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)Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Folding: The processes of RNA tertiary structure formation.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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, 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, 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)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.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.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, 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.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.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.RNA Viruses: Viruses whose genetic material is RNA.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.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).Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Riboswitch: Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.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.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.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.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, 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.5' Untranslated Regions: 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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.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, 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.Haloarcula marismortui: A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.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 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.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)RNA Splice Sites: 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.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Sulfuric Acid Esters: Organic esters of sulfuric acid.Introns: 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.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.CME-CarbodiimideEndoribonucleases: 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.-.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.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.Tetrahymena: A genus of ciliate protozoa commonly used in genetic, cytological, and other research.Nucleic Acid Denaturation: 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.RNA, Transfer, Asp: A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.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.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.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Frameshifting, Ribosomal: A directed change in translational READING FRAMES that allows the production of a single protein from two or more OVERLAPPING GENES. The process is programmed by the nucleotide sequence of the MRNA and is sometimes also affected by the secondary or tertiary mRNA structure. It has been described mainly in VIRUSES (especially RETROVIRUSES); RETROTRANSPOSONS; and bacterial insertion elements but also in some cellular genes.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.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.RNA, Ribosomal, 5S: Constituent of the 50S subunit of prokaryotic ribosomes containing about 120 nucleotides and 34 proteins. It is also a constituent of the 60S subunit of eukaryotic ribosomes. 5S rRNA is involved in initiation of polypeptide synthesis.RNA, Transfer, Phe: A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.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.Aristolochia: A plant genus of the family ARISTOLOCHIACEAE. Species of this genus have been used in traditional medicine but they contain aristolochic acid which is associated with nephropathy. These are sometimes called 'snakeroot' but that name is also used with a number of other plants such as POLYGALA; SANICULA; ASARUM; ARISTOLOCHIA; AGERATINA; and others.Azoarcus: A genus of gram-negative, facultatively anaerobic bacteria including species which are often associated with grasses (POACEAE) and which fix nitrogen as well as species which anaerobically degrade toluene and other mono-aromatic hydrocarbons.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.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.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Open Reading Frames: 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).Peptide Chain Initiation, Translational: A process of GENETIC TRANSLATION whereby the formation of a peptide chain is started. It includes assembly of the RIBOSOME components, the MESSENGER RNA coding for the polypeptide to be made, INITIATOR TRNA, and PEPTIDE INITIATION FACTORS; and placement of the first amino acid in the peptide chain. The details and components of this process are unique for prokaryotic protein biosynthesis and eukaryotic protein biosynthesis.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA, Neoplasm: RNA present in neoplastic tissue.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Sequence Homology, Nucleic Acid: 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.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 T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 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.Hydrogen Bonding: A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.Gene Products, tat: Trans-acting transcription factors produced by retroviruses such as HIV. They are nuclear proteins whose expression is required for viral replication. The tat protein stimulates LONG TERMINAL REPEAT-driven RNA synthesis for both viral regulatory and viral structural proteins. tat stands for trans-activation of transcription.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 Gene Products, Human Immunodeficiency Virus: Proteins encoded by the TAT GENES of the HUMAN IMMUNODEFICIENCY VIRUS.Anatomy, Artistic: The study of the structures of organisms for applications in art: drawing, painting, sculpture, illustration, etc.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)Models, Genetic: 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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.UridinePhylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.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, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.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.RNA, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Scattering, Small Angle: Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.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.Kinetics: The rate dynamics in chemical or physical systems.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Knowledge Bases: Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).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)HIV Long Terminal Repeat: Regulatory sequences important for viral replication that are located on each end of the HIV genome. The LTR includes the HIV ENHANCER, promoter, and other sequences. Specific regions in the LTR include the negative regulatory element (NRE), NF-kappa B binding sites , Sp1 binding sites, TATA BOX, and trans-acting responsive element (TAR). The binding of both cellular and viral proteins to these regions regulates HIV transcription.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.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.Aptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Anhydrides: Chemical compounds derived from acids by the elimination of a molecule of water.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.Picornaviridae: A family of small RNA viruses comprising some important pathogens of humans and animals. Transmission usually occurs mechanically. There are nine genera: APHTHOVIRUS; CARDIOVIRUS; ENTEROVIRUS; ERBOVIRUS; HEPATOVIRUS; KOBUVIRUS; PARECHOVIRUS; RHINOVIRUS; and TESCHOVIRUS.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.Nucleic Acid Heteroduplexes: Double-stranded nucleic acid molecules (DNA-DNA or DNA-RNA) which contain regions of nucleotide mismatches (non-complementary). In vivo, these heteroduplexes can result from mutation or genetic recombination; in vitro, they are formed by nucleic acid hybridization. Electron microscopic analysis of the resulting heteroduplexes facilitates the mapping of regions of base sequence homology of nucleic acids.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).Tetrahymena thermophila: A species of ciliate protozoa used in genetic and cytological research.Hepacivirus: A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Bromovirus: A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.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.Nucleotides: 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)Plant Viruses: Viruses parasitic on plants higher than bacteria.PseudouridineRNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.RNA-Directed DNA Polymerase: 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 Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.Codon, Initiator: A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.Guanosine: 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)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).Ribonucleoprotein, U1 Small Nuclear: A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U1 snRNP along with other small nuclear ribonucleoproteins (U2, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. The U1 snRNA forms base pairs with conserved sequence motifs at the 5'-splice site and recognizes both the 5'- and 3'-splice sites and may have a fundamental role in aligning the two sites for the splicing reaction.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)Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Hepatitis Delta Virus: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Oligoribonucleotides, Antisense: Short fragments of RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.Berberine Alkaloids: A group of related plant alkaloids that contain the BERBERINE heterocyclic ring structure.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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Foot-and-Mouth Disease Virus: The type species of APHTHOVIRUS, causing FOOT-AND-MOUTH DISEASE in cloven-hoofed animals. Several different serotypes exist.Gene Expression Regulation: 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.Protein Footprinting: A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.G-Quadruplexes: Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)Alternative Splicing: 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.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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Temperature: 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.Tombusvirus: 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.Molecular Dynamics Simulation: A computer simulation developed to study the motion of molecules over a period of time.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Exons: 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.RNA Probes: RNA, usually prepared by transcription from cloned DNA, which complements a specific mRNA or DNA and is generally used for studies of virus genes, distribution of specific RNA in tissues and cells, integration of viral DNA into genomes, transcription, etc. Whereas DNA PROBES are preferred for use at a more macroscopic level for detection of the presence of DNA/RNA from specific species or subspecies, RNA probes are preferred for genetic studies. Conventional labels for the RNA probe include radioisotope labels 32P and 125I and the chemical label biotin. RNA probes may be further divided by category into plus-sense RNA probes, minus-sense RNA probes, and antisense RNA probes.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Signal Recognition Particle: A cytosolic ribonucleoprotein complex that acts to induce elongation arrest of nascent presecretory and membrane proteins until the ribosome becomes associated with the rough endoplasmic reticulum. It consists of a 7S RNA and at least six polypeptide subunits (relative molecular masses 9, 14, 19, 54, 68, and 72K).Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.Gene Products, pol: Retroviral proteins coded by the pol gene. They are usually synthesized as a protein precursor (POLYPROTEINS) and later cleaved into final products that include reverse transcriptase, endonuclease/integrase, and viral protease. Sometimes they are synthesized as a gag-pol fusion protein (FUSION PROTEINS, GAG-POL). pol is short for polymerase, the enzyme class of reverse transcriptase.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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)Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Bacterial Proteins: Proteins found in any species of bacterium.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Adenosine Deaminase: An enzyme that catalyzes the hydrolysis of ADENOSINE to INOSINE with the elimination of AMMONIA.RNA, Small Cytoplasmic: Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.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.Phosphorus Radioisotopes: Unstable isotopes of phosphorus that decay or disintegrate emitting radiation. P atoms with atomic weights 28-34 except 31 are radioactive phosphorus isotopes.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Cross-Linking Reagents: Reagents with two reactive groups, usually at opposite ends of the molecule, that are capable of reacting with and thereby forming bridges between side chains of amino acids in proteins; the locations of naturally reactive areas within proteins can thereby be identified; may also be used for other macromolecules, like glycoproteins, nucleic acids, or other.Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Metals: Electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals. (Grant & Hackh's Chemical Dictionary, 5th ed)Norovirus: A genus in the family CALICIVIRIDAE, associated with epidemic GASTROENTERITIS in humans. The type species, NORWALK VIRUS, contains multiple strains.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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.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.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.RNA, Long Noncoding: 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.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.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
Chen, Yu, and Varani, Gabriele(Jun 2010) RNA Structure. In: eLS. John Wiley & Sons Ltd, Chichester. "RNA Structure". ... and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. RNA kissing ... Stem-loop Pseudoknot RNA Nucleic acid tertiary structure Three prime untranslated region Adaptation "A stem-loop "kissing" ... Ribonucleic acid (RNA) molecules perform their function in living cells by adopting specific and highly complex 3-dimensional ...
