AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
RNARNA, Small InterferingRNA, ViralRNA EditingRNA SplicingRNA, RibosomalRNA, BacterialDNA-Directed RNA PolymerasesRNA VirusesRNA InterferenceRNA, MessengerRNA, Double-StrandedRNA, CatalyticRNA FoldingRNA Polymerase IIRNA, FungalRNA StabilityRNA HelicasesRNA, AntisenseRNA Processing, Post-TranscriptionalRNA, TransferRNA, Small NuclearRNA PrecursorsRNA, UntranslatedNucleic Acid ConformationRNA CapsSequence Analysis, RNARNA, PlantRNA, ProtozoanBase SequenceRNA, NeoplasmRNA Ligase (ATP)DEAD-box RNA HelicasesRNA Polymerase IIIMolecular Sequence DataRNA Polymerase IRNA, NuclearRNA, GuideRNA, Ribosomal, 28SRNA, Ribosomal, 18SRNA-Binding ProteinsRNA, Ribosomal, 23SRNA TransportRNA, Spliced LeaderRNA, SatelliteRNA, Ribosomal, 16SAmino Acid SequenceRNA, ArchaealNucleic Acid HybridizationProtein BiosynthesisCell LineVirus ReplicationEscherichia coliRNA CleavageMutationOligoribonucleotidesRNA, Heterogeneous NuclearTranscription, GeneticRNA, Small CytoplasmicRNA 3' End ProcessingTemplates, GeneticRNA, Small UntranslatedHeLa CellsRibonucleoproteinsRibonucleasesPoly AGenome, ViralRNA, Ribosomal, 5.8SDNARNA, Long NoncodingRNA, Small NucleolarBinding SitesRNA Virus InfectionsProtein BindingRNA, ComplementaryUridinePromoter Regions, GeneticEndoribonucleasesCell NucleusRNA, ChloroplastModels, MolecularPlasmidsReverse Transcriptase Polymerase Chain ReactionKineticsSingle-Strand Specific DNA and RNA EndonucleasesBase PairingRNA, HelminthPlant VirusesDNA PrimersGene Expression RegulationSaccharomyces cerevisiaeTranscription FactorsRNA, Transfer, PheRNA, Transfer, LysRibosomesBlotting, NorthernDNA, ViralPolymerase Chain ReactionOligonucleotidesGene Silencing
SubunitRRNAEukaryoticProteinsHelicaseSequenceConformationRibosomeSecondary structureInteractionsStructuresFoldStructureBoundCellularTransferLargeSiteDomainChainTRNABacterialMoleculesNcRNAsPeptide bond formationMRNASubunitsNucleicNucleotidesProteinRibosomesSequencesGeneLinezolidPolypeptideFunctionalMathewsStructural diversityGenomicRolesRoleFormDiseasesIdentifyPotentialCellsDataToolsIncludes
Subunit10
  • 50S, roughly equivalent to the 60S ribosomal subunit in eukaryotic cells, is the larger subunit of the 70S ribosome of prokaryotes. (wikipedia.org)
  • The 50S subunit is primarily composed of proteins but also contains single-stranded RNA known as ribosomal RNA (rRNA). (wikipedia.org)
  • The large ribosomal subunit (50S) is approximately twice as massive as the small ribosomal subunit (30S). (wikipedia.org)
  • At tertiary structure level, the large subunit rRNA is a single gigantic domain while the small subunit contains three structural domains. (wikipedia.org)
  • Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. (embl.de)
  • In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. (embl.de)
  • A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. (embl.de)
  • A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. (colorado.edu)
  • Nuclear export with the pre-60S ribosomal subunit via individual atomic tiny holes affecting live. (chk-signal.com)
  • ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 exhibited high affinities for its cognate and wobble codons GUA and GUG, and for GUU in the A-site of the programmed 30S ribosomal subunit, whereas the unmodified ASL (Val3) UAC bound less strongly to GUA and not at all to GUG and GUU. (ncsu.edu)
RRNA9
  • rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome. (wikipedia.org)
  • The model of Hm 50S, determined in 2000 by Nenad Ban and colleagues in the laboratory of Thomas Steitz and the laboratory of Peter Moore, includes 2711 of the 2923 nucleotides of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structure of 27 of its 31 proteins. (wikipedia.org)
  • It shares the 50S size/sedimentation rate and the two rRNA count, but its 23S expansion segments have more in common with eukaryotes. (wikipedia.org)
  • Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. (embl.de)
  • In this way proteins serve to organise and stabilise the rRNA tertiary structure. (embl.de)
  • Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. (embl.de)
  • Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme. (colorado.edu)
  • Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins. (colorado.edu)
  • Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. (ncsu.edu)
Eukaryotic1
  • In many cases, they lack a number of the conserved or semi-conserved nucleotides that play important roles in creating the L-shaped tertiary structure of prokaryotic and eukaryotic cytoplasmic tRNAs (3Dirheimer G. Keith G. Dumas P. Westhof E. RajBhandary U. Soll D. tRNA: Structure, Biosynthesis and Function. (ncsu.edu)
