RNA Cleavage: 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.RNA: 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)Endoribonucleases: 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.-.RNA, Catalytic: 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.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA, Small Interfering: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA Processing, Post-Transcriptional: 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.RNA, Ribosomal: 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)DNA, Catalytic: Molecules of DNA that possess enzymatic activity.RNA-Induced Silencing Complex: A multicomponent, ribonucleoprotein complex comprised of one of the family of ARGONAUTE PROTEINS and the "guide strand" of the one of the 20- to 30-nucleotide small RNAs. RISC cleaves specific RNAs, which are targeted for degradation by homology to these small RNAs. Functions in regulating gene expression are determined by the specific argonaute protein and small RNA including siRNA (RNA, SMALL INTERFERING), miRNA (MICRORNA), or piRNA (PIWI-INTERACTING RNA).RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.RNA Editing: 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).RNA, Messenger: 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, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Double-Stranded: 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.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.DNA-Directed RNA Polymerases: 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).RNA Interference: 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.Ribonuclease H: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.RNA Stability: 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.Ribonuclease III: An endoribonuclease that is specific for double-stranded RNA. It plays a role in POST-TRANSCRIPTIONAL RNA PROCESSING of pre-RIBOSOMAL RNA and a variety of other RNA structures that contain double-stranded regions.Ribonuclease, Pancreatic: An enzyme that catalyzes the endonucleolytic cleavage of pancreatic ribonucleic acids to 3'-phosphomono- and oligonucleotides ending in cytidylic or uridylic acids with 2',3'-cyclic phosphate intermediates. EC 3.1.27.5.Amino Acid Sequence: 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.RNA Polymerase II: 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.Oligoribonucleotides: 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.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.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Transcription Factors, General: Transcription factors that form transcription initiation complexes on DNA, bind to specific DNA-DIRECTED RNA POLYMERASES and are required to initiate transcription. Although their binding may be localized to distinct sequence and structural motifs within the DNA they are considered non-specific with regard to the specific gene being transcribed.Kinetics: The rate dynamics in chemical or physical systems.Argonaute Proteins: A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.Transcriptional Elongation Factors: Transcription factors whose primary function is to regulate the rate in which RNA is transcribed.DNA Cleavage: A reaction that severs one of the covalent sugar-phosphate linkages between NUCLEOTIDES that compose the sugar phosphate backbone of DNA. It is catalyzed enzymatically, chemically or by radiation. Cleavage may be exonucleolytic - removing the end nucleotide, or endonucleolytic - splitting the strand in two.RNA Viruses: Viruses whose genetic material is RNA.Escherichia coli: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Mutation: 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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Templates, Genetic: 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.Poly A: 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.RNA Folding: The processes of RNA tertiary structure formation.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Cleavage Stage, Ovum: The earliest developmental stage of a fertilized ovum (ZYGOTE) during which there are several mitotic divisions within the ZONA PELLUCIDA. Each cleavage or segmentation yields two BLASTOMERES of about half size of the parent cell. This cleavage stage generally covers the period up to 16-cell MORULA.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.HeLa Cells: 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.RNA, Antisense: 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.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Protein Binding: 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.Protein Structure, Tertiary: 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.RNA, Transfer: 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.Cations, Divalent: Positively charged atoms, radicals or groups of atoms with a valence of plus 2, which travel to the cathode or negative pole during electrolysis.RNA, Small Nuclear: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Recombinant Proteins: Proteins prepared by recombinant DNA technology.RNA, Untranslated: 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.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.RNA Caps: 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.Nucleic Acid Hybridization: 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)Manganese: A trace element with atomic symbol Mn, atomic number 25, and atomic weight 54.94. It is concentrated in cell mitochondria, mostly in the pituitary gland, liver, pancreas, kidney, and bone, influences the synthesis of mucopolysaccharides, stimulates hepatic synthesis of cholesterol and fatty acids, and is a cofactor in many enzymes, including arginase and alkaline phosphatase in the liver. (From AMA Drug Evaluations Annual 1992, p2035)DNA Primers: 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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Conserved Sequence: 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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Magnesium: A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Saccharomyces cerevisiae: 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.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.DNA: 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).MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.RNA Replicase: An enzyme that catalyses RNA-template-directed extension of the 3'- end of an RNA strand by one nucleotide at a time, and can initiate a chain de novo. (Enzyme Nomenclature, 1992, p293)RNA Ligase (ATP): 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.RNA, Neoplasm: RNA present in neoplastic tissue.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Saccharomyces cerevisiae Proteins: 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.DEAD-box RNA Helicases: 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.RNA, Guide: 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.RNA Polymerase III: 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.Plasmids: 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.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.mRNA Cleavage and Polyadenylation Factors: Factors that are involved in directing the cleavage and POLYADENYLATION of the of MESSENGER RNA near the site of the RNA 3' POLYADENYLATION SIGNALS.