"As a graduate student at Duke… he used x-ray crystallography to study the three-dimensional structure of "transfer" RNA, which ... structure of a Cro repressor-DNA complex, and on the new David McKay and Thomas Steitz structure of a CAP-cAMP complex; David ... "Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement". Journal of Molecular Biology. 123 (4): ... "RNA expression analysis using a 30 base pair resolution Escherichia coli genome array". Nature Biotechnology. 18 (12): 1262-8. ...
Nucleic acid structure determination Nucleic acid structure prediction List of RNA structure prediction software. ... RNA structures form complex secondary and tertiary structures compared to DNA which form duplexes with full complementarity ... For example, tools to assess RNA-RNA interactions and restricted ensembles of structures. Furthermore, other features included ... for most stable structure) and generating suboptimal structures. A large number of structure prediction tools have been ...
"The Vienna RNA secondary structure package". Atri Rudra's course at The State University of New York, Buffalo. ... in that the existence of cyclic structure helps in reducing complexity and thus prevents secondary structure formation. i.e. ... In essence this algorithm shows how the presence of a cyclic structure in a DNA code reduces the complexity of the problem of ... This is also known as self-hybridization). The Nussinov-Jacobson algorithm is used to predict secondary structures and also to ...
Rivas E, Eddy S. (1999). "A dynamic programming algorithm for RNA structure prediction including pseudoknots". J Mol Biol 285(5 ... 2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proc Natl Acad Sci USA 102(23): 8080-5. ... Thus, popular secondary structure prediction methods like Mfold and Pfold will not predict pseudoknot structures present in a ... A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is ...
The D arm is a feature in the tertiary structure of transfer RNA (tRNA). It is composed of the two D stems and the D loop. The ... Smith, Drew; Yarus, Michael (April 1989). "Transfer RNA structure and coding specificity". Journal of Molecular Biology. 206 (3 ... It appears to play a large role in the stabilization of the tRNA's tertiary structure. Hardt, Wolf Dietrich; Schlegl, Judith; ...
ISBN 0-8493-8217-3. Venkstern, T.V. (1995). The Primary Structure of Transfer RNA. Boston, MA: Springer US. ISBN 1-4684-1971-4 ...
Chen, JL; Greider, CW (Jun 7, 2005). "Functional analysis of the pseudoknot structure in human telomerase RNA". Proceedings of ... as the growing RNA strand emerges from the RNA polymerase complex, it will create enough structural tension to cause the RNA ... Staple, DW; Butcher, SE (June 2005). "Pseudoknots: RNA structures with diverse functions". PLoS Biology. 3 (6): e213. doi: ... folds into a double-pseudoknot structure and self-cleaves its circular genome to produce a single-genome-length RNA. ...
At about the same time she pioneered folding algorithms for predicting RNA secondary structures. RNA folding was also ... Konings, D.A.M.; Hogeweg, P. (1989). "Pattern analysis for RNA secondary structure. Similarity and consensus of minimal-energy ... and has shown RNA increase in complexity as the result of interactions of secondary structure and spatial pattern formation. ... Hogeweg, Paulien (1969). "Structure of aquatic vegetation: a comparison of aquatic vegetation in India, the Netherlands and ...
Giedroc DP, Cornish PV (February 2009). "Frameshifting RNA pseudoknots: structure and mechanism". Virus Research. 139 (2): 193- ... Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other ... Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and ... Walczak R, Westhof E, Carbon P, Krol A (April 1996). "A novel RNA structural motif in the selenocysteine insertion element of ...
Unusual structure and restricted RNA distribution". The Journal of Biological Chemistry. 269 (8): 6016-25. PMID 8119947. ... Tan K, Casasnovas JM, Liu JH, Briskin MJ, Springer TA, Wang JH (Jun 1998). "The structure of immunoglobulin superfamily domains ... "Structure-function analysis of the integrin beta 7 subunit: identification of domains involved in adhesion to MAdCAM-1". ... 1 and 2 of MAdCAM-1 reveals novel features important for integrin recognition". Structure. 6 (6): 793-801. doi:10.1016/S0969- ...
... and small-RNA biology; DNA replication; RNA splicing; signal transduction; genome structure; non-coding RNAs; deep sequencing; ... Adrian Krainer, studies RNA splicing and developed nusinersen for treatment of spinal muscular atrophy (SMA). Robert ... James Watson, co-discoverer of structure of DNA, Nobel Laureate. Scott Lowe (currently at MSKCC), research on p53, Member of ... At the CSH Symposium in summer 1953, Watson made the first public presentation of DNA's double-helix structure. Nobel Prize ...
An emerging consensus for telomerase RNA structure. „Proc Natl Acad Sci U S A". 101 (41), s. 14683-4, Oct 2004. DOI: 10.1073/ ... Telomerase RNA structure and function: implications for dyskeratosis congenita. „Trends Biochem Sci". 29 (4), s. 183-92, Apr ... Functional analysis of the pseudoknot structure in human telomerase RNA. „Proc Natl Acad Sci U S A". 102 (23), s. 8080-5; ... Telomerase RNA levels limit the telomere length equilibrium. „Cold Spring Harb Symp Quant Biol". 71, s. 225-9, 2006. DOI: ...
As the 5′ UTR has a high GC content, secondary structures often occur within it. Hairpin loops are one such secondary structure ... RNA. 12 (5): 851-61. doi:10.1261/rna.2309906. PMC 1440912 . PMID 16540693. Araujo, Patricia R.; Yoon, Kihoon; Ko, Daijin; Smith ... The closed-loop structure inhibits translation. This has been observed in Xenopus laevis in which eIF4E bound to the 5′ cap ... RNA-binding proteins sometimes serve to prevent the pre-initiation complex from forming. An example is regulation of the msl2 ...
"RNA structure replaces the need for U2AF2 in splicing". Genome Research. 26 (1): 12-23. doi:10.1101/gr.181008.114. ISSN 1549- ... Structures, locations, and functions[edit]. A microsatellite is a tract of tandemly repeated (i.e. adjacent) DNA motifs that ... This method of RNA splicing is believed to have diverged from human evolution at the formation of tetrapods and to represent an ... 2003). "Microsatellites within genes: structure, function and evolution". Mol. Biol. Evol. 21 (6): 991-1007. doi:10.1093/molbev ...
A stem loop hairpin structure mediates the RNA editing. ADAR2 is likely to be the preferred editing enzyme at the I/V site. ... RNA editing[edit]. The pre-mRNA of this protein is subject to RNA editing.[11] ... A to I RNA editing is catalyzed by a family of adenosine deaminases acting on RNA (ADARs) that specifically recognize ... GABRA3 - a channel subunit which undergoes similar RNA editing. References[edit]. *^ a b c GRCh38: Ensembl release 89: ...
