-1620CrossRefPubMedGoogle ... Reductive treatment of RNA and RNA bisulfite sequencing. To reduce 5-formylcytosine to 5-hydroxmethlycytosine, RNA was treated ... RNA modifications have been shown to play important roles in the function and metabolism of all types of RNA in eukaryotes and ...
Catalytic RNA: Volume 120 Garrett A. Soukup 12 Dec 2013. Hardback. US$177.83 ... Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular ... Structure and Function in Promoter Escape by T7 RNA Polymerase. Ribonuclease Inhibitor: Structure and Function. show more ...
  • Among the molecular mechanisms that could account for these properties are those in which 5′-end binding by one enzyme subunit induces a protein structural change that accelerates RNA cleavage by another subunit. (pnas.org)
  • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. (nih.gov)
  • We have used this methodology in several human cell strains to reduce expression of the Prkdc ( DNA-PKcs ) gene coding for the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) that is involved in the nonhomologous end joining of DNA double-strand breaks. (aacrjournals.org)
  • Functional human telomerase complexes are minimally composed of the human telomerase RNA (hTR) and a catalytic subunit (human telomerase reverse transcriptase [hTERT]) containing reverse transcriptase (RT)-like motifs. (asm.org)
  • We have studied the expression of 4.5 S RNA and Fv Il RNA, the catalytic subunit of Escherchia coli RNase P, under various growth conditions. (diva-portal.org)
  • Here, we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. (elifesciences.org)
  • Most attention has focused on modifications of the regulatory C-terminal domain (CTD) of the large, catalytic subunit of RNAPII, which promote the ordered recruitment of numerous RNA packaging and processing factors to the nascent pre-mRNAs. (elifesciences.org)
  • We have previously reported the discovery of an islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) that is predominantly expressed in islet β-cells. (diabetesjournals.org)
  • Islet-specific glucose-6-phosphatase (G6Pase) catalytic subunit-related protein (IGRP) is a putative enzyme that is specifically expressed in the islets of Langerhans ( 1 - 3 ), where it is localized predominantly in insulin-producing β-cells ( 4 ). (diabetesjournals.org)
  • As its name implies, IGRP is a homologue of the catalytic subunit of G6Pase, the final enzyme in the glycogenolytic and gluconeogenic metabolic pathways ( 6 - 9 ). (diabetesjournals.org)
  • However, the favored model includes a catalytic subunit and transporters for G6P, glucose, and phosphate ( 6 - 9 ). (diabetesjournals.org)
  • Both the G6Pase catalytic subunit and IGRP are integral membrane proteins that are thought to span the endoplasmic reticulum membrane multiple times ( 1 , 3 ). (diabetesjournals.org)
  • The G6Pase catalytic subunit has its catalytic site oriented toward the lumen of the endoplasmic reticulum, so a G6P transporter is essential for delivering G6P from the cytosol to this active site ( 6 - 9 ). (diabetesjournals.org)
  • The spatial arrangement of the G6Pase system also serves to limit the function of the G6Pase catalytic subunit, which, in permeabilized microsomal membrane preparations, demonstrates relatively nonspecific phosphatase activity ( 6 - 9 ). (diabetesjournals.org)
  • Transcription in human mitochondria is carried out by a single-subunit, T7-like RNA polymerase assisted by several auxiliary factors. (researchwithrutgers.com)
  • Our data indicate that the transcriptional machinery in human mitochondria has evolved into a system that combines features inherited from self-sufficient, T7-like RNA polymerase and those typically found in systems comprising cellular multi-subunit polymerases, and provide insights into the molecular mechanisms of transcription regulation in mitochondria. (researchwithrutgers.com)
  • We have mapped the 5' and 3' boundaries of the region of the human telomerase RNA (hTR) that is required to produce activity with the human protein catalytic subunit (hTERT) by using in vitro assembly systems derived from rabbit reticulocyte lysates and human cell extracts. (nebraska.edu)
  • Telomerase was discovered in 1985 by Elizabeth Blackburn and Carol Greider, who also cloned and sequenced its template-containing RNA subunit. (hhmi.org)
  • The catalytic protein subunit, however, remained elusive. (hhmi.org)
  • Messenger RNAs are labile molecules whose longevity directly influences the synthesis rates of the proteins they encode. (pnas.org)
  • The N terminus of TERT proteins is unique to the telomerase family and has been implicated in catalysis, telomerase RNA binding, and telomerase multimerization, and conserved motifs have been identified by alignment of TERT sequences from multiple organisms. (asm.org)
  • We studied hTERT proteins containing N-terminal deletions or substitutions to identify and characterize hTERT domains mediating telomerase catalytic activity, hTR binding, and hTERT multimerization. (asm.org)
  • However, the association of hTERT proteins in immunoprecipitates may be indirect and could be mediated by other proteins or RNAs present in RRL. (asm.org)
  • His laboratory develops and exploits fundamental biophysical approaches to understanding the function of ribozymes (catalytic RNAs) and the interactions between RNA and proteins at the level of atomic structure. (nih.gov)
  • Much like green fluorescent protein (GFP) and its variants transformed the study of proteins, fluorescent RNAs have the potential to revolutionize the in vivo study of the tens of thousands of non-coding RNAs that have been discovered in the human transcriptome. (nih.gov)
  • In living cells, RNA in different configurations fulfills several important roles in the process of translating genetic information from deoxyribonucleic acid ( DNA ) into proteins . (newworldencyclopedia.org)
  • RNA would appear to be very poorly equipped to perform chemical catalysis, particularly when compared with proteins. (portlandpress.com)
  • Although the fusion proteins lacked the RNA sequence specificity of the natural enzyme, their activity was within 1-2 kcal.mol(-1) of a truncated alanyl-tRNA synthetase that has aminoacylation activity sufficient to sustain cell growth. (scripps.edu)
  • The male-specific lethal (MSL) complex contains at least five proteins and two noncoding roX (RNA on X) RNAs. (genetics.org)
  • In addition to interacting functions at the level of chromosome morphology, we also find that NURF complex and MSL proteins have opposing effects on roX RNA transcription. (genetics.org)
  • The MSL complex contains at least five proteins (MSL1, MSL2, MSL3, MLE, and MOF) and two noncoding RNAs ( roX1 and roX2 ). (genetics.org)
  • Whether roX genes contribute regionally to MSL targeting on the X chromosome is not evident, however, from the final colocalization of roX RNAs and MSL proteins along the length of the chromosome in wild type or roX1 or roX2 single mutant males. (genetics.org)
  • These are the "classic" genes that get transcribed into RNA that is subsequently spliced, processed and then exported into the cytoplasm where they are translated into proteins. (scienceblogs.com)
  • Although proteins are generally more versatile, RNA does have one advantage, it is a molecule that can pair up with complementary sequences found on other RNA or DNA molecules quite easily. (scienceblogs.com)
  • These 20ish nucleotide long RNA creatures employ this advantage to help recognize target RNA and/or DNA sequences that are then acted on by the real enzymes, proteins. (scienceblogs.com)
  • Cech and Altman showed in the early 1980s that RNA is more than simply a humble bearer of genetic information between DNA and proteins. (newscientist.com)
  • RNA had been observed to play a role in catalysis, a role that biochemists had hitherto attributed exclusively to proteins. (newscientist.com)
  • Following viral uncoating, genomic RNA (in a complex with the viral proteins integrase, polymerase and reverse transcriptase) enters the host cell cytoplasm (12-15). (bioscience.org)
  • However, unlike messenger RNAs, micro-RNAs are not translated to produce proteins. (innovations-report.com)
  • RNA, often thought of as merely the chemical messenger that helps decode DNA s genetic instructions for making proteins, can itself play a crucial role in regulating protein expression. (innovations-report.com)
  • Not surprisingly, this regulation occurs through proteins that bind to RNA. (innovations-report.com)