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA Polymerase I: 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, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.Caspases: A family of intracellular CYSTEINE ENDOPEPTIDASES that play a role in regulating INFLAMMATION and APOPTOSIS. They specifically cleave peptides at a CYSTEINE amino acid that follows an ASPARTIC ACID residue. Caspases are activated by proteolytic cleavage of a precursor form to yield large and small subunits that form the enzyme. Since the cleavage site within precursors matches the specificity of caspases, sequential activation of precursors by activated caspases can occur.Molecular Weight: The sum of the weight of all the atoms in a molecule.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Furin: A proprotein convertase with specificity for the proproteins of PROALBUMIN; COMPLEMENT 3C; and VON WILLEBRAND FACTOR. It has specificity for cleavage near paired ARGININE residues that are separated by two amino acids.Protein PrecursorsSerine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Virus Replication: 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.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.RNA 3' End Processing: 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.Cysteine Endopeptidases: ENDOPEPTIDASES which have a cysteine involved in the catalytic process. This group of enzymes is inactivated by CYSTEINE PROTEINASE INHIBITORS such as CYSTATINS and SULFHYDRYL REAGENTS.Caspase 3: A short pro-domain caspase that plays an effector role in APOPTOSIS. It is activated by INITIATOR CASPASES such as CASPASE 9. Isoforms of this protein exist due to multiple alternative splicing of its MESSENGER RNA.RNA, Satellite: 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)RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.Cell Nucleus: 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)Transfection: 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.Peptide Hydrolases: Hydrolases that specifically cleave the peptide bonds found in PROTEINS and PEPTIDES. Examples of sub-subclasses for this group include EXOPEPTIDASES and ENDOPEPTIDASES.RNA, Spliced Leader: 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).RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Oligonucleotides: 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)DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Proteolysis: Cleavage of proteins into smaller peptides or amino acids either by PROTEASES or non-enzymatically (e.g., Hydrolysis). It does not include Protein Processing, Post-Translational.Cholesterol Side-Chain Cleavage Enzyme: A mitochondrial cytochrome P450 enzyme that catalyzes the side-chain cleavage of C27 cholesterol to C21 pregnenolone in the presence of molecular oxygen and NADPH-FERRIHEMOPROTEIN REDUCTASE. This enzyme, encoded by CYP11A1 gene, catalyzes the breakage between C20 and C22 which is the initial and rate-limiting step in the biosynthesis of various gonadal and adrenal steroid hormones.Subtilisins: A family of SERINE ENDOPEPTIDASES isolated from Bacillus subtilis. EC 3.4.21.-Cells, Cultured: 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.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Amyloid Precursor Protein Secretases: Endopeptidases that are specific for AMYLOID PROTEIN PRECURSOR. Three secretase subtypes referred to as alpha, beta, and gamma have been identified based upon the region of amyloid protein precursor they cleave.DNA Restriction Enzymes: 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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Structure-Activity Relationship: 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.Recombinant Fusion Proteins: 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.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 3.4.21.4.Endonucleases: Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.Enzyme Activation: Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Single-Strand Specific DNA and RNA Endonucleases: 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.Blotting, Western: 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.RNA, Heterogeneous Nuclear: 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.RNA, Small Nucleolar: 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.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Aspartic Acid Endopeptidases: A sub-subclass of endopeptidases that depend on an ASPARTIC ACID residue for their activity.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Bacterial Proteins: Proteins found in any species of bacterium.Metalloendopeptidases: ENDOPEPTIDASES which use a metal such as ZINC in the catalytic mechanism.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Promoter Regions, Genetic: 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.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Reverse Transcriptase Polymerase Chain Reaction: 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.RNA, Small Cytoplasmic: Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.DNA, Complementary: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.UridineCell Line, Tumor: A cell line derived from cultured tumor cells.Cytoplasm: 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)Polymerase Chain Reaction: 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.Viral Nonstructural Proteins: 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.Ribonuclease P: 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.

Exposure of neurons to excitotoxic levels of glutamate induces cleavage of the RNA editing enzyme, adenosine deaminase acting on RNA 2, and loss of GLUR2 editing. (1/95)

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Identification of an hepatitis delta virus-like ribozyme at the mRNA 5'-end of the L1Tc retrotransposon from Trypanosoma cruzi. (2/95)

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Structural and functional basis for RNA cleavage by Ire1. (3/95)

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Cleavage of rRNA ensures translational cessation in sperm at fertilization. (4/95)

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Ribonuclease P. (5/95)

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Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. (6/95)

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Transcriptional activity regulates alternative cleavage and polyadenylation. (7/95)

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miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. (8/95)

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  • Here, we have identified a CRISPR-Cas effector complex that is comprised of small invader-targeting RNAs from the CRISPR loci (termed prokaryotic silencing (psi)RNAs) and the RAMP module (or Cmr) Cas proteins. (nih.gov)
  • RNase III dicer or dicer-like (DCL) proteins and their associated factors cleave precursor RNAs to produce duplex miRNAs or siRNAs. (asm.org)
  • 2′-5′ oligoadenylates, produced in response to interferon treatment and viral double-stranded RNA, are necessary to activate RNase L. In contrast, unfolded proteins in the endoplasmic reticulum activate Ire1p, a transmembrane serine/threonine kinase and endoribonuclease. (ucsf.edu)
  • Citation Query Cleavage of structural proteins during the assemble of the head of bacteriophage T4. (psu.edu)
  • Cleavage of structural proteins during the assemble of the head of bacteriophage T4. (psu.edu)
  • They comprise a ceramide- and cholesterol-rich lipid bilayer membrane ( 2 ), an array of membrane and cytosolic proteins ( 3 ) and selected RNA species ( 4 ). (aacrjournals.org)