"Common evolutionary trends for SINE RNA structures". Trends in Genetics. 23 (1): 26-33. doi:10.1016/j.tig.2006.11.005. PMID ... SINEs use an RNA intermediate and reverse transcriptase to transpose into new parts of the genome. SINEs do not encode a ... suggesting positive pressure to preserve structure and function of SINEs. While SINEs are present in many species of ... base pair internal regions which contain a tRNA-derived segment with A and B boxes that serve as an internal promoter for RNA ...
Acylation tRNA aminoacylation Transfer RNA-like structures. ...
The RNA adopts a double pseudoknotted structure. The cofactor is bound in a solvent-accessible pocket and the structure ... The Glucosamine-6-phosphate activated ribozyme ( glmS ribozyme) is an RNA structure that is both a ribozyme, since it catalyzes ... April 2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proc. Natl. Acad. Sci. U ... The structure of the GlmS ribozyme has been determined by X-ray crystallography. ...
... were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ... Although archaea only have one type of RNA polymerase, its structure and function in transcription seems to be close to that of ... Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. doi:10.1111/ ... and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic ...
Thurner C, Witwer C, Hofacker IL, Stadler PF (May 2004). "Conserved RNA Secondary Structures in Flaviviridae Genomes". J. Gen. ... However, the time interval between GBV-C infection and clearance of viraemia (detection of GBV-C RNA in plasma) is not known. ... It has a single stranded positive RNA genome of about 9.3 kb and contains a single open reading frame (ORF) encoding two ... Hepatitis G virus and GB virus C (GBV-C) are RNA viruses that were independently identified in 1995, and were subsequently ...
"Neutral networks of RNA Secondary Structures" (PDF). Hofacker, Ivo L.; Schuster, Peter; Stadler, Peter F. "Combinatorics of RNA ... An RNA secondary structure can be viewed as a diagram over N labeled vertices with its Watson-Crick base pairs represented as ... In the 1970s, Stein and M. Waterman laid the ground work for the combinatorics of RNA secondary structures. Waterman gave the ... M. Zuker, implemented algorithms for computation of MFE RNA secondary structures based on the work of Nussinov et al., Smith ...
Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, Cramer P: RNA polymerase II-TFIIB structure and mechanism of ... "Structure of transcribing mammalian RNA polymerase II". Nature. 529 (7587): 551-554. doi:10.1038/nature16482. Plaschka, C.; ... "RNA polymerase II-TFIIB structure and mechanism of transcription initiation". Nature. 462 (7271): 323-330. doi:10.1038/ ... Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P: Structure of transcribing mammalian RNA polymerase II. Nature. 2016 ...
StructureEdit. The structure of a mature eukaryotic mRNA. A fully processed mRNA includes a 5' cap, 5' UTR, coding region, 3' ... A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m7G cap) is a modified guanine nucleotide that has ... Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they ... Small interfering RNA (siRNA)Edit. Main article: siRNA. In metazoans, small interfering RNAs (siRNAs) processed by Dicer are ...
... and structure-specific RNA processing by a CRISPR endonuclease". Science. 329 (5997): 1355-8. Bibcode:2010Sci...329.1355H. doi: ... "RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex". Cell. 139 (5): 945-56. doi:10.1016/j.cell.2009.07.040. PMC ... Other RNA-guided Cas proteins cut foreign RNA.[9] CRISPR are found in approximately 50% of sequenced bacterial genomes and ... doi:10.4161/rna.24023. PMC 3737337. PMID 23445770.. *^ a b c Erdmann S, Garrett RA (September 2012). "Selective and hyperactive ...
除了蛋白質編碼基因之外,人類的基因組還包含了數千個RNA基因(製造非編碼RNA),其中包括用來轉錄轉運RNA(tRNA)、核糖體RNA(rRNA)與信使RNA(mRNA)的基因。其中轉錄rRNA的基因稱為rDNA,分佈在許多不同的染色體上。 ... Genome sequence, comparative analysis and haplotype structure of the domestic dog.. Nature. 2005, 438 (7069):
... has developed a computerised simulation model which can effectively predict the three-dimensional conformation of the RNA ... In many of these, its structure plays a crucial role. Structure is different and characteristic for each RNA depending on the ... Discovering the structure of RNA. Scuola Internazionale Superiore di Studi Avanzati. Journal. Nucleic Acids Research. Keywords ... Discovering the structure of RNA A new study develops an innovative simulation model able to efficiently predict the ...
... s Structure of Nucleic Acids. Learn exactly what happened in this chapter, scene, or section of Structure of Nucleic Acids and ... The main difference between the three-dimensional structures of DNA and RNA is that in RNA the three-dimensional structure is ... The primary structure of a nucleic acid refers to its sequence of base pairs. In RNA, the secondary structures are the two- ... The Three-Dimensional Structure of RNA Unlike DNA, RNA cannot adopt the B-form helix because the additional 2 hydroxyl ...
RNA (5-R(*AP*AP*AP*AP*AP*GP*UP*CP*CP*UP*C)-3)BiotinMagnesium Ion ... RNA (5- R(*AP*CP*CP*GP*UP*CP*AP*GP*AP*GP*GP*AP*CP*AP*CP*GP*GP*UP*U) -3) ... RNA (5- R(*ap*cp*cp*gp*up*cp*ap*gp*ap*gp*gp*ap*cp*ap*cp*gp*gp*up*u) -3) ... RNA (5-r(*ap*ap*ap*ap*ap*gp*up*cp*cp*up*c)-3) ... 1F27: Crystal Structure Of A Biotin-Binding Rna Pseudoknot. PDB ...
We use a new high-throughput RNA structure probing technology to identify RNA regions with tertiary folds and discover that ... RNA viruses usurp and reprogram host cells using short RNA genomes. RNA viruses encode the information required for their ... Higher-order RNA structures are pervasive and involve more than one-third of nucleotides in the DENV2 genomic RNA. These 3D ... Pervasive tertiary structure in the dengue virus RNA genome. Elizabeth A. Dethoff, Mark A. Boerneke, Nandan S. Gokhale, Brejnev ...
11 RNA.. CMCF Beamline Scientist Michel Fodje said the experiments were very successful in identifying the structure of the RNA ... With this information, researchers will continue to map the diverse structures of RNA and their roles in the design of novel ... RNA: Evaluation of a 50 Year‐Old Prediction. Angewandte Chemie International Edition.. Image: Structure of poly (rA) duplex ... RNA: Evaluation of a 50 year-Old Prediction.". "After 50 years of study, the identification of a novel nucleic acid structure ...
... there is a resurgence of research in using RNA primary sequences to predict their secondary structures, due to the... ... Due to the recent discovery of many RNAs with great diversity of functions, ... Song D., Deng Z. (2006) A Fuzzy Dynamic Programming Approach to Predict RNA Secondary Structure. In: Bücher P., Moret B.M.E. ( ... Here based on the fuzzy sets theory, we propose a fuzzy dynamic programming approach to predict RNA secondary structure, which ...
2001) Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II. J ... Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases Message Subject (Your Name) has sent you a ... Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. Bradley Zamft, Lacramioara Bintu, Toyotaka ... 1998) Transcriptional pausing at +62 of the HIV-1 nascent RNA modulates formation of the TAR RNA structure. Mol Cell 1:1033- ...
RNA secondary structure analysis using the Vienna RNA package.. Hofacker IL1. ... This Current Protocols in Bioinformatics unit documents how to use the Vienna RNA package for RNA secondary structure analysis ... Possible tasks include structure prediction for single sequences, prediction of consensus structures, and sequence design. ...