  • Researchers at Rockefeller University have now developed a method that allows scientists, for the first time, to develop complete lists of RNAs that are regulated by RNA binding proteins. (innovations-report.com)
  • We have developed and validated a new methodology we term CLIP to help scientists interested in the role of RNA binding proteins in biology and disease," says Darnell. (innovations-report.com)
  • We used CLIP to show that an RNA-binding protein called Nova regulates a biologically coherent -- that is, not a random -- set of RNAs whose proteins function at the synapse of nerve cells in the brain. (innovations-report.com)
  • This finding may help us better understand and treat the variety of diseases that involve the misregulation of RNA-binding proteins. (innovations-report.com)
  • RNA splicing is the process by which the initial RNA copy of any gene, known as pre-mRNA, is pieced together to produce a mature mRNA that codes for cellular proteins. (innovations-report.com)
  • More generally for Nova, and for all RNA-binding proteins that are important in biology and human disease, what we really want to know is what is the full array of RNAs that these proteins bind to -- the complete list. (innovations-report.com)
  • Once the complementary RNA is bound, Argonaute proteins either slice the RNA directly, or recruit additional factors to silence the RNA. (kenyon.edu)
  • For example, the sugars can be linked to form polysaccharides such as starch and glycogen , the amino acids can be linked to form proteins , the nucleotides can be linked to form the DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) of chromosomes , and the fatty acids can be linked to form the lipids of all cell membranes . (britannica.com)
  • As with proteins, the specific sequence of nucleotide subunits in an RNA chain gives each macromolecule a unique character. (britannica.com)
  • RNA molecules are much less frequently used as catalysts in cells than are protein molecules, presumably because proteins, with the greater variety of amino acid side chains, are more diverse and capable of complex shape changes. (britannica.com)
  • The paper focuses on the latest developments in our understanding of the interactions between different types of DNA, RNA and proteins and their relevance to the function and health of a range of different organisms. (otago.ac.nz)
  • Francis Crick and Leslie Orgel proposed the idea that RNA once did the work of DNA and proteins in 1968. (wikibooks.org)
  • RNA's catalytic properties do not only apply to itself, but it also catalyzes transesterification-a process necessary for protein synthesis that allows specific peptide sequences and proteins to arise. (wikibooks.org)
  • RNA is the ribosome's tool for synthesizing proteins and catalyzing the formation of peptide bonds. (wikibooks.org)
  • One may ask, if RNA was the precursor of DNA and proteins, how did this evolution occur? (wikibooks.org)
  • N Structural Biochemistry/Transcription Regulation by Mediator ‎ (Created page with '=Human Mediator Complex= The Mediator complex in humans has roles in regulating RNA polymerase II's ability to express genes for proteins. (wikibooks.org)
  • This discovery has quickly resulted in the widespread use of artificial interfering RNAs as an important laboratory research technique for altering the amount of specific proteins inside cells. (wikiversity.org)
  • Several proteins (colored ovals) are required for efficient RNA interference. (wikiversity.org)
  • The siRNA can form a molecular complex with proteins that first strip away the sense strand of RNA, making the antisense inhibitory RNA (iRNA) available for base pairing with messenger RNA (mRNA). (wikiversity.org)
  • DNA, RNA, and proteins) with high molecular absorption and quantum yeild, and good thermal and photo-stability. (sigmaaldrich.com)
  • Scientists have speculated that life on Earth originated in an "RNA world," where RNA fulfilled the dual role of carrying genetic information and conducting metabolism before the dawn of DNA or proteins. (eurekalert.org)
  • Catalytic RNA (ribonucleic acid) are RNA molecules that have enzyme activity. (nature.com)
  • Since the discovery of catalytic RNA molecules (ribozymes), intense research has been devoted to understand their structure and activity. (rsc.org)
  • Among RNA molecules, the large ribozymes, namely group I and group II introns and RNase P, are of special importance. (rsc.org)
  • The RNA moieties of ribonuclease P purified from both E. coli (M1 RNA) and B. subtilis (P-RNA) can cleave tRNA precursor molecules in buffers containing either 60 mM Mg2+ or 10 mM Mg2+ plus 1 mM spermidine. (nih.gov)
  • There are roughly 450 molecules of 4.5 S RNA and 80 molecules of M1 RNA per cell at 0.4 doubling per hour, and this is increased to 5300 and 1060 molecules per cell, respectively, at 2.7 doublings per hour. (diva-portal.org)
  • Ribonucleic acids (RNA) are remarkable molecules. (nih.gov)
  • Furthermore, since RNA molecules are simultaneously capable of carrying genetic information and functioning as catalysts, they can be subjected to evolutionary selection pressures and may have formed the basis for ancestral life. (nih.gov)
  • Dr. Ferré-D'Amaré studies RNA molecules in their many guises. (nih.gov)
  • Dr. Ferré-D'Amaré is also interested in the role of RNA molecules in gene regulation and signal transduction (e.g., riboswitches, non-coding mRNA domains that directly bind to specific small molecules or macromolecules and control transcription, translation, or splicing). (nih.gov)
  • He and his colleagues focus on the way RNA molecules fold into three-dimensional structures and how they are modified post-transcriptionally, and use this information rationally to design new molecular tools. (nih.gov)
  • Finally, he uses the dual function of RNA molecules as information carriers and catalytic agents to artificially evolve them, study their properties, and engineer them. (nih.gov)
  • The "hammerhead" RNA self-cleaving domain can be assembled from two RNA molecules: a large (approximately 34 nucleotide) ribozyme RNA containing most of the catalytically essential nucleotides and a small (approximately 13 nucleotide) substrate RNA containing the cleavage site. (scripps.edu)
  • RNA also serves as a genetic blueprint for certain viruses , and some RNA molecules (called ribozymes) are also involved in the catalysis of biochemical reactions. (newworldencyclopedia.org)
  • RNA molecules may comprise as few as 75 nucleotides or more than 5,000 nucleotides, while a DNA molecule may comprise more than 1,000,000 nucleotide units. (newworldencyclopedia.org)
  • Catalytic experiments have demonstrated that the presence of the coordinated hydroxide anion and water molecules in precatalyst (2) substantially lowered the catalytic activity of the system prepared from (2) in butadiene and isoprene polymerization compared to the catalytic system based on the neodymium tris[bis(2,6-diisopropylphenyl) phosphate] complex, which contains neither OH nor HO ligands. (americanelements.com)
  • Ribozymes are catalytic RNA molecules, some of which catalyze extremely important cellular reactions, notably processing tRNA and mRNA [ 1 ], and condensation of amino acids to form polypeptides [ 2 - 5 ]. (portlandpress.com)
  • We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. (biomedcentral.com)
  • Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life's history. (biomedcentral.com)
  • Ribozymes are catalytic RNA molecules with enzyme-like cleavage properties, that can be designed to target specific RNA sequences within the HIV-1 genome. (bioscience.org)
  • Researchers at Oregon State University have made an important advance in the understanding of "micro-RNA" molecules, which are tiny bits of genetic material that were literally unknown 10 years ago but now represent one of the most exciting new fields of study in biology. (innovations-report.com)
  • In transcription, single-stranded "messenger RNA" molecules that correspond to each expressed gene are produced. (innovations-report.com)
  • Key to the catalytic property of an enzyme is its tendency to undergo a change in its shape when it binds to its substrate, thus bringing together reactive groups on substrate molecules. (britannica.com)
  • However, RNA molecules are thought to have preceded protein molecules during evolution and to have catalyzed most of the chemical reactions required before cells could evolve ( see below The evolution of cells ). (britannica.com)