  • One of the major goals of our present study was to design and develop an RNA interference-based therapy to inhibit mannan-binding lectin (MBL)-associated serine proteases (MASPs) to determine whether these proteins would play an important role in the pathogenesis of experimental RA and might be appropriate therapeutic targets for human RA ( 6 ). (jimmunol.org)
  • The dimerization and cleavage of caspase-8 in the DISC are the critical upstream events in TNF family ligand-induced apoptosis ( 9 - 12 ), and ubiquitination of proteins in the DISC regulates these biochemical processes ( 13 ). (aacrjournals.org)
  • Finally, our RNP IP and RNA transcriptome analysis of HuR under IR revealed that the HuR cleavage product-1 (HuR-CP1) associates and promotes the expression of mRNAs encoding proteins involved in apoptosis. (omicsdi.org)
  • The CRISPR/Cas system functions as an acquired bacterial immune defense system as Cas proteins associate with transcribed spacer DNA (RNA) to target foreign viral DNA. (kenyon.edu)
  • If viral DNA is identified via hybridization with the CRISPR RNA, CRISPR/Cas proteins' nuclease activity will cleave the DNA, inducing a double stranded break (DSB) and rendering the phage DNA inactivate. (kenyon.edu)
  • The goal of this tutorial is to elucidate how Streptococcus pyogenes Cas9, one of the the most widely used Cas proteins in gene engineering, binds target DNA via sgRNA and executes the chemical reactions required for cleavage. (kenyon.edu)
  • With recent advances in LLPS in biological research fields, studies have found that macromolecular droplets composed of proteins and RNAs are formed within living cells via moderate interactions among the biomolecules ( 6 - 10 ). (sciencemag.org)
  • Although several in vitro studies have reproduced droplet formation by changing the concentrations of proteins/RNAs and salts ( 8 , 9 , 12 , 13 ), no study has demonstrated the control of dynamic behavior of macromolecular droplets by varying the biological information encoded in the biopolymer sequence. (sciencemag.org)
  • snRNA are often divided into two classes based upon both common sequence features as well as associated protein factors such as the RNA-binding LSm proteins. (wikipedia.org)
  • The spliceosome is a large, protein-RNA complex that consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and over 150 proteins. (wikipedia.org)
  • MMP-2 enhanced peritoneal adhesion of OvCa cells through cleavage of ECM proteins fibronectin (FN) and vitronectin (Vn) into small fragments and increased binding of OvCa cells to these FN and Vn fragments and their receptors, α 5 β 1 and α V β 3 integrin. (jci.org)
  • At 24 and 48 hpi of GUY11, 32 and 16 proteins in CN-4b were up-regulated, among which 16 and five were paralleled with the expression of their corresponding RNAs. (mdpi.com)
  • These proteins are 'serpin' protease inhibitors, which function via a pseudosubstrate mechanism involving initial interactions between the protease and a cleavage site within the serpin. (portlandpress.com)
  • The retention of Spi-2 proteins' caspase-8 specificity during chordopoxvirus evolution, despite this function being readily lost through cleavage site mutagenesis, suggests that caspase-8 inhibition is crucial for poxviral pathogenesis and spread. (portlandpress.com)
  • The proteins that constitute these complexes are recruited to the cleavage site by cleavage and polyadenylation specificity factor and cleavage stimulatory factor, and form a larger complex that also includes polyadenine polymerase (PAP), which performs the polyadenylation reaction. (wikipedia.org)
  • Involved in the earliest step for the formation of the active cleavage complex, the CFIm complex is formed by three proteins of 25, 59 and 68 kDa, respectively: CFIm25 (or CPSF5/NUDT21) CFIm59 (or CPSF7) CFIm68 (or CPSF6) CFIm25 and CFIm68 are sufficient for the activity of the complex, proving the expected redundancy of CFIm68 and CFIm59, which share great sequence similarity. (wikipedia.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)
  • Additional analysis suggests that an interaction of the ribosome with a stop codon might affect the site of cleavage by RNase LS in an mRNA molecule. (genetics.org)
  • During characterization of RNase LS activity after infection of a T4 dmd mutant, we found cleavages in T4 soc mRNA when two successive ochre codons were introduced into the open reading frame ( K ai and Y onesaki 2002 ). (genetics.org)
  • Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. (uni-muenchen.de)
  • Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. (bcm.edu)
  • This observation is inconsistent with sequencing error and leads us to propose that the changes arise predominantly from post-transcriptional RNA-editing activity operating on miRNA:target mRNA complexes. (bcm.edu)
  • MicroRNAs are short stretches of RNA that can regulate gene expression by inhibiting translation of mRNA into a protein and directing the destruction of mRNA before it can be used to make more protein. (mit.edu)
  • Researchers from the National Agricultural Research and Innovation Centre, Hungary describe a method that enables the high-throughput identification of cleaved mRNA targets of ARGONAUTE/small RNA complexes. (rna-seqblog.com)
  • After the sequence-specific miRNA-induced RNA cleavage, the 3′ cleavage product of the mRNA contains a 5′-monophosphate and a poly(A) tail. (rna-seqblog.com)
  • RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA a" by Phillip D. Zamore, Thomas Tuschl et al. (umassmed.edu)
  • Double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi). (umassmed.edu)
  • Processing of the dsRNA to the small RNA fragments does not require the targeted mRNA. (umassmed.edu)
  • Cleavage occurs at sites 21-23 nucleotides apart, the same interval observed for the dsRNA itself, suggesting that the 21-23 nucleotide fragments from the dsRNA are guiding mRNA cleavage. (umassmed.edu)
  • By simple adjustment of ring size of caged asODNs, we could successfully photoregulate their hybridization with mRNA and target RNA hydrolysis by RNase H with light activation. (bjmu.edu.cn)
  • Cleavage factors are two closely associated protein complexes involved in the cleavage of the 3' untranslated region of a newly synthesized pre-messenger RNA (mRNA) molecule in the process of gene transcription. (wikipedia.org)
  • The cleavage is the first step in adding a polyadenine tail to the pre-mRNA, which is one of the necessary post-transcriptional modifications necessary for producing a mature mRNA molecule. (wikipedia.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)
  • A comparative RNase H digestion study showed that modifications of the same type ( North-East type or North type) in different sequences gave rise to similar cleavage patterns. (diva-portal.org)
  • Nucleotide Sequences of the RNA Subunit of RNase P from Several Mammals,"Genomics 18(2):418-422 (1993). (patentgenius.com)
  • Aside from revealing directly metal ion-binding sites these techniques also provide structural information for longer RNA sequences that are out of range to be analyzed with other techniques such as NMR. (uzh.ch)
  • 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. (mdpi.com)
  • Thus, in contrast to ZFNs and TALENs, this modified CRISPR RNA/Cas9 system directs a common nuclease to specific DNA sequences by a short, readily generated RNA. (genetics.org)