... is an RNA virus with the largest genome among all such viruses. This 30 kb size virus has caused many difficulties for ... Comparing RNA Secondary Structures. In a new study out of Yale University and published on the preprint server bioRxiv* ... Since RNA structure is essential for viral function and for higher-order compaction, the current study focuses on this aspect ... Researchers map RNA structure throughout SARS-CoV-2 genome. *Download PDF Copy ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows ... Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex. Sainsbury, S., Niesser, J., Cramer, P.. ( ... DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1. A. 1733. Saccharomyces cerevisiae. Mutation(s): 0 EC: ...
... label guanosine in single-strand RNAs in live cells that could be used to determine transcriptome-wide RNA secondary structures ... N3-kethoxal-based chemistry allows efficient RNA labeling under mild conditions and transcriptome-wide RNA secondary structure ... RNA secondary structure is critical to RNA regulation and function. We report a new N3-kethoxal reagent that allows fast and ... RNA secondary structure is critical to RNA regulation and function. We report a new N3-kethoxal reagent that allows fast and ...
Representative RNA 3D Structure Sets All RNA Structures. Representative sets of RNA-containing 3D structures. Resolution cutoff ... RNA Search Options:. Polymer. All. RNA Only Protein RNA Complexes. Drug RNA Complexes Hybrids and Chimera Peptide Nucleic Acid ... The role of RNA structure in translational regulation by L7Ae protein in archaea.. RNA pp. - 2018. ... Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence ...
Empirical measurement of RNA secondary structure is an invaluable tool that has provided a more complete understanding of the ... RNA life cycle and functionality of this extremely important molecule. In... ... RNA genomics RNA secondary structure Posttranscriptional regulation Transcriptome Nuclease probing Abbreviations. RBP. RNA ... high-throughput sequencing for chemical probing of RNA structure. RNA 20:713-720CrossRefPubMedGoogle Scholar ...
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 ... SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE C. 5 synthetic 5-MER ...
... and functional aspects of DNA and RNA research. ... U5 RNA), 4.5S RNA I (Alu RNA), 4.5S RNA II (U6), and 4.5S RNA ... pppNp) for primary transcripts such as 4.5S RNA I, 5S RNA, and Alu RNA. (pNp) 5′ end for processed RNAs such as Alu RNA, 5S RNA ... Small nucleolar RNA (C/D box RNA, H/ACA RNA)sdRNA: sno-derived RNAsmoRNA: MicroRNA-offset RNAstel-sRNA: Telomere small RNAs ... Lnc RNA: Long Noncoding RNA (~0.5 to 100 kb) (1) Specific Long Noncoding RNA. TR/TERC: Telomerase RNA/telomerase RNA component ...
... are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate ... secondary structure-specific nucleases, inline probing, and SHAPE chemistry, ... Methods to probe RNA secondary structure, such as small molecule modifying agents, ... Improving RNA secondary structure prediction with structure mapping data Methods Enzymol. 2015;553:91-114. doi: 10.1016/bs.mie. ...
... Don Gilbert gilbertd at bio.indiana.edu Thu Sep 4 19: ... an application for visualizing RNA secondary structure version 2.07b, August 1997 loopDloop is a tool for drawing RNA secondary ... Options allow you to modify, adorn and edit the structure. Standard application functions to save, print, edit and manage ... It reads files of biosequence data with base pairing information, and displays graphic views of the secondary structure. ...
... a Rosetta framework for predicting and designing noncanonical motifs that define RNA tertiary structure. In a test set of ... thirty-two 6-20-nucleotide motifs, FARFAR recapitulated 50% of the experimental structures at near-atomic … ... We present fragment assembly of RNA with full-atom refinement (FARFAR), ... Atomic accuracy in predicting and designing noncanonical RNA structure Nat Methods. 2010 Apr;7(4):291-4. doi: 10.1038/nmeth. ...
Advanced cryo-EM imaging reveals high-resolution side and top views of the viral RNA replication "crown" complex structure. ... "We hope to continue to improve the RNA replication complex crown structure to provide additional important refinements in ... This protein contains RNA polymerase and RNA capping domains- two enzymatic domains that are conserved across numerous positive ... In each positive-strand RNA virus, most of the viral genes are devoted to a single process: replicating the viral RNA genome. ...
Download past episodes or subscribe to future episodes of Rna Structure and Function 2014 by International Centre for Genetic ... Topics include RNA structure, structure prediction, ribozymes, transport, RNA- protein recognition, translation, processing, ... CleanVideoJ. E. Dahlberg - What makes RNA special? - RNA Structure and Function 2014 James E. Dahlberg, University of Wisconsin ... CleanVideoM. Yusupov - Crystal structure of bacterial and yeast ribosome -RNA Structure and Function 2014 Marat Yusupov IGBMC, ...
Home , Printer-friendly , Discovering the structure of RNA. Discovering the structure of RNA. A new study develops an ... In many of these, its structure plays a crucial role. Structure is different and characteristic for each RNA depending on the ... And yet RNA, or ribonucleic acid, plays an essential role in many biological processes: not only as messenger molecule with the ... has developed a computerised simulation model which can effectively predict the three-dimensional conformation of the RNA ...
... to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full- ... M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination. ... cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA ... Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable ...
The RNA secondary structure problem To view this video please enable JavaScript, and consider upgrading to a web browser that ... This is an RNA sequence, this is another RNA sequence and so on. ... An RNAs, an RNA sequence has only one, each one of the letters ... The main focus of these tasks is to understand interaction between the algorithms and the structure of the data sets being ... forms a secondary structure where it moves onto itself or it falls onto itself. ...
For most RNAs, elimination of the cap structure causes a loss of stability, especially against exonuclease degradation, and a ... Also a cap requirement has been observed for splicing eukaryotic substrate RNAs. A method using E. coli RNA Polymerase primed ... Larger amounts of capped RNAs are produced by transcription systems using SP6 RNA polymerase primed with m7G(5´)ppp(5´)G. ... Certain prokaryotic mRNAs containing a 5´ terminal cap structure are translated as efficiently as or more efficiently than ...
Preassembled Cas9 ribonucleoproteins (RNPs) composed of the recombinant Cas9 protein and in vitrotranscribed (IVT) guide RNA ... Modification of CRISPR guide RNA structure prevents immune response in target cells. Cold Spring Harbor Laboratory Press ... Modification of CRISPR guide RNA structure prevents immune response in target cells ... CRISPR RNAs trigger innate immune responses in human cells. Genome Res doi: 10.1101/gr.231936.117 ...