  • Those modifications led to more efficient sequences of RNA molecules. (wikibooks.org)
  • This work is an extension of our previous studies carried out to investigate the possible catalytic role of minerals in the abiotic synthesis of biologically important molecules. (cambridge.org)
  • Researchers reporting in ACS Nano have found that short RNA molecules can form liquid crystals that encourage growth into longer chains. (eurekalert.org)
  • It was first identified in the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where it catalyzes self-cleavage and joining (ligation) reactions to process the products of rolling circle virus replication into linear and circular satellite RNA molecules. (wikipedia.org)
  • The hairpin ribozyme is an RNA motif that catalyzes RNA processing reactions essential for replication of the satellite RNA molecules in which it is embedded. (wikipedia.org)
  • Both cleavage and end joining reactions are mediated by the ribozyme motif, leading to a mixture of interconvertible linear and circular satellite RNA molecules. (wikipedia.org)
  • These reactions are important for processing the large multimeric RNA molecules that are generated by rolling circle replication. (wikipedia.org)
  • At the end of the replication cycle, these large intermediates of satellite RNA replication are processed down to unit length molecules (circular or linear) before they can be packaged by viruses and carried to other cells for further rounds of replication. (wikipedia.org)
  • Ferris JP (2006) Montmorillonite catalyzed formation of RNA oligomers: the possible role of catalysis in the origins of life. (springer.com)
  • In this work, we examined a fragment of Escherichia coli alanyl-tRNA synthetase, which catalyzes aminoacyl adenylate formation but is virtually inactive for catalysis of RNA microhelix aminoacylation. (scripps.edu)
  • Catalysis is relevant to many aspects of environmental science , e.g. the catalytic converter in automobiles and the dynamics of the ozone hole . (wikipedia.org)
  • We have now moved out of this RNA world to investigate other long noncoding RNAs, where catalysis is carried out by RNPs (RNA-protein complexes). (hhmi.org)
  • Over the past decade, there have been a variety of fundamental insights into ribozymes which have changed the perspective on RNA catalysis. (springer.com)
  • Cech TR (1987) The chemistry of self-splicing RNA and RNA enzymes. (springer.com)
  • Although monomeric forms of RNase E and RNase G can cut RNA, the ability of these enzymes to discriminate between RNA substrates on the basis of their 5′ phosphorylation state requires the formation of protein multimers. (pnas.org)
  • The greater susceptibility of 5′-monophosphorylated RNAs to cleavage by these enzymes may help to ensure the rapid degradation of the downstream products of initial endonucleolyic cleavage, which differ from their primary-transcript precursors in being 5′-monophosphorylated rather than 5′-triphosphorylated. (pnas.org)
  • Within the catalytic domain of these enzymes, there presumably is a site that can interact productively with RNA 5′ ends that are monophosphorylated but not with those that bear a triphosphate or hydroxyl, yet the presence of such a 5′-end-binding site has not been verified empirically. (pnas.org)
  • Some sequences of RNA can catalyze biochemical reactions, much like protein enzymes. (sciencebuddies.org)
  • The RNA acts as a true catalyst under these conditions whereas the protein moieties of the enzymes alone show no catalytic activity. (nih.gov)
  • RNAPs (RNA polymerases) are key enzymes of the cellular gene expression machineries of all organisms. (biochemsoctrans.org)
  • Catalytic RNAs, known as ribozymes, act as true enzymes and are implicated in important biological processes, such as protein synthesis, mRNA splicing, transcriptional regulation and retroviral replication. (eurekaselect.com)
  • RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes, some of them guided by non-coding RNAs. (newworldencyclopedia.org)
  • The protein enzymes catalyze a wide variety of reactions and can generate huge catalytic rate enhancements. (portlandpress.com)
  • Protein enzymes are just better - they are smaller and much more versatile then their RNA counterparts. (scienceblogs.com)
  • The RNA enzymes that are still with us are probably too central to biological function for them to be replaced. (scienceblogs.com)
  • Remarkably, the plant-specific RNA silencing enzymes, Pol IV and Pol V differ from Pols I, II and III at ~140 of these positions, yet remain capable of RNA synthesis. (indiana.edu)
  • Viral reverse transcriptase and polymerase enzymes convert the genomic RNA to cDNA, and a dsDNA copy is transported to the cell nucleus and then integrated into the host genome by the action of the viral integrase protein. (bioscience.org)
  • Much of the mammalian genome is transcribed into long non-coding RNAs, but their biological roles -- such as transcriptional regulation via recruitment of histone-modifying enzymes - are only beginning to be discovered. (keystonesymposia.org)
  • Most of the catalytic macromolecules in cells are enzymes . (britannica.com)
  • Some enzymes are macromolecules of RNA , called ribozymes. (britannica.com)
  • ORNL process improves catalytic rate of enzymes by 3,0. (bio-medicine.org)
  • Studies of this reaction in multiple ribozymes have served to establish that the reaction chemistry (catalytic mechanism) is an endogenous property of the RNA molecule itself and is not mediated by metal ions, as is true for some protein enzymes and some other ribozymes. (wikipedia.org)
  • These catalytic RNA sequences are called ribozymes. (sciencebuddies.org)
  • Four such hammerheads that contained identical catalytic core sequences but differed in the base composition of the helices that are involved in substrate binding had been reported to vary in cleavage rates by more than 70-fold under similar reaction conditions. (scripps.edu)
  • This polymerase-based mechanism may result in portions of noncoding RNA sequences being evolutionarily conserved for efficient folding during transcription. (pnas.org)
  • Upstream catalytic targeting of specific RNA sequences offers an alternative platform for drug discovery to achieve more potent and selective treatment through antisense interference with disease-relevant RNAs. (novelconjugates.com)
  • Zeng, Y. & Cullen, B.R. Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. (nature.com)
  • Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. (biomedcentral.com)
  • They found that at high concentrations, short RNA sequences (either 6 or 12 nucleotides long) spontaneously ordered into liquid crystal phases. (eurekalert.org)
  • The hairpin ribozyme has been identified in only 3 naturally occurring sequences: satellite RNA of tobacco ringspot virus (sTRSV) satellite RNA of chicory yellow mottle virus (sCYMV) satellite RNA of arabis mosaic virus (sARMV) Smaller artificial versions of the hairpin ribozyme have been developed to enable a more detailed experimental analysis of the molecule. (wikipedia.org)
  • RNAPs (RNA polymerases) are complex molecular machines containing structural domains that co-ordinate the movement of nucleic acid and nucleotide substrates through the catalytic site. (biochemsoctrans.org)
  • The direct physical contacts between all these key players immediately suggest that conformational changes in any of them (especially in the bridge-helix) can be 'sensed' by numerous active elements within the catalytic site and thus directly influence many enzymatic parameters of the nucleotide addition cycle (and other chemistries) in a co-ordinated manner. (biochemsoctrans.org)
  • Ribonucleic acid or RNA is a polymer or chain of nucleotide units, each comprising a nitrogenous base ( adenine , cytosine , guanine , or uracil ), a five-carbon sugar ( ribose ), and a phosphate group. (newworldencyclopedia.org)
  • and other types of RNA, microRNAs (miRNAs) play a role in regulating gene expression, while small nuclear(sn) RNA helps with assuring that mRNA contains no nucleotide units that would lead to formation of a faulty protein. (newworldencyclopedia.org)
  • Furthermore, RNA uses the nucleotide uracil in its composition, instead of the thymine that is present in DNA. (newworldencyclopedia.org)
  • RNA is a nucleic acid , a complex, high-molecular-weight macromolecule composed of nucleotide chains whose sequence of bases conveys genetic information . (newworldencyclopedia.org)