  • 30-nt RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (betaTC-3) reveals that approximately 50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences. (bcm.edu)
  • Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies ("intranomics") can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs. (bcm.edu)
  • Cellular RNAi components slice and destroy invading double-stranded RNA sequences and also help snip and process microRNAs, RNA sequences encoded by the genome that play key roles in gene regulation. (mit.edu)
  • The aims of the present study concern the amino acids sequences comparison with reference strain A/equine/Miami/1963(H3N8) of the HA2 subunit including the cleavage site of three equine influenza viruses (H3N8) isolated in Morocco: A/equine/Nador/1/1997(H3N8), A/equine/Essaouira/2/2004 (H3N8) and A/equine/Essaouira/3/2004 (H3N8). (biomedcentral.com)
  • 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)
  • That is to say, these short RNA strings allowed RNA to be copied without enzymes if they had a chemical group at one end that made them more reactive.Each short catalyst helped copy one of the four RNA letters, and adding several into one reaction meant that longer sequences containing all four RNA letters could be copied. (elifesciences.org)
  • Further work is now needed to see if it is possible to copy other RNA sequences, and especially longer ones, without enzymes. (elifesciences.org)
  • To identify new miRNAs and regulation in Arabidopsis ( Arabidopsis thaliana ), 27 small RNA libraries were constructed and sequenced from various tissues, stresses, and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. (plantphysiol.org)
  • 1961. An unstable intermediate sequences for the RNA polymerase. (ximicat.com)
  • Based on the ever-increasing number of RNA sequences, it was determined that most coding RNAs mature as a result of alternative splicing. (hindawi.com)
  • Cis-acting regulatory sequence elements are sequences contained in the 3′ and 5′ untranslated region, introns, or coding regions of precursor RNAs and mature mRNAs that are selectively recognized by a complementary set of one or more trans-acting factors to regulate posttranscriptional gene expression. (intechopen.com)
  • RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. (nih.gov)
  • The psiRNA-Cmr protein complexes cleave complementary target RNAs at a fixed distance from the 3' end of the integral psiRNAs. (nih.gov)
  • The recombinant protein PvNCED1 catalyzes the cleavage of 9- cis -violaxanthin and 9′- cis -neoxanthin, so that the enzyme is referred to as 9- cis -epoxycarotenoid dioxygenase. (pnas.org)
  • After the discovery of catalytic RNA ( 1 , 2 ), it became clear that nucleic acid molecules of a particular sequence and 3-dimensional structure are able to carry out specific chemical reactions, often with an efficiency comparable to that of protein enzymes ( 3 ). (pnas.org)
  • We are also interested in (3) protein-RNA complexes along the microRNA (miRNA) biogenesis pathway that mediate processing of primary miRNAs to their precursor counterparts, and processes associated with miRNA guide strand-mediated cleavage, translation inhibition or degradation of target RNAs. (mskcc.org)
  • One strand of the small RNA duplex is subsequently loaded onto the Argonaute protein to yield an active RNA-induced silencing complex. (mskcc.org)
  • We show that N-terminal post-translational cleavage products of the prion protein (PrP) induce a quiescent state, halting NSC cellular growth, migration, and neurite outgrowth. (springer.com)
  • Full-depth explants of human OA knee articular cartilage from arthroplasty were cultured with exogenous DFO (1-50 μ M). Type II collagen cleavage and phospho-adenosine monophosphate-activated protein kinase (pAMPK) concentrations were measured using ELISAs. (hindawi.com)
  • Now, researchers at Whitehead Institute have uncovered how small changes in the fish Argonaute (Ago) protein, an RNA slicing protein, that happened in its lineage an estimated 300 million years ago greatly diminished the efficiency of RNAi in these animals, while another ancestral feature, in a critical pre-microRNA, was retained that enabled the microRNA to still be produced despite the fish's impaired Ago protein. (mit.edu)
  • Since Chen had discovered that zebrafish lack an efficient Ago protein, it was mysterious as to how are fish were able to produce Ago cleavage-dependent miR-451. (mit.edu)
  • The Ago protein must process miR-451 by slicing the sequence out of a longer strand of RNA that has folded up on itself, forming a hairpin structure. (mit.edu)
  • Our study showed that prodigiosin (500 μM) (extracted from Serratia marcescens culture) and a prodigiosin/copper(II) (100 μM each) complex have strong RNA and dsDNA cleaving properties while they have no pronounced effect on protein. (frontiersin.org)
  • The typical form of pre-miRNA processed by the Drosha protein is a hairpin RNA with 2-nt 3' overhangs. (biomedcentral.com)
  • In this study, we show that human recombinant DICER protein (rDICER) processes a hairpin RNA with 5' overhangs in vitro and generates an intermediate duplex with a 29 nt-5' strand and a 23 nt-3' strand, which was eventually cleaved into a canonical miRNA duplex via a two-step cleavage. (biomedcentral.com)
  • In the death-inducing signaling complex, the C-terminal zinc finger (Znf) domain of the A20 ubiquitin ligase mediates receptor-interacting protein 1 polyubiquitination through lysine-63-linked polyubiquitin chains, which bind to the caspase-8 protease domain and inhibit caspase-8 dimerization, cleavage, and the initiation of TRAIL-induced apoptosis in glioblastoma-derived cell lines and tumor-initiating cells. (aacrjournals.org)
  • We demonstrated that the presence of superpower (SP) protein cleavage is responsible for the diversity of superpowers in a tissues-specific manner within The Incredibles family. (ubc.ca)
  • The extraction was performed with the AllPrep DNA/RNA/Protein Mini Kit (Qiagen Inc, Valencia, CA, USA) according to a modified manufacturer's protocols. (ubc.ca)
  • A well-studied RNA-binding protein Hu Antigen-R (HuR), controls post-transcriptional gene regulation and undergoes stress-activated caspase-3 dependent cleavage in cancer cells. (omicsdi.org)
  • The current understanding related to the production of small ribonucleic acid (RNAs), the process concerning their loading into the protein complexes and the repression of the gene expression is reviewed. (readabstracts.com)
  • With the anti-PARP Caspase Cleavage Product Antibody you will specifically detect only the small apoptotic PARP-1 cleavage fragment, but not the full-length protein, in samples of human, mouse, or rat origin. (bio-medicine.org)
  • Intracellular redistribution of truncated La protein produced by poliovirus 3Cpro-mediated cleavage. (semanticscholar.org)
  • The La autoantigen (also known as SS-B), a cellular RNA binding protein, may shuttle between the nucleus and cytoplasm, but it is mainly located in the nucleus. (semanticscholar.org)
  • Contents: CONTENTS:1.Introduction 2.Cellular Basis of Development 3.DNA, RNA and Protein Synthesis 4.Male Gonads and Spermatogenesis 5. (abebooks.com)
  • Elbasvir targets the NS5A protein, which effectively prevents the transcription of the HCV RNA and also prevents virion assembly. (wikipedia.org)
  • The protein-containing complex was named "RNA-induced silencing complex", RISC. (wikiversity.org)
  • 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)