  • This can have an important impact on basic research, to help shed light on the relationship between structure and function of these molecules, but also on application realms, above all in the medical and therapeutic sector. (eurekalert.org)
  • This work suggests that tertiary structure elements might be common in large RNAs, and that these regions might contain pockets targetable by small molecules in the design of antiviral therapeutics. (pnas.org)
  • The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. (nature.com)
  • Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. (nature.com)
  • RNA molecules usually possess a variety of single-stranded and double-stranded regions that give rise to complex three-dimensional structures. (thermofisher.com)
  • These structures are involved in the molecule's interactions with other nucleic acids, proteins, and small molecules. (thermofisher.com)
  • The Cap Analog is used for synthesis of 5´-capped RNA molecules. (thermofisher.com)
  • The lag between the protein and RNA modeling fields is partly explained by differences in how protein and RNA molecules fold. (sciencemag.org)
  • Cold Spring Harbor, N.Y. - Most of the DNA in the nucleus of each of our cells is converted into RNA, but only a small fraction of these RNA molecules serve as coding templates for the synthesis of proteins. (scienceblog.com)
  • Professor David L. Spector, Ph.D., and a team led by graduate student Hongjae Sunwoo at Cold Spring Harbor Laboratory (CSHL), have expanded our knowledge of ncRNA functions by uncovering a unique structure-building role for two ncRNA molecules. (scienceblog.com)
  • The idea that some of these structures might somehow be supported by RNA molecules first surfaced in studies in the 1970s," according to Professor Spector. (scienceblog.com)
  • In addition, when the scientists depleted the levels of the ncRNAs and blocked the production of new ncRNA molecules, paraspeckles failed to form suggesting that the ncRNAs were essential to both initiate and maintain these nuclear structures. (scienceblog.com)
  • RNA, just like DNA, is a long chain composed of nucleotides, the building blocks that contain nucleobases, the letters that encode the information contained in these molecules. (nanowerk.com)
  • The team began by looking for patterns in this cloverleaf structure, using detailed data from hundreds of molecules representing viruses and each of the three superkingdoms of life: archaea, bacteria and eukarya. (phys.org)
  • Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. (mdpi.com)
  • PhysOrg.com) -- For the first time, it's possible to experimentally capture a global snapshot of the conformation of thousands of RNA molecules in a cell. (phys.org)
  • The application is cool, but it's just window dressing for the real advance: For the first time, it's possible to experimentally capture a global snapshot of the conformation of thousands of RNA molecules in a cell. (phys.org)
  • Finally, they found that RNA molecules that had similar functions often have similar structures - perhaps to better direct them to specific locations within the cell. (phys.org)
  • The researchers tested their technique on baker's yeast because it is a well-studied organism with a relatively limited number of RNA molecules in action at any one time (about 3,000 vs. 10,000 in humans). (phys.org)
  • Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. (ebscohost.com)
  • High hydrostatic pressure (HHP) is a convenient tool in an analysis of the role of small molecules in the structure stabilization of biological macromolecules. (ebscohost.com)
  • Instead the functions of these genes depend on the RNA itself, which can be unstructured or adopt functional secondary structures through internal base pairing or pairing to other RNA molecules. (biomedcentral.com)
  • Thus, delivery of these large self-replicating RNA molecules require definition with respect to translation of different genes, rather than just the GOI as is the norm, for identifying optimal delivery for the desired immune activation in vivo. (ovid.com)
  • Emerging data points to fundamental roles for many of these molecules in development and disease, so we believe that determining the structure of lncRNAs is critical for understanding how they function,' explained Laurie Boyer, the senior author of the study and the Irwin and Helen Sizer Career Development Associate Professor of Biology and Biological Engineering at MIT. (labroots.com)
  • We use a new high-throughput RNA structure probing technology to identify RNA regions with tertiary folds and discover that roughly one-third of the dengue virus RNA genome forms higher-order interactions, many in regions functionally important for replication. (pnas.org)
  • The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is currently at the heart of a pandemic that has cost the world more than 550,000 lives, 12 million infections, and uncounted years of productivity, is an RNA virus with the largest genome among all such viruses. (news-medical.net)
  • Previous reports have suggested that this virus also forms genome-scale ordered RNA structures (GORS) like other coronaviruses . (news-medical.net)
  • Since RNA structure is essential for viral function and for higher-order compaction, the current study focuses on this aspect of the viral genome. (news-medical.net)
  • In a new study out of Yale University and published on the preprint server bioRxiv * researchers assessed the folding stability of the RNA genome of this virus in comparison to other known systems, to explore the biological contributions made by these structural features. (news-medical.net)
  • The study shows that the RNA folding stability of this genome is twice that of the HCV, hitherto the hallmark of stable secondary structure. (news-medical.net)
  • Distribution of well-defined RNA structures across the SARS-CoV-2 genome. (news-medical.net)
  • A) The percentage of nucleotides in well-defined structured regions (high BPC/low Shannon) was calculated in 100-nt bins tiling the genome and is plotted as a function of the genomic coordinate (gray curve). (news-medical.net)
  • For example, valine binds to the tRNA-like structure of the turnip yellow mosaic virus genome whilst tyrosine binds to the tRNA-like structure of the barley stripe mosaic virus genome. (wikipedia.org)
  • Newswise - For the first time, scientists at the Morgridge Institute for Research have generated near atomic resolution images of a major viral protein complex responsible for replicating the RNA genome of a member of the positive-strand RNA viruses, the large class of viruses that includes coronaviruses and many other pathogens. (newswise.com)
  • In each positive-strand RNA virus, most of the viral genes are devoted to a single process: replicating the viral RNA genome. (newswise.com)
  • Given this massive investment of resources, viral RNA genome replication is arguably one of the most important processes in infection, and It is already a major target for virus control," Ahlquist says. (newswise.com)
  • Ahlquist and his team previously showed that in each such genome replication complex, a copy of the viral RNA genome or chromosome is protected inside the spherule vesicle to function as a replication template. (newswise.com)
  • Hangauer, M. J., Vaughn, I. W. & McManus, M. T. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. (nature.com)
  • Preassembled Cas9 ribonucleoproteins (RNPs) composed of the recombinant Cas9 protein and in vitrotranscribed (IVT) guide RNA complexes can be delivered into cells without risk of foreign DNA integration into the host genome and with fewer off-target effects. (eurekalert.org)
  • Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. (eurekalert.org)
  • We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD. (frontiersin.org)
  • In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the synthesis of viral enzymes), replication, transcription and encapsidation into progeny virions. (leidenuniv.nl)
  • The sg mRNAs of two nidovirus families, arteri- and coronaviruses, consist of two RNA stretches that are noncontiguous in the genome. (leidenuniv.nl)
  • Research on the genome of the virus that causes severe acute respiratory syndrome (SARS) has revealed an unusual molecular structure that looks like a promising target for antiviral drugs. (innovations-report.com)
  • In SARS and related viruses, however, one segment of the RNA genome--known as the s2m RNA--remains virtually unchanged. (innovations-report.com)
  • To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. (uni-muenchen.de)
  • CG was found to be the most informative dinucleotide and could be used to identify regions of the picornavirus genome, which corresponded to the 5'UTR, 3'UTR and Cre, as well as further new structures. (bl.uk)
  • When the transcription start signal of the second gene was exchanged with the transcription start signal of the first gene, transcription of the second gene also was regulated by VP30, indicating that the stem-loop structure of the first transcription start site acts autonomously and independently of its localization on the RNA genome. (asm.org)
  • The RNA genome of EBOV is 19 kb in length and has a coding capacity for eight proteins encoded by seven genes ( 8 ). (asm.org)
  • Since the genome organizations of the different nonsegmented negative-sense RNA viruses are quite similar, it is presumed that the transcription process follows a general mechanism. (asm.org)