  • The most common nucleotide bases are the purines adenine and guanine and the pyrimidines cytosine and thymine (or uracil in RNA). (newworldencyclopedia.org)
  • The RNA polymer features a ribose and phosphate backbone with one of four different nucleotide bases- adenine , guanine , cytosine , and uracil -attached to each ribose-phosphate unit. (newworldencyclopedia.org)
  • Through this process, a 50 nucleotide minimal catalytic domain and a 14 nucleotide substrate were identified. (wikipedia.org)
  • Almost nothing is known about the mechanism by which a monophosphate at the 5′ end of an RNA molecule is able to influence the rate of ribonuclease cleavage at an internal site that may be far downstream. (pnas.org)
  • Anastassios Vourekas, Dimitra Kalavrizioti, Constantinos Stathopoulos and Denis Drainas, " Modulation of Catalytic RNA Biological Activity by Small Molecule Effectors", Mini-Reviews in Medicinal Chemistry (2006) 6: 971. (eurekaselect.com)
  • RNA is usually single stranded, while DNA naturally seeks its stable form as a double stranded molecule. (newworldencyclopedia.org)
  • Not only that, many biologists now suspect that RNA was the first kind of information-carrying molecule to have emerged at the origin of life itself. (newscientist.com)
  • This enzyme is a molecule built from a protein and an RNA. (newscientist.com)
  • The team focused on studies of the maturation of an RNA molecule found in ribosomes, cellular bodies where protein synthesis takes place. (newscientist.com)
  • On this frontier of biology, experts say, the most intriguing new component is micro-RNA, a minuscule type of regulatory molecule that had seemed insignificant even in the extraordinarily tiny, microscopic world of cell biology. (innovations-report.com)
  • At the same time, bacterial non-coding RNAs are being found to function as small-molecule-sensing riboswitches and as elements of the CRISPR defense system. (keystonesymposia.org)
  • RNA as a catalytic and regulatory molecule. (otago.ac.nz)
  • This proposes that there may be a pre-RNA molecule that used RNA or by change created RNA as a side product. (wikibooks.org)
  • In the 1970s, Cech was studying the splicing of RNA in a single-celled organism, Tetrahymena thermophila , when he discovered that an unprocessed RNA molecule could splice itself. (wikibooks.org)
  • These nucleotides sequenced spontaneously and randomly, eventually forming an RNA molecule (or a similar molecule) with catalytic characteristics. (wikibooks.org)
  • Therefore, this points to the fact that RNA is multifunctional, and can act as a synthesizer, transporter, messenger, and ribosome molecule. (wikibooks.org)
  • Since DNA is a more stable molecule than RNA, it makes sense for DNA to adapt to the environment and take over this job of RNA. (wikibooks.org)
  • This is a commonly used strategy for separating those parts of a self-processing RNA molecule that are essential for the RNA processing reactions from those parts which serve unrelated functions. (wikipedia.org)
  • When the precursor to E. coli 4.5S RNA is used as a substrate, only the enzyme complexes formed with M1 RNA from E. coli and the protein moieties from either bacterial species are active. (nih.gov)
  • section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes. (uniprot.org)
  • Finally, RNA's central role in life suggests that its potential therapeutic value is barely tapped but already clinically validated: approximately 80 percent of antibiotics in use today target a single type of RNA-containing enzyme, the ribosome, and most do so by targeting its non-coding RNA component. (nih.gov)
  • RNA polymerase (RNAP) is the essential enzyme responsible for transcribing genetic information stored in DNA to RNA. (elsevier.com)
  • Sutherland, C & Murakami, KS 2018, ' An Introduction to the Structure and Function of the Catalytic Core Enzyme of Escherichia coli RNA Polymerase ', EcoSal Plus , vol. 8, no. 1. (elsevier.com)
  • In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. (port.ac.uk)
  • RNA polymerase II (also called RNAP II and Pol II ) is an enzyme found in eukaryotic cells. (wikipedia.org)
  • RNA-splicing enzyme,' recalls Cech. (newscientist.com)
  • With this as a model, Agarwal's team theorized that it should be possible to improve the catalytic efficiency of enzyme reactions by attaching chemical elements on the surface of an enzyme and manipulating them with the use of tuned light. (bio-medicine.org)
  • To investigate the mechanism by which 5′-terminal phosphorylation can influence distant cleavage events, we have developed fluorogenic RNA substrates that allow the activity of RNase E and RNase G to be quantified much more accurately and easily than before. (pnas.org)
  • Kinetic analysis of the cleavage of these substrates by RNase E and RNase G has revealed that 5′ monophosphorylation accelerates the reaction not by improving substrate binding, but rather by enhancing the catalytic potency of these ribonucleases. (pnas.org)
  • Furthermore, the presence of a 5′ monophosphate can increase the specificity of cleavage site selection within an RNA. (pnas.org)
  • In view of the homology of RNase G to the catalytic domain of RNase E, it is not surprising that they have a similar cleavage site specificity, with both preferring to cut RNA within single-stranded regions that are AU-rich ( 8 , 9 ). (pnas.org)
  • Remarkably, such substrates are cleaved by full-length RNase E, N-RNase E, or RNase G more than an order of magnitude faster than otherwise identical RNAs bearing a 5′-terminal triphosphate or hydroxyl group, even though cleavage may occur far from the 5′ end ( 9 - 11 ). (pnas.org)
  • The antibiotics also disrupted structural contacts that have been proposed to bring the 5' cleavage site of the intron into proximity to the catalytic core. (sciencemag.org)
  • The nucleolytic ribozymes are a diverse group of smaller RNA species that generate site-specific cleavage and ligation of RNA. (portlandpress.com)
  • Ligation is the reverse of this reaction [ 26 - 30 ] and occurs if the cleavage product RNA is held in place by the structure of the ribozyme. (portlandpress.com)
  • Hybridization of the DCs bearing two spatially-separated recognition motifs with the target tRNAPhe placed the peptide adjacent to a single-stranded RNA region and promoted cleavage within the 'action radius' of the catalytic peptide. (novelconjugates.com)
  • RNA cleavage without hydrolysis. (qub.ac.uk)
  • Preferred RNA oligonucleotide multimers contain ribozymes capable of both cis (autolytic) and trans cleavage. (google.com)
  • The catalytic activity of the trans cleaving hammerhead ribozyme 2as-Rz12, with long antisense flanks of 128 and 278 nt, was tested under a wide range of different reaction conditions for in vitro cleavage of a 422 nt RNA transcript derived from human immunodeficiency virus type 1 (HIV-1). (biomedsearch.com)
  • In common with several other ribozymes and protein ribonucleases, the cleavage reaction of the hairpin ribozyme generates RNA fragments with termini consisting of a 2',3'-cyclic phosphate and a 5'-hydroxyl group. (wikipedia.org)
  • The ligation reaction appears to be a simple reversal of cleavage, i.e. covalent joining of RNA fragments ending with a 2',3'-cyclic phosphate and a 5'-hydroxyl group to generate the ordinary 3'-5' phosphodiester linkage used in both RNA and DNA. (wikipedia.org)
  • The function of a ribozyme depends upon the primary sequence of the RNA which folds into a 3-D structure. (sciencebuddies.org)
  • In a previous contribution, we discovered a variant of the Azoarcus group I ribozyme that represents a local peak in the RNA fitness landscape. (royalsocietypublishing.org)
  • The glmS ribozyme is being studied as a potentially valuable target for novel antibiotics, and also an experimental platform with which to understand how RNA targets can evolve antibiotic resistance. (nih.gov)
  • By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca 2+ ion as a sign for the more catalytically useful Mg 2+ ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. (biomedcentral.com)
  • In addition to the genomic RNA, several RNA intermediates, including splice variants, can be targeted by a single ribozyme. (bioscience.org)
  • The basic mechanisms of antisense (AS), ribozyme (Rz), and RNA interference (RNAi) approaches to PTGS will be presented here. (hindawi.com)
  • Comparison of the properties of antisense, ribozyme, and RNA i . (hindawi.com)
  • 11. The method of claim 10 wherein the ribozyme is a hairpin, hammerhead-motif, or hepatitis delta catalytic ribozyme. (google.com)