  • RNA interference can be used to selectively reduce the level of expression of a specific protein. (wikiversity.org)
  • Aβ generation depends on proteolytic cleavage of the amyloid precursor protein (APP) by two unknown proteases: β-secretase and γ-secretase. (sciencemag.org)
  • D ) Schematic of the co-transcriptional DNA cleavage assay of a dsDNA substrate containing the nes target. (nih.gov)
  • Arrowheads indicate the approximate cleavage site detected in panel E. The red circle identifies the radiolabeled 5' end of substrate and products. (nih.gov)
  • Surprisingly, RNase L and Ire1p showed mutually exclusive RNA substrate specificity and partially overlapping but not identical requirements for phylogenetically conserved amino acid residues in their nuclease domains. (ucsf.edu)
  • The results provide evidence that drought-induced ABA biosynthesis is regulated by the 9- cis -epoxycarotenoid cleavage reaction and that this reaction takes place in the thylakoids, where the carotenoid substrate is located. (pnas.org)
  • Because the carotenoid substrate is abundantly available in photosynthetic tissues ( 13 ), it follows by the process of elimination that the cleavage of 9- cis -epoxycarotenoids is the rate-limiting step in the ABA biosynthetic pathway. (pnas.org)
  • An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions. (pnas.org)
  • The RNA substrate is bound through Watson-Crick base pairing and is cleaved at a particular phosphodiester located between an unpaired purine and a paired pyrimidine residue. (pnas.org)
  • We sought to develop a DNA enzyme that could be made to cleave almost any RNA substrate, efficiently and specifically under physiological conditions. (pnas.org)
  • In a previous study, DNA was shown to catalyze the Mg 2+ -dependent cleavage of an RNA phosphoester embedded within an otherwise all-DNA substrate ( 6 ). (pnas.org)
  • Although that DNA enzyme was unable to cleave an all-RNA substrate, its properties suggested that a DNA enzyme with general purpose RNA cleavage activity might be attainable. (pnas.org)
  • When this mutation was combined with a second mutation that induces a bulge in the exon binding site 1/intron binding site 1 (EBS1/IBS1) duplex, the base-pairing register of the EBS1/IBS1 duplex was shifted and the cleavage site moved to a downstream position on the substrate. (nih.gov)
  • We also provide new insights into the interaction between E. coli RNase P RNA and the -1 residue in the substrate. (diva-portal.org)
  • A subset of these enzymes recognizes structural features of the RNA substrate, such as in tRNA, while others act on unstructured polymers ( Li and Deutscher, 1996 ). (elifesciences.org)
  • The previously identified endogenous pre-miRNA with 5' overhangs, pre-mmu-mir-1982 RNA, is also determined to be a substrate of rDICER through the same two-step cleavage. (biomedcentral.com)
  • Previous work indicated that the degree of substrate cleavage by caspase-8 determines whether a cell dies or survives in response to a death stimulus. (omicsdi.org)
  • DNA cleavage by a deoxyribozyme uses to main mechanisms, either they cleaved their DNA substrate by hydrolysis or via deglycosylation, a carbohydrate (sugar) is detached from the DNA subtrate which is the followed by two β-eliminations. (openwetware.org)
  • Efforts are in progress ( 15 , 16 ) to enhance the specificity of DNA targeting by Cas9 for potential therapeutic applications ( 17 , 18 ), which requires detailed mechanistic understanding of substrate-dependent activation of Cas9 for DNA cleavage. (sciencemag.org)
  • The comparative study showed that a single modified nucleotide in the AON with North-East locked sugar (oxetane-T and azetidine-T) lowered the affinity for the complementary RNA whereas North locked sugars (LNA-T, aza-ENA-T, carbocyclic-ENA-T, and carbocyclic-LNA-T) significantly improved the affinity. (diva-portal.org)
  • A key mediator of RNA silencing is several classes of 21- to 24-nucleotide (nt) small RNAs. (asm.org)
  • Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. (elifesciences.org)
  • The nonenzymatic replication of RNA is a potential transitional stage between the prebiotic chemistry of nucleotide synthesis and the canonical RNA world in which RNA enzymes (ribozymes) catalyze replication of the RNA genomes of primordial cells. (elifesciences.org)
  • together with the fact that DXZ4 expresses ~85 nucleotide long RNAs ( Chadwick 2008 ), we investigated whether small RNAs are expressed from DXZ4 . (g3journal.org)
  • Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. (ebi.ac.uk)
  • A mistake in even a single nucleotide can be devastating to the cell, and a reliable, repeatable method of RNA processing is necessary to ensure cell survival. (wikipedia.org)
  • DNA target recognition requires a short protospacer adjacent motif (PAM) sequence (5′-NGG-3′ for Streptococcus pyogenes Cas9) ( 5 ) and complementary base pairing with the 20-nucleotide (nt) targeting sequence of the guide RNA. (sciencemag.org)
  • In fact, in the in vitro cleavage reaction ( O tsuka and Y onesaki 2005 ), Dmd inhibits the activity of RNase LS (Y. O tsuka and T. Y onesaki , unpublished results). (genetics.org)
  • Type III CRISPR-Cas immunity requires target transcription, and whereas genetic studies demonstrated DNA targeting, in vitro data have shown crRNA-guided RNA cleavage. (nih.gov)
  • In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions," Genes and Dev. (patentgenius.com)
  • We then used in vitro transcription, with either 5'-dideuterated, 4' deuterated, 3' deuterated, or 2' deuterated GTP or ATP, along with the other three ribonucleoside triphosphates, to prepare a 29mer analog of the Sarcin-Ricin loop, a key structural feature of 28S ribosomal RNA. (jbsdonline.com)
  • This inverse correlation between caspase-3 glutathiolation and cleavage was further confirmed by the observation that in vitro glutathiolation of caspase-3 inhibited its cleavage with recombinant caspase-8. (ahajournals.org)
  • Also the (32)P-labeled pCMV/T7-NCRC luc (containing the gene sequence of the whole 5'-NCR and part core of HCV RNA ) transcripts as target-RNAs were transcribed in vitro . (bvsalud.org)
  • Furthermore, we demonstrate both in vitro and in vivo that exogenous MMP-7 enhances proNGF cleavage and provides neuroprotection following kainic acid treatment. (jneurosci.org)
  • In this study, for example, it was directed to cleave synthetic RNAs corresponding to the start codon region of HIV-1 gag / pol , env , vpr , tat , and nef mRNAs. (pnas.org)
  • Precise selection of cleavage sites by RNase III enzymes is critical, with Drosha and Dicer recognizing specific RNA structures and cleave a fixed distance away from that structural element. (mskcc.org)
  • The targeting CRISPR RNA (sgRNA) can be synthesized to match a specific eukaryotic genomic locus, enabling the CRISPR/Cas system to cleave the locus of interest. (kenyon.edu)
  • RIBONUCLEASE LS ( l ate-gene s ilencing in bacteriophage T4) plays a role in Escherichia coli RNA metabolism ( O tsuka and Y onesaki 2005 ), although its effect seems modest in comparison to that of RNase E ( K ushner 2002 ). (genetics.org)
  • The effects of donor groups of dizinc complexes, formed from a 2:1 mixture of Zn(II) and a dinucleating ligand, on adenylyl(3′-5′)adenosine (ApA) cleavage have been studied. (springer.com)
  • The cleavage pattern derived from in-line probing experiments reflects local and overall conformational changes in RNA upon the addition of metal ions, metal complexes, or other ligands. (uzh.ch)