  • Once bound to the genome, the transcription complex scans the viral RNA for the conserved transcription start and stop signals, where transcription initiation and termination of the individual genes occur. (asm.org)
  • The nucleocapsid proteins have a dual function in the viral replication cycle: they are involved in virus morphogenesis as structural components ( 22 ), and they catalyze replication and transcription of the RNA genome. (asm.org)
  • Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. (osti.gov)
  • We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human neuroblastoma cell line SK-N-AS. (biomedcentral.com)
  • Amesse, L. S., Pridgen, C.L., Kingsbury, D. W.: Sendai virus DI RNA species with conserved virus genome termini and extensive internal deletions. (springer.com)
  • Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. (semanticscholar.org)
  • Long noncoding RNA (lncRNA) refers to the RNA copied from an area of the genome thought of as junk DNA. (labroots.com)
  • The results showed several unique and interesting features of the s2m RNA, including a distinctive fold that appears to be capable of binding to certain proteins involved in regulating protein synthesis in cells. (innovations-report.com)
  • The structure gives us strong hints about the function, because it forms a fold that has been implicated in binding a certain class of proteins," Scott said. (innovations-report.com)
  • Messenger RNA is the intermediary that carries genetic information from the DNA in the chromosomes to the cellular protein factories, called ribosomes, where the genetic information is translated into proteins. (innovations-report.com)
  • The SARS s2m RNA is in an untranslated section at one end of each of the messenger RNAs that direct the production of viral proteins in infected cells. (innovations-report.com)
  • This part of the ribosome and the proteins that bind to it are involved in the regulation of protein synthesis, leading Scott and his coauthors to hypothesize that the s2m RNA, by mimicking the ribosomal binding site, may serve to hijack the host cell's protein-synthesis machinery for use by the virus. (innovations-report.com)
  • By interacting with precursor and mature mRNA transcripts, RNA binding proteins (RBP) regulate the expression level and isoform of proteins within the cell in an often spatially and temporally dependent manner. (washington.edu)
  • Of the thousands of RNAs so far identified, transfer RNA (tRNA) is the most direct intermediary between genes and proteins. (phys.org)
  • Like many other RNAs (ribonucleic acids), tRNA aids in translating genes into the chains of amino acids that make up proteins. (phys.org)
  • These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus sigma NS. (uni-muenchen.de)
  • To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. (uni-muenchen.de)
  • DNA in the cell is associated with histone proteins to form nucleosomal arrays that are compacted into a highly ordered protein-DNA structure known as chromatin ( 32 ). (asm.org)
  • The Swi-Snf complex can remodel nucleosome structure to facilitate the access of DNA-binding proteins to DNA ( 34 , 58 ). (asm.org)
  • CsrA family RNA-binding proteins are widely distributed in bacteria and regulate gene expression at the posttranscriptional level. (asm.org)
  • IMPORTANCE The CsrA family of RNA-binding proteins is widely conserved in bacteria and plays important roles in the posttranscriptional regulation of protein synthesis. (asm.org)
  • RNA-binding proteins play an integral role in the posttranscriptional regulation of protein synthesis by altering translation initiation, mRNA stability, and/or RNA processing. (asm.org)
  • The CsrA family of RNA-binding proteins regulates carbon metabolism, virulence factor production, and motility in a number of Gram-negative bacteria ( 1 - 5 ). (asm.org)
  • From nuclear magnetic resonance (NMR) studies of the free L11 RNA binding domain (L11-C76), it was known that the protein folds into three α-helices that are superimposable on the α-helices of the homeodomain class of DNA binding proteins. (asmscience.org)
  • In the last decade rRNA has taken center stage as the functional component of ribosomes, and it has been suggested that the primary role of ribosomal proteins is to promote RNA folding. (asmscience.org)
  • In this way RNA can act as enzymes, structural scaffolds and cofactors for proteins. (biomedcentral.com)
  • However, after investigating 182 non-redundant protein-RNA complexes, we find that it would be unsuitable for a certain amount of complexes since the distances between proteins and RNAs vary widely. (springer.com)
  • Si J, Cui J, Cheng J, Wu R (2015) Computational prediction of RNA-binding proteins and binding sites. (springer.com)
  • Besides coding for proteins, RNAs perform various essential roles-most prominently in regulating gene expression-in all kingdoms of life, in many cases mediated by their three-dimensional structures (Mercer et al. (deepdyve.com)
  • RNA nucleotides have a uracil base instead of thymine. (sparknotes.com)
  • When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. (rcsb.org)
  • Once the RNA grows to 12-13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. (rcsb.org)
  • The data revealed that the functional ARE2197 is located in a hairpin loop structure and most nucleotides are highly reactive. (sigmaaldrich.com)
  • To investigate the role of secondary structure in the binding, we mutated specific nucleotides in both functional AREs. (sigmaaldrich.com)
  • In comparison to DNA - a relatively inflexible, double strand of paired nucleotides that spiral around one another in a helix formation - RNA is a veritable circus contortionist. (phys.org)
  • T4 RNA ligase can also be used to synthesize the fifteen nucleotide long anticodon arm region of yeast tRNA('phe) complete with modified nucleotides and a four base pair helical stem. (illinois.edu)
  • In describing the structure, it is interesting to note how conservation and variation of different nucleotides and amino acids serve as a guide to critical features of the complex, and the authors use the extreme conservation of some bases to speculate about functional surfaces of the rRNA domain. (asmscience.org)
  • By solving the genotype-phenotype (GP) map for RNA secondary structure for systems up to length $L=126$ nucleotides (where the set of all possible RNA strands would weigh more than the mass of the visible universe) we show that the GP map strongly constrains the evolution of non-coding RNA (ncRNA). (arxiv.org)
  • We present fragment assembly of RNA with full-atom refinement (FARFAR), a Rosetta framework for predicting and designing noncanonical motifs that define RNA tertiary structure. (nih.gov)
  • In a test set of thirty-two 6-20-nucleotide motifs, FARFAR recapitulated 50% of the experimental structures at near-atomic accuracy. (nih.gov)
  • Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure. (inria.fr)
  • Despite extensive algorithmic development in recent years, modeling of noncanonical base pairs of new RNA structural motifs has not been achieved in blind challenges. (sciencemag.org)
  • When adapted to RNA structure modeling, analogous methods have consistently achieved nucleotide resolution in the RNA-Puzzle blind trials but have not yet reached atomic accuracy, aside from previously solved motifs that happen to recur in new targets ( 2 ). (sciencemag.org)
  • To produce de novo models of small RNA motifs through Fragment Assembly of RNA with Full Atom Refinement (FARFAR). (rosettacommons.org)
  • This method has been demonstrated to reach atomic accuracy for small motifs (12 residues or less) - the current bottleneck for larger RNAs is the difficulty of complete conformational sampling (as in other applications in Rosetta to, e.g., protein de novo modeling). (rosettacommons.org)
  • Intergenic regions of Borrelia species carry evolutionarily stable RNA secondary structure motifs. (pubmedcentralcanada.ca)
  • Small repeat elements carry a variety of motifs at either the DNA, transcribed RNA or translated protein levels and they may be engines for evolutionary change [ 16 , 17 ]. (pubmedcentralcanada.ca)
  • Background There are a growing number of RNA gene families and RNA motifs [1, (sciweavers.org)
  • A fundamental property of RNA is that its secondary structure and even some tertiary contacts are highly stable, which gives rise to independent modular RNA motifs and makes RNAs prone to adopting misfolded intermediates. (utexas.edu)
  • This result underscores the modular nature of RNA motifs and provides insight into how structured RNAs can arrange helices and contacts in multiple ways to achieve and stabilize functional structures. (utexas.edu)
  • In contrast, regulation of the elongation phase is spatially distributed throughout the transcribed gene and involves the modulation of the dynamics of RNA synthesis by cis - and trans -acting factors. (pnas.org)
  • TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. (rcsb.org)
  • TFIIB then prevents the emerging DNA-RNA hybrid duplex from tilting, which would impair RNA synthesis. (rcsb.org)
  • For most RNAs, elimination of the cap structure causes a loss of stability, especially against exonuclease degradation (4), and a decrease in the formation of the initiation complex of mRNAs for protein synthesis (4,5). (neb.com)
  • We have developed an extensive portfolio of products for the synthesis and modification of RNA in order to further understand the role of RNA structure. (thermofisher.com)
  • It was demonstrated that primary and higher order RNA structures play a crucial role during the synthesis of these special sg mRNAs. (leidenuniv.nl)