  • Twin ribozyme mediated removal of nucleotides from an internal RNA site. (sigmaaldrich.com)
  • The hairpin ribozyme is a small section of RNA that can act as a ribozyme. (wikipedia.org)
  • Like the hammerhead ribozyme it is found in RNA satellites of plant viruses. (wikipedia.org)
  • Domain B (helix 3 - loop B - helix 4) is larger and contains the primary catalytic determinants of the ribozyme. (wikipedia.org)
  • These data suggest that the expression of both 4.5 S RNA and M1 RNA genes are growth-rate regulated, but not through the same mechanism. (diva-portal.org)
  • We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome. (port.ac.uk)
  • The mechanism of the nucleolytic ribozymes and potential catalytic strategies. (portlandpress.com)
  • Tom Cech and his research group are studying the structure and mechanism of long noncoding RNAs and RNA-protein complexes, including telomerase and complexes that regulate transcription. (hhmi.org)
  • They reveal for the first time a new mechanism by which micro-RNA can stop the function of messenger-RNA by literally cutting it in half, interfering with the normal function of specific messenger RNAs in gene expression. (innovations-report.com)
  • We propose a catalytic mechanism in which lysine-180 acts as a catalytic base and deprotonates the reactive hydroxyl group of caffeoyl-CoA. (plantphysiol.org)
  • Collectively, these data give a new perspective on the catalytic mechanism of CCoAOMTs and provide a basis for the functional diversity exhibited by type 2 plant OMTs that contain a unique insertion loop (residues 208-231) conferring affinity for phenylpropanoid-CoA thioesters. (plantphysiol.org)
  • RNA interference was discovered as a mechanism used by cells for regulating gene expression . (wikiversity.org)
  • Parallels between these results and previously observed protection of 16S ribosomal RNA by aminoglycosides raise the possibility that group I intron splicing and transfer RNA selection by ribosomes involve similar RNA structural motifs. (sciencemag.org)
  • Fundamental to the life and destiny of every cell is the regulation of protein synthesis through ribosome biogenesis, which begins in the nucleolus with the production of ribosomal RNA (rRNA). (biologists.org)
  • Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. (port.ac.uk)
  • This first class of RNAs, which include ribosomal RNAs, tRNAs and snRNAs, are the most ancient genes in all of biology. (scienceblogs.com)
  • There is by far more ribosomal RNA in every cell then there is DNA or protein. (scienceblogs.com)
  • The first thing to do was to isolate the precursor ribosomal RNA, so that splicing could be observed cleanly in the test tube. (newscientist.com)
  • Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA. (biomedsearch.com)
  • Catalytic RNAs are involved in a number of biological processes, including RNA processing and protein synthesis. (nature.com)
  • These results suggest that if RNA was somehow incorporated into a primitive form of RNA-based thermophilic life, either it must be protected from random hydrolytic events, or the rate of synthesis must exceed the rate of hydrolysis. (springer.com)
  • During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a template for the production of more vRNAs. (rcsb.org)
  • Deletion of both relA and spoT, the two genes that are responsible for synthesis of ppGpp, does not affect the rate of synthesis of either RNA species. (diva-portal.org)
  • the structural factors that direct nucleolar assembly and disassembly are just as important in controlling rRNA synthesis as are the catalytic activities that synthesize rRNA. (biologists.org)
  • Dr. Ferré-D'Amaré's second translational research focus is on the role of a catalytic RNA-glmS-in controlling the synthesis of the bacterial cell wall. (nih.gov)
  • Dr. Ferré-D'Amaré and colleagues elucidated the structural basis for fluorescence of several RNA-chromophore complexes, and are leveraging this knowledge to generate optimized tools to study the synthesis, maturation, targeting, localization and turnover of RNAs that play essential roles in metabolism, development and disease progression. (nih.gov)
  • The connectedness of living organisms can be seen in the ubiquitousness of RNA in living cells and in viruses throughout nature, and in the universal role of RNA in protein synthesis. (newworldencyclopedia.org)
  • When compared with Mg 2+ -induced refolding of full-length RNAs, two obvious properties that influence RNA folding during transcription are the 5′ to 3′ polarity of RNA synthesis and the transcriptional speed of the RNA polymerase ( 4 - 8 ). (pnas.org)
  • These results show that, starting with an activity for adenylate synthesis, barriers are relatively low for building catalytic units for aminoacylation of RNA helices. (scripps.edu)
  • They have been known by the biological community for the past 40 years and have some of the most important activities inside the cell, such as protein synthesis and RNA splicing. (scienceblogs.com)
  • It is thus involved in maintaining cellular guanine deoxy- and ribonucleotide pools needed for DNA and RNA synthesis. (genecards.org)
  • The present invention provides methods for synthesis and therapeutic use of DNA and RNA oligonucleotides and analogs. (google.com)
  • The RNA synthesis is performed by combining a circular single-stranded. (google.com)
  • The RNA synthesis is performed by combining a circular single-stranded oligonucleotide template with an effective RNA polymerase and at least two types of ribonucleotide triphosphate to form an RNA oligonucleotide multimer comprising multiple copies of the desired RNA oligonucleotide sequence. (google.com)
  • In addition, bacterial RNA polymerases pause during transcriptional elongation ( 9 , 10 ). (pnas.org)
  • Catalytic subunits of DNA-dependent RNA polymerases of bacteria, archaea and eukaryotes share hundreds of ultra-conserved amino acids. (indiana.edu)
  • In the paused complexes, the nascent RNAs form labile structures that sequester these upstream portions in a manner to possibly guide folding. (pnas.org)
  • Dinuclear neodymium and lanthanum bis(2,6-diisopropylphenyl) phosphate complexes bearing a hydroxide ligand: catalytic activity of the Nd complex in 1,3-diene polymerization. (americanelements.com)
  • Together, the studies reviewed herein reveal the versatility and programmability of RNA-induced silencing complexes and emphasize the importance of both upstream biogenesis and downstream silencing factors. (nature.com)
  • These observations demonstrate that the secondary structure of substrate RNA can be a major determinant of hammerhead catalytic efficiency. (scripps.edu)
  • These contribute to or even provide the catalytic activity and substrate specificity of the complex. (waw.pl)
  • Unexpectedly, catalytic autolabeling reveals that TFB2 interacts with the priming substrate, suggesting that TFB2 acts as a transient component of the catalytic site of the initiation complex. (researchwithrutgers.com)
  • Mineral components of the Murchison meteorite were investigated in terms of potential catalytic effects on synthetic and hydrolytic reactions related to ribonucleic acid. (springer.com)
  • The RNA World Hypothesis speculates that the origin of life began with ribonucleic acid ( RNA ) because of its ability to serve both as a storage for genetic information and enzymatic activity. (wikibooks.org)
  • In Arabidopsis, DNA methylation can be induced by double-stranded RNA through the RNA interference (RNAi) pathway, a response known as RNA-directed DNA methylation. (nih.gov)
  • Since its relatively recent discovery, RNA interference (RNAi) has emerged as a potent, specific and ubiquitous means of gene regulation. (nature.com)
  • This section and the next few sections briefly introduce RNA interference (RNAi) and will orient you towards the activities . (wikiversity.org)
  • Elucidating these mechanisms is crucial for explaining how RNA sequence and structure control mRNA lifetimes. (pnas.org)
  • Despite intense research, there is still an astonishing degree of uncertainty concerning the catalytic mechanisms of RNAPs. (biochemsoctrans.org)
  • Identifying the mechanisms of telomerase assembly and catalytic function is essential for understanding the role of telomerase in immortalization. (asm.org)
  • Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. (portlandpress.com)
  • In this Review, we focus on mechanisms and structures that govern RNA silencing in higher organisms. (nature.com)