  • Kaczmarek A, Alvarez Porebski PW, Mortier T, Lynen F, Van Deun R, Van Hecke K. Near-infrared luminescence and RNA cleavage ability of lanthanide Schiff base complexes derived from N,N'-bis (3-methoxysalicylidene)ethylene-1,2-diamine ligands. (ugent.be)
  • We show that A20-mediated ubiquitination inhibits caspase-8 cleavage and TRAIL-induced apoptosis in glioblastoma through 2 signaling complexes. (aacrjournals.org)
  • In the nucleus, small RNA-Argonaute complexes recruit epigenetic modifying activities to genomic sites. (g3journal.org)
  • The most common snRNA components of these complexes are known, respectively, as: U1 spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, and U6 spliceosomal RNA. (wikipedia.org)
  • The lists of conserved cis-elements have been expanding over the past decade, but the mechanisms of the precise assembly of RNA-binding complexes in an orchestrated temporal and spatial manner have not been comprehensively described. (intechopen.com)
  • Altman, et al, "Catalysis by the RNA Subunit of RNase P--A Minireview," Gene 82:63-64 (1989). (patentgenius.com)
  • In this process, we detected a gene encoding cleavage stimulation factor, 3′ pre-RNA, subunit 2, 64 kDa (CSTF2) as a candidate. (aacrjournals.org)
  • Because there is a significant correlation of cleavage stimulation factor, 3′ pre-RNA, subunit 2, 64 kDa (CSTF2) expression with poor prognosis for patients with lung cancers, CSTF2 positivity in resected specimens could be an index that provides useful information to physicians in applying adjuvant therapy and intensive follow-up to the cancer patients who are likely to relapse. (aacrjournals.org)
  • This systematic approach revealed that cleavage stimulation factor, 3′ pre-RNA, subunit 2, 64 kDa ( CSTF2 ) gene was frequently transactivated in the majority of primary lung cancers. (aacrjournals.org)
  • The Rpc11p subunit of Pol III shows homology with the zinc ribbon of TFIIS and is known to mediate RNA 3′ cleavage and to be important for termination. (pubmedcentralcanada.ca)
  • On the other side, terbium(III) cleavage experiments are applied to locate specific metal ion-binding sites in RNA molecules. (uzh.ch)
  • Small nuclear ribonucleic acid (snRNA), also commonly referred to as U-RNA, is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. (wikipedia.org)
  • One of the strands is incorporated into the RNA-induced silencing complex (RISC) to guide sequence-specific cleavage of a target RNA or inhibition of translation or into an RNA-induced initiator of transcriptional silencing complex to guide DNA methylation ( 1 , 6 , 14 , 19 , 26 , 39 , 42 , 58 , 85 ). (asm.org)
  • In type II CRISPR systems, a CRISPR RNA (crRNA), which contains sequence complementary to invading virus or plasmid DNA, and a trans -activating CRISPR RNA (tracrRNA) interact with a CRISPR-associated nuclease (Cas9) to direct sequence-specific cleavage of exogenous DNA. (genetics.org)
  • Our long-term goals are to structurally characterize and mechanistically define events associated with (1) processing of long double-stranded RNAs into siRNAs by the endonuclease acvtivity of Dicer and (2) guide-strand-mediated cleavage of target RNAs by Argonaute, the key component exhibiting slicer activity, within the RNA-induced silencing complex (RISC). (mskcc.org)
  • Baksa I, Szittya G. (2017) Identification of ARGONAUTE/Small RNA Cleavage Sites by Degradome Sequencing . (rna-seqblog.com)
  • Here, we describe in human somatic cells a potential link between the expression of small RNAs from the macrosatellite DXZ4 and Argonaute-dependent DNA methylation of this locus. (g3journal.org)
  • A subpopulation of these RNAs is bound by Argonaute. (g3journal.org)
  • We hypothesize that the RNAs are involved in Argonaute-dependent methylation of DXZ4 DNA. (g3journal.org)
  • In somatic cells, we detected the expression of a wide range of small RNAs from this locus with a subpopulation associating with Argonaute. (g3journal.org)
  • By combining small RNA expression analysis with ARGONAUTE immunoprecipitation data and global target cleavage data from Parallel Analysis of RNA Ends, a much more complete picture of Arabidopsis miRNAs was obtained. (plantphysiol.org)
  • In particular, the discovery of ARGONAUTE loading and target cleavage biases gave important insights into tissue-specific expression patterns, pathogen responses, and the role of sequence variation among closely related miRNA family members that would not be evident without this combinatorial approach. (plantphysiol.org)
  • The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. (asm.org)
  • We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. (asm.org)
  • The predominant plus-strand polarity and genomic map locations suggest that small RNAs are derived mostly from structured regions of genomic RNAs of several tested positive-strand RNA viruses ( 59 ) and the structured region of defective interfering (DI) RNAs ( 82 ). (asm.org)
  • Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean ( Phaseolus vulgaris ). (frontiersin.org)
  • Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing. (frontiersin.org)
  • DXZ4 was found to express a wide range of small RNAs potentially representing several classes of small RNAs. (g3journal.org)
  • MicroRNAs ( miRNAs ) are a class of small RNAs that typically function by guiding the cleavage of target messenger RNAs. (plantphysiol.org)
  • Small RNAs are a type of noncoding RNA that regulate gene expression at the transcriptional or posttranscriptional level. (plantphysiol.org)
  • The two major classes of small RNAs are small interfering RNAs ( siRNAs ) and microRNAs ( miRNAs ). (plantphysiol.org)
  • We describe a rapid genome-scale approach, MORE (mapping by overexpression of an RNase in Escherichia coli) RNA-seq, for defining the cleavage specificity of endoribonucleolytic toxins. (uniprot.org)
  • MicroRNAs (miRNAs) are produced by cleavage of hairpin RNA precursors encoded by the genome of an organism. (asm.org)
  • We have adapted a bacterial CRISPR RNA/Cas9 system to precisely engineer the Drosophila genome and report that Cas9-mediated genomic modifications are efficiently transmitted through the germline. (genetics.org)
  • In the past few months, the simplified CRISPR RNA-guided Cas9 nuclease has shown broad potential for genome engineering in metazoans. (genetics.org)
  • May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. (uniprot.org)
  • The Cas9 endonuclease is widely used for genome engineering applications by programming its single-guide RNA, and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. (sciencemag.org)
  • By manipulating the sequence of the single-guide RNA (sgRNA), Cas9-sgRNA can be programmed to target any DNA sequence flanked by a PAM ( 6 , 8 - 10 ), making it a powerful genome-editing tool. (sciencemag.org)
  • Recent technical and conceptual advances, such as the establishment of genome editing and improved phylogenetic resolution, are paving the way for a fresher and deeper look into this fascinating early cleavage mode. (biologists.org)
  • Altman, "RNA enzyme-directed gene therapy," Proc. (patentgenius.com)
  • Directed Evolution of an RNA Enzyme," Science,257:635-641 91992). (patentgenius.com)
  • Efficient enzyme-free copying of all four pre-activated nucleobases, templated by immobilized RNA, was reported [ 24 ]. (mdpi.com)