  • The central role of templated RNA synthesis in biological information flow was predicted by Jacob and Monod, and the enzymatic activity promoting formation of RNA polymers was reported in eubacteria and eukaryotes at that time by several groups. (cancer.gov)
  • rRNA is the RNA component of the ribosome that is essential for protein synthesis in all living organisms. (varsitytutors.com)
  • Carter, M.J., Mahy, B. W.J.: Synthesis of RNA segments 1-3 during generation of incomplete influenza A (Fowl plague) vims. (springer.com)
  • The RNA serves as a template for telomere DNA synthesis and may also be important for enzyme structure or catalysis. (epfl.ch)
  • The study conducted a comparative structural analysis of SARS-CoV-2 genomic RNA as well as of the previously known most highly structured RNA virus, the hepatitis C virus (HCV), the West Nile virus which is considered to be lacking overall RNA structure, and a set of human mRNAs which do not have internal structure. (news-medical.net)
  • Two copies of unspliced human immunodeficiency virus (HIV)-1 genomic RNA (gRNA) are preferentially selected for packaging by the group-specific antigen (Gag) polyprotein into progeny virions as a dimer during the late stages of the viral lifecycle. (mdpi.com)
  • Olson ED, Cantara WA, Musier-Forsyth K. New Structure Sheds Light on Selective HIV-1 Genomic RNA Packaging. (mdpi.com)
  • To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. (osti.gov)
  • This research project is a collaboration between two experts in the fields of mRNA translation/initiation (Dr Julie Aspden) and cryo-EM (Dr Juan Fontana), combining genetic, biochemical, genomic and structural approaches to tackle an important, outstanding question on the structure-function relationship of specialised ribosomes. (rnasociety.org)
  • Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. (semanticscholar.org)
  • Architecture of a gamma retroviral genomic RNA dimer. (semanticscholar.org)
  • They constructed a workflow and the tools to decipher the base pair content from the secondary structure of any long RNA as well as to pick up any structural definition in a transcript containing kb of base pairs. (news-medical.net)
  • Using this, they identified the highly complex structural regions of RNA, so as to compare predicted structures among the domains of this large RNA. (news-medical.net)
  • Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. (rutgers.edu)
  • In general, methods for probing structural information involve treating RNA with either a chemical or an enzyme that preferentially targets regions of the RNA in a single- or double-stranded conformation (ssRNA and dsRNA, respectively). (springer.com)
  • Goodarzi H et al (2012) Systematic discovery of structural elements governing stability of mammalian messenger RNAs. (springer.com)
  • In cellular RNA metabolisms, RNA maturation is performed through various structural alterations that include chemical modifications of constituent components. (hindawi.com)
  • These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput. (nature.com)
  • In this review, we discuss the methodologies employed to define Xist RNA structures and the tight interplay between structural clues and functionality of lncRNAs. (frontiersin.org)
  • Genetic analysis of a predicted structure in the 3D-encoding region of HPe V s, was carried out by making two mutants, with 3 or 6 mutations in one of the structural domains. (bl.uk)
  • Structural studies of antibiotics not only provide a short cut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding 1 , 2 . (pubmedcentralcanada.ca)
  • Smaller chimeras allow 3D RNA algorithms for structural design and biophysical investigation of hhRz structure/function performance. (arvojournals.org)
  • An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. (ebscohost.com)
  • RNA-sequencing (RNA-seq) data from eight equine tissue samples (34-day whole embryo, full term placental villous, adult testes, adult cerebellum, adult articular cartilage, adult LPS-stimulated articular cartilage, adult synovial membrane, and adult LPS-stimulated synovial membrane) were used to refine the structural annotation of protein-coding genes in the horse and for a preliminary assessment of tissue-specific expression patterns. (biomedcentral.com)
  • A consensus set of equine protein-coding gene structures was defined by consolidation of gene sets predicted by Ensembl and NCBI (containing 20,322 and 17,610 genes respectively) and structural annotation derived from the RNA-seq experiments. (biomedcentral.com)
  • Next, structural boundaries for the resulting loci were compared to 75,116 expressed structures defined by the RNA-seq tag alignments. (biomedcentral.com)
  • The structural data suggest a mechanism of RNA recognition and cleavage that explains the enzyme's preference for substrates possessing a 5'-monophosphate and accounts for the protective effect of a triphosphate cap for most transcripts. (epfl.ch)
  • Consequently, in addition to stabilizing the native structure relative to the unfolded species (defined here as stability), RNAs are faced with the challenge of stabilizing the native structure relative to alternative structures (defined as structural specificity). (utexas.edu)
  • Our results suggest that the structural rigidity and intricate networks of contacts inherent to structured RNAs can allow them to evolve exquisite structural specificity without explicit negative selection, even against closely-related alternative structures. (utexas.edu)
  • 2. The method according to claim 1 wherein the target gene specific silencing activity is a transcriptional gene silencing (TGS) activity or a post-transcriptional gene silencing (PTGS) activity preferably selected from RNA interference and/or translational attenuation. (freepatentsonline.com)
  • When they were discovered in 2002, it was believed they were involved in controlling gene activity "post-transcriptionally," i.e., after a gene's DNA has been converted into RNA. (scienceblog.com)
  • The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. (mdc-berlin.de)
  • 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. (arvojournals.org)
  • This suggests an RNA structure driven biophysical approach for enhanced hhRz-based gene therapeutics. (arvojournals.org)
  • Now we know that RNAs control many aspects of gene regulation and function. (phys.org)
  • Experimentally derived RNA-seq annotation superceded the in silico predictions in reaching consensus gene models. (biomedcentral.com)
  • Some of these can be assigned to known RNA gene families such as tRNA, rRNAs, snoRNAs and miRNAs, while others have no assigned functions. (biomedcentral.com)
  • The 2014 IMB Meeting on Nuclear RNA, Gene Regulation, and Chromatin Structure took place from the 9th till the 12th of October at the Institute for Molecular Biology (IMB) in Mainz, Germany. (epigenie.com)
  • Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects the measurement (or even utility) of the resulting patterns of gene expression. (biomedcentral.com)
  • Here we determine how complex composite tissue structure affects measures of gene expression using RNA-seq. (biomedcentral.com)
  • RNA-seq is revolutionizing the study of gene expression. (biomedcentral.com)
  • While the technical and experimental logistics of how best to use RNA-seq are being addressed in a variety of contexts [ 17 - 20 ], one question that has received relatively little attention is the extent to which structure specific extractions are necessary for an accurate determination of gene expression. (biomedcentral.com)
  • First, if genes are expressed in many different structures within the composite structure, then signals of gene expression from the different organs may interfere with one another. (biomedcentral.com)
  • For example, if the structure of interest is small relative to the size of the rest of the structure (a gland within a whole larva, for example), then a strong difference in gene expression within the gland may be washed out by different patterns of expression elsewhere. (biomedcentral.com)
  • Of the remaining RNAs, known as "non-coding" RNAs (ncRNA), the functions of a scant few are known: they inhibit the activity of genes or modify them by altering the way in which DNA is packaged within cells. (scienceblog.com)
  • The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. (mdpi.com)
  • A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. (mdpi.com)
  • Small regulatory RNA genes are also abundantly found in regions between protein coding genes [ 2 - 7 ]. (pubmedcentralcanada.ca)
  • This shows a rapid evolutionary trend in these regions and perhaps plasmid intergenic regions are where new protein and RNA genes and other functional units may evolve. (pubmedcentralcanada.ca)
  • A small number of Borrelia non-coding RNA genes have been detected [ 24 , 25 ]. (pubmedcentralcanada.ca)
  • Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. (biomedcentral.com)
  • Using this strategy, we identify thousands of human candidate RNA genes. (biomedcentral.com)
  • To further verify the expression of these genes, we focused on candidate genes that had a stable hairpin structures or a high level of covariance. (biomedcentral.com)
  • A common theme seems to be that many noncoding RNA genes have a very restricted expression. (biomedcentral.com)
  • This may be especially true for RNA genes expressed in the brain, which is a very complex organ estimated to have thousands of different cell types. (biomedcentral.com)