  • Wilson, R.C. & Doudna, J.A. Molecular mechanisms of RNA interference. (nature.com)
  • To gain insights into the molecular mechanisms underlying PKR's growth regulatory properties, we examined the biological and biochemical properties of PKR variants containing either a mutation in catalytic domain II (PKR-M1) or a deletion of RNA binding domain I (PKR-M7) in both reticulocyte translation extracts and in vitro kinase assays with purified reagents and compared these results with those using the same mutants stably expressed in vivo. (elsevier.com)
  • Two generally accepted mechanisms of AS ODN inhibition of gene expression are both dependent upon strong annealing to the target RNA (Figure 1 ). (hindawi.com)
  • Gene silencing is one of a number of mechanisms for post transcriptional regulation of RNA within eukaryotic cells. (kenyon.edu)
  • The genes that encode the two roX RNAs are positioned at distinct locations, near the tip ( roX1 ) and the middle ( roX2 ) of the euchromatic portion of the X chromosome ( Figure 1A ). (genetics.org)
  • RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein -coding genes in living cells. (wikipedia.org)
  • Now apparently the new model is that the DNA encodes more than genes, it has all sorts of weird stuff mostly noncoding-RNAs, and that there is mass confusion in the biomedical sciences. (scienceblogs.com)
  • 2 - Genes that specify non-coding RNAs (ncRNAs). (scienceblogs.com)
  • These genes produce two types of RNAs, catalytic RNAs that act like molecular machines and are known as ribozymes and non catalytic small RNAs that modify the expression of classic genes. (scienceblogs.com)
  • So now we have the second class of genes that specify, ncRNAs, the newly discovered small regulatory RNAs. (scienceblogs.com)
  • 3 - DNA elements that modulates how genes are transcribed into RNA and how the genome is organized. (scienceblogs.com)
  • They had just discovered that virtually all genes from higher organisms carried 'inert', non-coding regions - introns - that had to be removed when the RNA message was formed. (newscientist.com)
  • And we re now also learning the role of micro-RNA in controlling expression of some important genes. (innovations-report.com)
  • Micro-RNAs are actually produced by the transcription of tiny genes, in regions of the genome that were previously thought to be vacant or useless DNA. (innovations-report.com)
  • Base pair-complementary RNA strands (ssRNA) can be produced by transcription of both template DNA strands of some genes (Figure 1). (wikiversity.org)
  • Biochemical and biophysical investigations, supported by recent findings from X-ray crystal structures, allow clarifying and rationalizing both the structural and catalytic roles of metal ions in large ribozymes. (rsc.org)
  • Finally, Dr. Ferré-D'Amaré's interest in non-coding RNA biology has led him to structural and molecular engineering studies of fluorescent RNAs. (nih.gov)
  • RNA is very similar to DNA, but differs in a few important structural details. (newworldencyclopedia.org)
  • At the centre of the PNPase ring is a tapered channel with an adjustable aperture where RNA bases stack on phenylalanine side chains and trigger structural changes that propagate to the active sites. (port.ac.uk)
  • I formed the idea that the RNA was important not just as a structural component but as the catalytic agent,' said Altman. (newscientist.com)
  • Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. (rutgers.edu)
  • These results indicate that catalytic nucleic acids can effectively cleave Smn target RNA in an environment closely resembling that present in the cell and thus have potential for interference with Smn gene expression in cells and in vivo. (ox.ac.uk)
  • Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans . (nature.com)
  • Castel, S.E. & Martienssen, R.A. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. (nature.com)
  • RNA interference requires that two base pair-complementary strands of RNA to come together to form double stranded RNA [2] . (wikiversity.org)
  • The Nobel Prize in Physiology or Medicine in 2006 was awarded to Andrew Z. Fire and Craig C. Mello for their research on RNA interference [3] . (wikiversity.org)
  • The goal of this learning project is to complement the Wikipedia article about RNA interference in two ways. (wikiversity.org)
  • This means providing learning resources for people who would normally be unable to understand a technical Wikipedia article on the topic of RNA interference. (wikiversity.org)
  • Explore a user-friendly introduction to the practical medical implications of RNA interference that arise from the Nobel Prize-winning scientific research of Andrew Z. Fire and Craig C. Mello. (wikiversity.org)
  • If you were able to read and appreciate the Wikipedia article about RNA interference then continue reading below and participate in further exploration of this subject. (wikiversity.org)
  • There is also active study of the potential value of RNA interference for medical applications [4] . (wikiversity.org)
  • The normal function of RNA interference inside cells depends on the production of double stranded RNA (dsRNA). (wikiversity.org)
  • An important aspect of RNA interference is its role in protecting organisms from some deleterious effects of viruses [8] . (wikiversity.org)
  • Such a role for RNA interference was first found in plants, but has also been found in some animals [9] . (wikiversity.org)
  • RNA interference is now a widely used biology research technique that can be applied to both cultured cells [10] and whole animals [11] . (wikiversity.org)
  • RNA interference can be used to selectively reduce the level of expression of a specific protein. (wikiversity.org)
  • Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. (nature.com)
  • 9. The method of claim 8 wherein the biologically active RNA oligonucleotide comprises a catalytic RNA, an antisense RNA, or a decoy RNA. (google.com)
  • In other cases, the protein-coding RNA sense strand might be produced by a virus and the antisense RNA strand produced by the host cell. (wikiversity.org)
  • The sense and antisense RNA strands form double strand RNA (Figure 2, top) that is processed to small (about 20 base pairs long) inhibitory RNA (siRNA). (wikiversity.org)
  • In the majority of RNAP X-ray structures from bacterial, archaeal and eukaryotic sources, the bridge-helix takes up a more or less straight α-helical conformation and thus appears as a rod-like structure next to the catalytic site [ 8 - 16 ]. (biochemsoctrans.org)
  • The eukaryotic RNA exosome: same scaffold but variable catalytic subunits. (waw.pl)
  • Here, we review the latest findings concerning catalytic subunits of eukaryotic exosomes, and we discuss the apparent need for differential composition and subcellular distribution of exosome variants. (waw.pl)
  • The PKR- M1 variant was able to reverse the translational inhibitory effects and increased eukaryotic initiation factor (eIF)-2α phosphorylation levels caused by addition of double-stranded RNA to reticulocyte extract, whereas PKR-M7 could not. (elsevier.com)
  • Influenza RNA polymerase is composed of three subunits: PB1, PB2 and PA. (rcsb.org)
  • In the presence of low concentrations of Mg2+, in vitro, the RNA and protein subunits from one species can complement subunits from the other species in reconstitution experiments. (nih.gov)
  • Notably, its catalytic potential, derived exclusively from associated subunits, differs between the nuclear and cytoplasmic versions of the complex. (waw.pl)
  • RNase E is an endonuclease that plays a central role in RNA processing and degradation in Escherichia coli . (pnas.org)
  • We show that efficient folding during transcription of three conserved noncoding RNAs from Escherichia coli , RNase P RNA, signal-recognition particle RNA, and tmRNA is facilitated by their cognate polymerase pausing at specific locations. (pnas.org)
  • A previous work on the folding during transcription of a circularly permuted version of the Bacillus subtilis RNase P RNA demonstrated that pausing at a specific site alters its folding during transcription by Escherichia coli RNA polymerase ( 11 ). (pnas.org)
  • Single-stranded RNA is similar to the protein polymer in its natural propensity to fold back and double up with itself in complex ways assuming a variety of biologically useful configurations. (newworldencyclopedia.org)