  • Cullin 3 (CUL3), an E3 ligase, adds K48- and K63-linked polyubiquitin chains to caspase-8 and facilitates its dimerization and cleavage in the DISC, where A20 deubiquitinating enzyme removes the polyubiquitin chains from caspase-8 ( 23 ). (aacrjournals.org)
  • then used these short catalysts to copy an RNA molecule that itself acts a bit like an enzyme, and confirmed that a significant portion of this molecule could be copied without any polymerases. (elifesciences.org)
  • The cleavage activity of the chimeric ribozyme increased with the prolongation of reaction time and increment of enzyme concentration. (bvsalud.org)
  • In the figure below you can observe 8-17, an RNA cleaving DNA enzyme. (openwetware.org)
  • In this study, we demonstrate that, following kainic acid-induced seizures, the proNGF processing enzyme matrix metalloproteinase 7 (MMP-7) and its inhibitor TIMP-1 (tissue inhibitor of matrix metalloproteinase 1) are regulated in a manner that prevents proneurotrophin cleavage and leads to increased proNGF in the extracellular milieu. (jneurosci.org)
  • Overexpression of this protease, termed BACE (for beta-site APP-cleaving enzyme) increased the amount of β-secretase cleavage products, and these were cleaved exactly and only at known β-secretase positions. (sciencemag.org)
  • Here, we demonstrate that RNase LS cleaves soc RNA at the same site even when only a single ochre codon is present or is replaced with either an amber or an opal codon. (genetics.org)
  • Indeed, some cleavages by RNase LS are introduced only when the target is translatable, while others are independent of translation ( K ai and Y onesaki 2002 ). (genetics.org)
  • Here, we present a line of evidence indicating that the cleavages are tightly linked with translation termination and present insights into the selection of cleavage sites by RNase LS. (genetics.org)
  • Structure and Transcription of a Human Gene for H1 RNA the RNA Component of Human RNase," Nucleic Acids Res. (patentgenius.com)
  • Identification and characterization of an RNA molecule that copurifies with RNase P activity from HeLa cells," Genes Dev. (patentgenius.com)
  • We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. (uni-muenchen.de)
  • RNase III enzymes play central roles in RNA silencing by processing double-stranded RNA precursors into small RNA duplexes. (mskcc.org)
  • Our findings will be discussed using a model where bacterial RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal(II)-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond. (diva-portal.org)
  • an N-terminal DExH-box RNA helicase-like domain, a DUF283 domain, a PAZ domain, two RNase III domains (RIIIa and RIIIb), and a dsRNA binding motif domain (DARM) [ 24 ]. (biomedcentral.com)
  • Each RNase has a specificity for a different cleavage site. (encyclopedia.com)
  • Recent findings suggest that cellular RNA may be a therapeutically relevant locus. (elsevier.com)
  • The ready accessibility of cellular RNAs to xenobiotic agents, the high selectivity of bleomycin action on RNAs, and the paucity of mechanisms for RNA repair suggest that RNA may be a therapeutically relevant target for bleomycin. (elsevier.com)
  • The exosome is a major eukaryotic nuclease located in both the nucleus and the cytoplasm that contributes to the processing, quality control and/or turnover of a large number of cellular RNAs. (waw.pl)
  • Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. (elifesciences.org)
  • Small interfering RNA-mediated knockdown (KD) of ADAM9 resulted in up-regulation of membrane-bound MICA expression on the HepG2 and PLC/PRF/5 cellular surfaces and down-regulation of soluble MICA levels in their culture supernatant. (wiley.com)
  • In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. (hindawi.com)
  • A key element in the study of cellular RNA metabolism is the molecular characterization of RNA. (hindawi.com)
  • Cellular RNAs are posttranscriptionally modified at various points in the primary RNA transcript as well as processed. (hindawi.com)
  • In cellular RNA metabolisms, RNA maturation is performed through various structural alterations that include chemical modifications of constituent components. (hindawi.com)
  • Such a molecule could be used to inactivate a target RNA, probe a structured RNA, or assist in the manipulation of recombinant RNA. (pnas.org)
  • To study the cleavage activity on the HCV RNA of a chimeric recombinant of HCV specific ribozyme and U1 small nuclear RNA , which compartmentalizes within the nucleolus. (bvsalud.org)
  • Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures. (asm.org)
  • However, the mechanisms that regulate caspase-3 cleavage remain elusive. (ahajournals.org)
  • however, the underlying molecular mechanisms facilitating caspase-3 activation and HuR cleavage remains unknown. (omicsdi.org)
  • The mechanisms that regulate cleavage of proNGF, therefore, are critical determinants of whether this factor promotes neuronal survival or death. (jneurosci.org)
  • Computational approaches including classical molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and free energy simulations were employed to study the cleavage mechanisms and explain experimental observations such as the thio effects and metal ion rescue effects. (illinois.edu)
  • These results suggest that RNA silencing targets several genes from T-DNA of A. rhizogenes in hairy roots of common bean. (frontiersin.org)
  • Base pair-complementary RNA strands (ssRNA) can be produced by transcription of both template DNA strands of some genes (Figure 1). (wikiversity.org)
  • What they determined was that in the pre-miR-451 hairpin in zebrafish, at a critical position in the miRNA, they found a "G-G" pairing mismatch that actually appears to facilitate cleavage by the impaired zebrafish Ago. (mit.edu)
  • On the other hand, production of mature miRNA from an endogenous hairpin RNA with 5' overhangs has also been reported, although the mechanism for this process is unknown. (biomedcentral.com)
  • The two-step cleavage of a hairpin RNA with 5' overhangs shows that DICER releases double-stranded RNAs after the first cleavage and binds them again in the inverse direction for a second cleavage. (biomedcentral.com)
  • Photomodulating RNA cleavage using photolabile circular antisense oligodeoxynucleotides[J]. NUCLEIC ACIDS RESEARCH,2010,38(11):3848-3855. (bjmu.edu.cn)
  • 2010).Photomodulating RNA cleavage using photolabile circular antisense oligodeoxynucleotides. (bjmu.edu.cn)
  • A structural model of the DNA/RNA non-specific endonuclease NucA from Anabaena sp. (kpfu.ru)
  • The RNA-guided endonuclease Cas9 is responsible for recognizing, unwinding, and cutting double-stranded DNA (dsDNA) targets as part of the type II CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) adaptive immune system ( 1 - 4 ). (sciencemag.org)
  • Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. (asm.org)
  • Arenavirus infection induces discrete cytosolic structures for Rna replication. (springer.com)
  • Effectively grazoprevir prevents cleavage of the necessary polyproteins for replication. (wikipedia.org)
  • However, it was only in 1998 that experiments were described showing the unexpected power of double stranded RNA to block gene expression . (wikiversity.org)
  • Our results demonstrate the importance of caspase-mediated RIPK1 cleavage during embryonic development and show that caspase cleavage of RIPK1 not only inhibits necroptosis but also maintains inflammatory homeostasis throughout life. (nature.com)