  • Jacobsen lectured on the RNA dependent DNA Methylation (RdDM) pathway that Arabidopsis thaliana utilizes to maintain and probably establish cytosine DNA methylation in order to silence genes and transposons. (epigenie.com)
  • For each of the three structures, we used RNA-seq to identify differentially expressed genes between two developmental stages, nurse bees and foragers. (biomedcentral.com)
  • Based on RNA-seq for each structure-specific extraction, we found that RNA-seq with composite structures leads to many false negatives (genes strongly differentially expressed in particular structures which are not found to be differentially expressed within the composite structure). (biomedcentral.com)
  • We also found a significant number of genes with one pattern of differential expression in the tissue-specific extraction, and the opposite in the composite extraction, suggesting multiple signals from such genes within the composite structure. (biomedcentral.com)
  • The present study suggests that RNA-seq studies of composite structures are prone to false negatives and difficult to interpret positive signals for genes with variable patterns of local expression. (biomedcentral.com)
  • In general, our results suggest that RNA-seq on large composite structures should be avoided unless it is possible to demonstrate that the effects shown here do not exist for the genes of interest. (biomedcentral.com)
  • Noller, an expert on the ribosome, noticed that a sharp, 90-degree bend in the s2m RNA structure is similar to a part of the ribosome. (innovations-report.com)
  • The RNA ligase catalyzed addition of radioactively labeled cytidine 3',5'-bisphosphate has been used to probe the availability of the 3' ends of rRNAs in the ribosome under varying conditions. (illinois.edu)
  • Noller HF (2005) RNA structure: reading the ribosome. (springer.com)
  • In vitro transcribed-CRISPR guide RNAs trigger innate immune response in cells, but can be prevented by removing the triphosphate moiety. (eurekalert.org)
  • In a blind challenge, SWM models predicted nucleotide-resolution chemical mapping and compensatory mutagenesis experiments for three in vitro selected tetraloop/receptors with previously unsolved structures (C7.2, C7.10, and R1). (sciencemag.org)
  • In this work, we found that a version of the intron that was generated by in vitro selection for enhanced stability also displayed enhanced specificity against a stable misfolded structure that is globally similar to the native state, despite the absence of selective pressure to increase the energy gap between these structures. (utexas.edu)
  • In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA. (semanticscholar.org)
  • Presently, snRNA research is making progresses involved in enzymology of snRNA modifications, molecular evolution, mechanism of spliceosome assembly, chemical mechanism of intron removal, high-order structure of snRNA in spliceosome, and pathology of splicing. (hindawi.com)
  • These works are destined to reach final pathway of work "Function and Structure of Spliceosome" in addition to exciting new exploitation of other noncoding RNAs in all aspects of regulatory functions. (hindawi.com)
  • The yeast splicing factor Cwc2 contacts several catalytically important RNA elements in the active spliceosome, suggesting that Cwc2 is involved in determining their spatial arrangement at the spliceosome's catalytic centre. (embopress.org)
  • The positive-strand RNA viruses addressed in this work are the largest of six genetic classes of viruses and include many important pathogens such as the Zika, dengue and chikungunya viruses, as well as coronaviruses like SARS-CoV-2, cause of the current COVID-19 pandemic. (newswise.com)
  • Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. (sciencemag.org)
  • The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition. (sciencemag.org)
  • Internal flexibility within the quaternary structure is also observed, a finding that has implications for recognition of structured RNA substrates and for the mechanism of internal entry for a subset of substrates that are cleaved without 5'-end requirements. (epfl.ch)
  • We knew Braveheart was critical for heart muscle cell development, but we didn't know the detailed molecular mechanism of how this lncRNA functioned, so we hypothesized that determining its structure could reveal new clues,' explained lead author Zhihong Xue, an MIT postdoc. (labroots.com)
  • Until today, predictive models have concentrated primarily on the study of RNA parts which form double helices. (eurekalert.org)
  • However, the ubiquity of RNA elements with higher-order folds-in which helices pack together to form complex 3D structures-and the extent to which these elements affect viral fitness are largely unknown. (pnas.org)
  • Protein structures are largely defined by how α helices and β sheets pack together. (sciencemag.org)
  • Elucidating the RNA features responsible for selective recognition of the full-length gRNA in the presence of an abundance of other cellular RNAs and spliced viral RNAs remains an area of intense research. (mdpi.com)
  • I also apply my technique to suggest changes to a RNA recognition motif aimed at re-targeting the domain to specifically bind a target involved in dysregulation in certain cancers. (washington.edu)
  • Here based on the fuzzy sets theory, we propose a fuzzy dynamic programming approach to predict RNA secondary structure, which takes advantage of the fuzzy sets theory to reduce parameter sensitivity and import qualitative prior knowledge through fuzzy goal distribution. (springer.com)
  • One of the first attempts to predict RNA secondary structure was made by Ruth Nussinov and co-workers who used dynamic programming method for maximising the number of base-pairs [ 1 ]. (openwetware.org)
  • Stepwise structure formation, as encoded in the SWM method, enables modeling of noncanonical RNA structure in a variety of previously intractable problems. (sciencemag.org)
  • The theory enables predictions for the free energy landscapes and conformational transitions for simple RNA tertiary folds and pseudoknots. (umsystem.edu)
  • Target hRHO fragment cDNA (510 nt RNA) containing the hhRz cleavage site was cloned into pBlueScript. (arvojournals.org)
  • RNaseH cleavage of the O. nova RNA in extracts by use of a complementary oligonucleotide leads to loss of telomerase activity, supporting the identification. (epfl.ch)
  • As a final test, SWM blindly and correctly predicted all noncanonical pairs of a Zika virus double pseudoknot during a recent community-wide RNA-Puzzle. (sciencemag.org)
  • However in practice, energy minimization is mostly limited to pseudoknot-free structures or rather simple pseudoknots, not covering many biologically important structures such as kissing hairpins. (deepdyve.com)
  • Results We present a CCJ-type algorithm, Knotty, that handles the same comprehensive pseudoknot class of structures as CCJ with improved space complexity of Θ(n3+Z)-due to the applied technique of sparsification, the number of 'candidates', Z, appears to grow significantly slower than n4 on our benchmark set (which include pseudoknotted RNAs up to 400 nt). (deepdyve.com)
  • 2013), most often pseudoknot-free structure prediction methods are applied in biological research-severely limiting the practical capabilities to correctly predict, recognize and compare pseudoknotted structures. (deepdyve.com)
  • This simple decomposition scheme allows predicting the MFE pseudoknot-free secondary structure by dynamic programming (DP) in Θ(n3) time and Θ(n2) space for standard energy models (Nussinov and Jacobson, 1980). (deepdyve.com)
  • A disappointing theme in recent RNA-Puzzle assessments is that the rate of accurate prediction of noncanonical base pairs is typically 20% or lower, even for models with correct global folds ( 2 ). (sciencemag.org)
  • The new higher resolution cryo-EM images and complementary results show that the crown is composed of twelve copies of the key viral RNA replication protein arranged like staves in a barrel. (newswise.com)
  • 14. The method of any of claims 1 to 13, wherein the antisense strand is completely complementary to said target RNA, wherein complementarity comprises Watson-Crick and base pairs and Wobble (G-U, U-G) base pairs. (freepatentsonline.com)
  • Also found are the hydration sites around unpaired RNA bases and non replication of atom positions of complementary bases in the Watson-Crick pairs. (ebscohost.com)
  • His research is focused on mechanisms of epigenetic inheritance in plants, including the genetics and genomics of DNA methylation, histone methylation as well as small RNA driven silencing pathways. (epigenie.com)
  • The detailed 3D structure of poly (rA)11 was published by the laboratory of McGill Biochemistry professor Kalle Gehring, in collaboration with George Sheldrick, University of Göttingen, and Christopher Wilds, Concordia University. (mcgill.ca)
  • To explore further how RNAs gain stability from intricate architectures, we examined a novel group I intron from red algae (Bangia). (utexas.edu)
  • This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. (elsevier.com)
  • RNA structure and expected dynamics of a small hhRz within an RNA scaffold strongly impacts enzymatic function. (arvojournals.org)
  • Here, we describe an approach that utilizes a combination of ssRNA- and dsRNA-specific nuclease (ss- and dsRNase, respectively) treatments along with high-throughput sequencing technology to provide comprehensive and robust measurements of RNA secondary structure across entire plant transcriptomes. (springer.com)