  • [5] Many of them are involved in the formation of a preinitiation complex , which, together with RNA polymerase II , bind to and read the single-stranded DNA gene template. (wikipedia.org)
  • Single-stranded ODNs are transfected or transduced into cells where they diffuse and encounter target RNAs in either the nucleus or cytoplasm. (hindawi.com)
  • Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism. (genecards.org)
  • RNA nucleotides contain ribose while DNA nucleotides contain the closely related sugar deoxyribose . (newworldencyclopedia.org)
  • Otherwise, RNA does not remain in a helical ring, as does DNA, since the chain of nucleotides would be easily broken apart. (wikibooks.org)
  • Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. (nih.gov)
  • There are also numerous modified bases and sugars found in RNA that serve many different roles. (newworldencyclopedia.org)
  • RNA modifications have been shown to play important roles in the function and metabolism of all types of RNA in eukaryotes and in bacteria. (springer.com)
  • The biochemical roles of the two noncoding RNAs in the MSL complex, roX1 and roX2 , are largely unknown. (genetics.org)
  • The catalytically active amino-terminal half of the protein (N-RNase E: residues 1-498) is alone sufficient for the enzyme's ribonuclease activity, whereas the carboxyl half of the protein (residues 499-1061) contains both an arginine-rich region and a carboxy-terminal domain that serves as a scaffold for the assembly of a multiprotein complex known as the RNA degradosome ( 4 , 5 ). (pnas.org)
  • Chemically stabilized hammerhead ribozymes are nuclease-resistant, RNA-based oligonucleotides that selectively bind and cleave specific target RNAs. (aacrjournals.org)
  • RNA oligonucleotides are synthesized using a small, circular DNA template which lacks an RNA polymerase promoter sequence. (google.com)
  • Preferably, the RNA oligonucleotide multimer is cleaved to produce RNA oligonucleotides having well-defined ends. (google.com)
  • RNA self-ligation: from oligonucleotides to full length ribozymes. (sigmaaldrich.com)
  • The initial aim of this work was therefore to determine whether and how Bre5 and Ubp3 are linked to nuclear RNA metabolism. (elifesciences.org)
  • Our lab's early work on catalytic RNAs (ribozymes) helped to establish that RNA is not restricted to being a passive carrier of genetic information, but can have an active role in cellular metabolism. (hhmi.org)
  • All three RNAs, RNase P RNA,signal-recognition particle (SRP) RNA, and tmRNA, contain numerous long-range helices. (pnas.org)
  • Single mutations in the Asp-Asp-His catalytic motif of AGO4 do not affect siRNA-binding activity but abolish its catalytic potential. (nih.gov)
  • siRNA accumulation and non-CpG DNA methylation at some loci require the catalytic activity of AGO4, whereas others are less dependent on this activity. (nih.gov)
  • First, AGO4 can recruit components that signal DNA methylation in a manner independent of its catalytic activity. (nih.gov)
  • Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects. (nih.gov)
  • a href='/help/catalytic_activity' target='_top'>More. (uniprot.org)
  • In addition, many mutations within this domain cause a substantial increase in the RNAP catalytic activity ('superactivity'), suggesting that the RNAP active site is conformationally constrained. (biochemsoctrans.org)
  • PdN /C, which is closely related to the catalytic activity results. (thefreedictionary.com)
  • From the figure it is clear that the catalytic activity increased with prolonged the immobilization time and the maximum value was obtained under immobilization allowed to proceeding for 5h. (thefreedictionary.com)
  • The catalytic activity revealed by samples of natural alumosilicates depends most likely on content of the porous component as zeolite one. (thefreedictionary.com)
  • 4] loading on the catalytic activity of the unmodified zeolite P(wt. (thefreedictionary.com)
  • The mixed 10VSi presented low catalytic activity for the conversion of NO into [N. (thefreedictionary.com)
  • deposited very small 3-10 nm sized AuNPs on metal oxides, such as TiO2, Fe2O3, Co3O4 and NiO, which displayed surprisingly high catalytic activity for CO oxidation at low temperature (-70 0C) [24]. (thefreedictionary.com)
  • The effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons (which reduce the catalytic activity) or promoters (which increase the activity and also affect the temperature of the reaction). (wikipedia.org)
  • Our results show that residues Cys 48 and Cys 96 are required for catalytic activity. (biochemj.org)
  • Isolated RNA inhibits the catalytic activity of topo II beta in vitro through the interaction with a specific 50-residue region of the CTD (termed the CRD). (okayama-u.ac.jp)
  • Taken together, these results suggest that both the subnuclear distribution and activity regulation of topo II beta are mediated by the interplay between cellular RNA and the CRD. (okayama-u.ac.jp)
  • GO annotations related to this gene include RNA binding and oxidoreductase activity . (genecards.org)
  • TFIIE affects TFIIH's catalytic activity. (wikipedia.org)
  • A TUT7 CM structure trapped in the monoU activity staterevealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins to favor monoU addition. (proteopedia.org)
  • Simulations performed on Jaguar also allowed researchers to better understand how the enzyme's internal motions control the catalytic activity. (bio-medicine.org)
  • This case was different from the circularly permuted P RNA study, in that pausing did not alter the structure of the RNA in the paused complex. (pnas.org)
  • Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. (nih.gov)
  • In marked contrast, the potential catalytic resources of RNA are limited to four similar nucleobases, ribose with a secondary alcohol (2′-hydroxyl) and an anionic phosphodiester with associated hydrated metal ions that can bind site-specifically (inner sphere complex) or more dynamically in atmospheric mode. (portlandpress.com)
  • [6] The cluster of RNA polymerase II and various transcription factors is known as a basal transcriptional complex (BTC). (wikipedia.org)
  • The TFIID-TFIIA-TFIIB (DAB)-promoter complex subsequently recruits RNA polymerase II and TFIIF. (wikipedia.org)
  • The RNA exosome is a versatile ribonucleolytic protein complex that participates in a multitude of cellular RNA processing and degradation events. (waw.pl)
  • So when a miRNA binds to a region of an mRNA, the RISC protein complex can then direct this mRNA to P-bodies where the RNA is silenced. (scienceblogs.com)
  • Telomerase is a fascinating biochemical system because a large DNA-protein complex (the chromosome end) must interact productively with an RNA-protein complex (telomerase). (hhmi.org)
  • HIV-1 is a lentivirus, a separate genus of the Retroviridae, which are complex RNA viruses that integrate into the genome of host cells and replicate intracellularly. (bioscience.org)
  • Unique long double stranded RNA's are processed into microRNA (miRNA) which are then uptaken by the RNA induced silencing complex (RISC). (kenyon.edu)
  • The protein-containing complex was named "RNA-induced silencing complex", RISC. (wikiversity.org)
  • Diagram showing how the anti-sense RNA (the yellow strand in this diagram) of the RISC complex targets destruction of complementary mRNA. (wikiversity.org)
  • One strand from the miRNA duplex (miR-5p/miR-3p duplex) containing the less stable 5′ end is preferentially selected and loaded onto the RNA-induced silencing complex (RISC) to produce a functional, mature miRNA (MIR) [Khvorova et al. (wiley.com)
  • Ribozymes are non-coding RNAs that can precisely position reactants and accelerate chemical reactions by preferentially stabilizing their transition states. (nih.gov)
  • Catalysts may bind to the reagents to polarize bonds, e.g. acid catalysts for reactions of carbonyl compounds, or form specific intermediates that are not produced naturally, such as osmate esters in osmium tetroxide -catalyzed dihydroxylation of alkenes , or cause dissociation of reagents to reactive forms, such as chemisorbed hydrogen in catalytic hydrogenation . (wikipedia.org)
  • Catalytic reactions are preferred in environmentally friendly green chemistry due to the reduced amount of waste generated, [4] as opposed to stoichiometric reactions in which all reactants are consumed and more side products are formed. (wikipedia.org)
  • WHEN Tom Cech announced in 1982 that RNA catalyses biochemical reactions, he received instant acclaim from his peers. (newscientist.com)