  • Detection of a 89-kDa or 24-kDa caspase cleavage fragment of PARP-1 was shown to be a hallmark of apoptosis . (bio-medicine.org)
  • After 5 hours, the untreated cells (Figure 1, left panel) and CD95-stimulated cells (Figure 1, right panel) were stained for PARP cleavage using the anti-PARP Caspase Cleavage Product-Fluorescein antibody (1 g/ml), and analyzed for TUNEL staining using the In Situ Cell Death Detection Kit, TMR red. (bio-medicine.org)
  • To gain new insights into apoptotic pathways particularly in situ Roche Applied Science now offers the anti- PARP Caspase Cleavage Product-Fluorescein antibody. (bio-medicine.org)
  • The antibody can serve as an early marker of apoptosis since it is directed against the caspase cleavage site of PARP-1 and specifically recognizes an epitope that is generated by caspases, but is not accessible in nonapoptotic cells. (bio-medicine.org)
  • Mutation of the proteolytic cleavage site often has profound implications for disease progression ( 17 , 18 ). (cdc.gov)
  • The alpha- and beta-cleavage events remove the flexible, unstructured N-terminus from the structured C-terminal region, producing N1/C1 and N2/C2 fragments, respectively (Fig. 1 a). (springer.com)
  • long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
  • 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. (mdpi.com)
  • The other three (C20, C30 and C40) without stable secondary structures have the middle 20 deoxynucleotides complementary to 40-mer RNA. (bjmu.edu.cn)
  • Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity. (nih.gov)
  • Here, we show that transcription across the targets of the Staphylococcus epidermidis type III-A CRISPR-Cas system results in the cleavage of the target DNA and its transcripts, mediated by independent active sites within the Cas10-Csm ribonucleoprotein effector complex. (nih.gov)
  • Our studies reveal a highly versatile mechanism of CRISPR immunity that can defend microorganisms against diverse DNA and RNA invaders. (nih.gov)
  • A CRISPR View of Cleavage. (nih.gov)
  • RNAs from the CRISPR loci are hypothesized to guide the CRISPR-Cas defense response based on their potential to base pair with invading nucleic acids. (pubmedcentralcanada.ca)
  • Nonetheless, to date the CRISPR RNA/Cas9 system has not been adapted for Drosophila , a key genetic model, and germline transmission of Cas9-induced changes has not been achieved in any organism. (genetics.org)
  • Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. (asm.org)
  • It is noted that RNA sequencing can aid the determination of the molecular pathogenesis of diseases. (hindawi.com)
  • This study reports the effects of the iron chelator deferoxamine (DFO) on collagen cleavage, inflammation, and chondrocyte hypertrophy in relation to energy metabolism-related gene expression in osteoarthritic (OA) articular cartilage. (hindawi.com)
  • 3. The nucleic acid molecule according to claim 2, wherein said ribonucleic acid molecule having endonucleasc activity is a ribozyme, preferably a hammerhead ribozyme which specifically cleaves heparanase RNA and thereby inhibits the expression of heparanase. (freepatentsonline.com)
  • The building blocks of RNA are commonly referred to using single letters: A, C, G and U. Previous studies have shown that it is possible to copy RNA without enzymes, but for only two of the four RNA letters, namely C and G. (elifesciences.org)
  • The enzymes were incubated with the target RNAs under different conditions and autoradiographed after denaturing gel- electrophoresis . (bvsalud.org)
  • Cotranscriptional cleavage mediated by a hammerhead ribozyme can affect alternative splicing if interposed between an exon and its intronic regulatory elements. (ox.ac.uk)
  • Our results suggest that targeted hammerhead ribozyme cleavage within introns can be used as a tool to define splicing regulatory elements. (ox.ac.uk)
  • Finally, by immobilizing the primer and template on a bead and adding individual monomers in sequence, we synthesize a significant part of an active hammerhead ribozyme, forging a link between nonenzymatic polymerization and the RNA world. (elifesciences.org)
  • The third stem-loop sequence of human U1 snRNA (position 95-116) within pBSIISK+ U1 was substituted by hammerhead ribozyme against HCV RNA by PCR and cloning methods , and the constructed plasmid was named pBSIISK+ (U1-Rz). (bvsalud.org)
  • This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). (mdpi.com)
  • The researchers discovered that while, as might be expected, a G-G mismatch slows Ago binding, it significantly enhances both slicing efficiency as well as the release of the bound product, more than off-setting the slower binding reaction kinetics and suggesting that non- "Watson-Crick" base pairing creates an exceptionally favorable geometry for the cleavage and release parts of the reaction. (mit.edu)
  • A conformational change within the serpin interrupts the cleavage reaction, deforming the protease active site and preventing dissociation. (portlandpress.com)
  • The glmS ribozyme regulates the level of glucosamine-6-phosphate (GlcN6P) in bacteria by catalyzing a self-cleavage reaction. (illinois.edu)
  • The data indicate that Rpc11p limits RNA 3′-U length and that this significantly restricts pre-tRNAs to a La-independent pathway of maturation in fission yeast. (pubmedcentralcanada.ca)
  • Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. (asm.org)
  • Exploring the effects of a seed sequence mismatch on Ago-catalyzed cleavage kinetics further, they then tested its ability to slice other bound transcripts. (mit.edu)
  • Taken together, this evidence suggests that small RNA pathways can regulate gene expression by chromatin modification in somatic cells. (g3journal.org)
  • The role of dT n extends beyond termination, since it provides a means to link Pol III transcripts to La, an abundant and ubiquitous nuclear phosphoprotein that binds these RNAs in a 3′-oligo(U) length-dependent manner and promotes their posttranscriptional processing ( 27 , 32 , 37 ). (pubmedcentralcanada.ca)
  • Caspase-3 cleavage and activation are known to play central roles in apoptosis. (ahajournals.org)
  • TRAF2 and RIP1 then detach from TNFR1 and recruit FADD and caspase-8 for the assembly of the cytoplasmic complex II ( 19 ), where the deubiquitinating cylindromatosis removes the polyubiquitin chains from RIP1 to promote caspase-8 cleavage for TNF-α-induced apoptosis ( 20 ). (aacrjournals.org)
  • We determined that oral cancer cells overexpressing cyclooxygenase-2 (COX-2) limited the cleavage of both caspase-3 and HuR, which in turn, reduced the rate of apoptosis in paclitaxel treated cells. (omicsdi.org)
  • In contrast to measuring active caspase 3, which is degraded during apoptosis via the ubiquitin/proteosome pathway, measuring PARP-1 cleavage might allow sustained signal detection even in late stages of apoptosis. (bio-medicine.org)
  • Furthermore, providing exogenous MMP-7 after injury promoted proNGF cleavage and neuroprotection, suggesting a novel regulatory mechanism for p75 NTR -mediated apoptosis. (jneurosci.org)
  • Consistent with this suggestion, the cleavage dependency on an amber codon was considerably reduced in the presence of amber-codon-suppressing tRNA. (genetics.org)
  • The original RNA sequencing data are uploaded and available at the Gene Expression Omnibus (GEO) under accession GSE127572 . (nature.com)
  • Small noncoding RNAs play several roles in regulating gene expression. (g3journal.org)