  • Since their discovery, RNA has been shown to catalyse a series of important reactions. (newscientist.com)
  • In the presence of montmorillonite, a member of the phyllosilicate group minerals that are abundant on Earth and identified on Mars, activated RNA monomers, namely 5′-phosphorimidazolides of nucleosides (ImpNs), undergo condensation reactions in aqueous electrolyte solution producing oligomers with similar structures to short RNA fragments. (cambridge.org)
  • Here we show that AGO4 binds to small RNAs including small interfering RNAs (siRNAs) originating from transposable and repetitive elements, and cleaves target RNA transcripts. (nih.gov)
  • However, in plants, most siRNAs are generated by RNA-dependent RNA polymerase [1] . (wikiversity.org)
  • RNA-dependent RNA polymerase which is responsible for replication and transcription of virus RNA segments. (rcsb.org)
  • In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. (rcsb.org)
  • However, there is also evidence that RNA processing events can affect the transcription machinery. (elifesciences.org)
  • RNA folding in the cell occurs during transcription. (pnas.org)
  • Particularly challenging for RNA folding during transcription is the formation of duplexes composed of two strands located far apart in sequence. (pnas.org)
  • In light of the result that E. coli and B. subtilis RNA polymerase have very distinct pausing properties ( 9 ), a coevolutionary relationship between the RNA polymerase and folding during transcription remains unanswered. (pnas.org)
  • Transcriptional pausing at a specific location also affects the folding of the FMN-responsive riboswitch by providing FMN with a greater time window to bind the RNA during transcription ( 7 ). (pnas.org)
  • i ) For naturally evolved RNAs, how do pause sites affect folding during transcription by their cognate RNA polymerase? (pnas.org)
  • The PIC helps position RNA polymerase II over gene transcription start sites , denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription. (wikipedia.org)
  • Most scientist believe that the actual content of this RNA is probably not important although some believe that the actual act of transcription itself may actually play a role in regulating how the genome is organized. (scienceblogs.com)
  • Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. (biomedsearch.com)
  • This study provides the strong position for future development of highly selective RNA-targeting agents that can potentially be used for disease-selective treatment at the level of messenger, micro, and genomic viral RNA. (novelconjugates.com)
  • This proviral DNA is then a stable component of the host cell genome and it may remain dormant or become actively transcribed to genomic or subgenomic viral RNA yielding mature virions which are released by budding (12, 13). (bioscience.org)
  • We use 'state-of-the art' genomic technologies to analyse DNA and RNA and help students develop the highly sought after bioinformatics skills required to interpret these data. (otago.ac.nz)
  • DNA complements the RNA sequence and stores genomic information. (wikibooks.org)
  • Various backbone formulations have been used with the intent of resisting nuclease degradation outside or inside cells, enhancing, the binding energy to the target RNA, reducing the strong electrostatic repulsive energies during annealing, and enhancing specificity of RNase H attack. (hindawi.com)
  • Group I introns may also insert into the natural intron insertion site at the RNA level, and subsequently become stably integrated into the host genome. (biomedsearch.com)
  • Another important property shared by these two endonucleases is their preference for RNA substrates that bear a single phosphate group at an unpaired 5′ end. (pnas.org)
  • this binding is stabilized by hydrogen bonds, contacts to the phosphate backbone of the RNA, and Van der Waals contacts with the sugar bases. (kenyon.edu)
  • The RNA cytosine methyltransferase NSUN3 was recently shown to generate 5-methylcytosine in the anticodon loop of mitochondrial tRNA Met . (springer.com)
  • A form of RNA known as transfer RNA (tRNA) is responsible for delivering free amino acids to the ribosome and growing peptide chain. (wikibooks.org)
  • Further evidence that the RNA World Hypothesis has clout is found through the function of present day ribosomes. (wikibooks.org)
  • We describe a procedure for selecting effective DNAzymes (DZ) and ribozymes (RZ) based on their ability to cleave the full length Smn mRNA at low magnesium concentrations, after a short time period, and at a low catalytic nucleic acid to target ratio. (ox.ac.uk)
  • The minerals had little or no effect in promoting hydrolysis of RNA (24mer of polyadenylic acid) at 80°C over a pH range from 4.2 to 9.3. (springer.com)
  • We identified two RNA interaction domains, RID1 and RID2, the latter containing a vertebrate-specific RNA binding motif. (asm.org)
  • Like its E. coli homolog RNase G, RNase E shows a marked preference for cleaving RNAs that bear a monophosphate, rather than a triphosphate or hydroxyl, at the 5′ end. (pnas.org)
  • Tommaso Bellini and colleagues wondered if liquid crystals could help guide short RNA precursors to form longer strands. (eurekalert.org)
  • Double-stranded RNA-dependent protein kinase (PKR) is suggested to play an important role in both the antiviral and antiproliferative arms of the interferon response. (elsevier.com)
  • Through a number of pathways that are conserved in eukaryotes from yeast to humans, small noncoding RNAs direct molecular machinery to silence gene expression. (nature.com)
  • Instead, researchers are finding that these micro-RNAs have critical functions in controlling the process of gene expression. (innovations-report.com)
  • However, it was only in 1998 that experiments were described showing the unexpected power of double stranded RNA to block gene expression [6] . (wikiversity.org)
  • RNA binding elements are imagined to have been added so that early RNA substrates could be docked proximal to the activated amino acid. (scripps.edu)
  • RNA microhelices that recapitulate the acceptor stem of modern tRNAs are potential examples of early substrates. (scripps.edu)
  • Seven years after Cech announced his finding during a symposium at the Cold Spring Harbor Laboratory in New York, the importance of RNA in biochemistry is indisputable. (newscientist.com)
  • Scientists have previously shown that defects in RNA binding underlie several human brain disorders, but their RNA targets have been a mystery. (innovations-report.com)
  • Whether these amino acid changes in Pols IV and V alter their catalytic properties in comparison to Pol II, from which they evolved, is unknown. (indiana.edu)
  • And in translation, the messenger RNA is decoded, resulting in the production of a protein made from some combination of 20 amino acids. (innovations-report.com)
  • For one thing, Carrington said, micro-RNAs might be intimately involved in the normal function of stem cells, those biologically unique cells that, when reproducing, can produce either more stem cells or begin a line of cells that is differentiated into something else, a brain, lung or liver cell. (innovations-report.com)
  • 8. The method of claim 5 wherein the RNA oligonucleotide is biologically active. (google.com)
  • In some recent studies, other scientists found that micro-RNAs can bind to specific messenger RNAs to block the translation or decoding process. (innovations-report.com)
  • Reporting in the Nov. 14 issue of the journal Science, a team of scientists led by Robert B. Darnell, M.D., Ph.D., a professor at Rockefeller and an investigator at the Howard Hughes Medical Institute, showed that their new technique, called CLIP, can rapidly identify all the RNAs that bind to a protein that has been linked to the brain disorder POMA, or paraneoplastic opsoclonus myoclonus ataxia. (innovations-report.com)
  • These antibodies bind a segment of Nova called the KH domain and inhibit Nova s interaction with RNA. (innovations-report.com)
  • RNA has properties of autocatalytic self-replication and assembly, contributing to its exponential increase in number. (wikibooks.org)
  • Scientists today have assumed that replication was not perfect in the time of primitive life, and therefore variations of RNA developed. (wikibooks.org)
  • Some of the peptides formed may have supported the self-replication of RNA and provided the possibility of undergoing modifications. (wikibooks.org)

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