Proteins6
  • Most of the proteins interact with multiple RNA elements, often from different domains. (embl.de)
  • While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. (embl.de)
  • Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. (biomedcentral.com)
  • Similar to proteins, functional RNA molecules fold into specific three-dimensional conformations essential for performing their biological activity. (biomedcentral.com)
  • Nonetheless, it is common knowledge that RNA 3D structure is more conserved than RNA sequence and that such principle could be used for comparative RNA structure prediction in a similar way it is done for proteins [ 11 ]. (biomedcentral.com)
  • Ribosomes are nano-machines that translate information coded in a messenger RNA into proteins in all living organisms. (biorxiv.org)
Helicase1
Sequence2
  • The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. (biomedcentral.com)
  • However, to date no general large-scale study has systematically addressed the quantitative analysis of the relationship between sequence and structure conservation in RNA molecules. (biomedcentral.com)
Conformation1
  • The stems of the unmodified ASL (Val3) UAC and that with cmo (5)U 34 and N (6)-methyladenosine, m (6)A 37, adopted an A-form RNA conformation (rmsd approximately 0.6 A) as determined with NMR spectroscopy and torsion-angle molecular dynamics. (ncsu.edu)
Ribosome2
  • About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. (embl.de)
  • Ribosome-nascent chain complexes (RNCs) studied by cryo-EM provided us with "snapshots" of most-stable states of NCs within the ribosomal tunnel 9-13. (biorxiv.org)
Secondary structure2
  • The secondary structure of 23S is divided into six large domains, within which domain V is most important in its peptidyl transferase activity. (wikipedia.org)
  • A new method that relies on secondary structure information to align homolog RNA sequences was also recently developed [ 49 ]. (biomedcentral.com)
Interactions3
  • New insights about the evolution, recognition and structural modularity of GNRA and A-minor RNA-RNA interactions are proposed. (cnrs.fr)
  • However, chemical and enzymatic probing has lead to the idea that these tRNAs have retained the basic cloverleaf structure of canonical tRNAs but that they lack several conserved tertiary interactions leading to a weaker three-dimensional structure (4Watanabe Y.-I. Kawai G. Yokogawa T. Hayashi N. Kumazawa Y. Ueda T. Nishikawa K. Hirao I. Miura K.-I. Watanabe K. Nucleic Acids Res. (ncsu.edu)
  • The D-loop is somewhat small and lacks the G residues at positions 18 and 19 that facilitate interactions with the T-loop in the tertiary structure. (ncsu.edu)
Structures1
  • In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. (biomedcentral.com)
Fold1
  • Nonetheless, nascent polypeptides with more complex tertiary structure fold close to and outside the tunnel, as found for spectrin - a three-helix bundle protein, and titin, an all beta-sheet immunoglobulin domain 10,13. (biorxiv.org)
Structure2
  • Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction. (biomedcentral.com)
  • Finally, with the aim of characterizing RNA structure diversity, Abraham and co-workers recently studied the RNA conservation at three levels: primary, secondary, and tertiary structure. (biomedcentral.com)
Bound1
  • The amino group of an aminoacyl-tRNA (binds to A site) attacks the carbon of a carbonyl group of a peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site and a deacylated tRNA in the P site. (wikipedia.org)
Cellular2
  • RNA molecules are now known to carry a large repertory of biological functions such as transfer of information, enzymatic catalysis and regulation of cellular processes [ 4 ]. (biomedcentral.com)
  • The nascent chain (NC), emerges into the cellular milieu via the ribosomal exit tunnel, which is an active component that regulates the NC passage. (biorxiv.org)
Transfer2
  • Complementary oligonucleotide binding to the anticodon loop of fMet-transfer RNA. (colorado.edu)
  • Complementary oligonucleotide binding to transfer RNA. (colorado.edu)
Large1
  • Where indicated the normal U8 or 8U→C mutated hmtRNAs were phosphorylated with cold ATP using polynucleotide kinase (New England Biolabs) prior to large scale aminoacylation.To measure ternary complex formation, reaction mixtures (50 ;l) were prepared as reported (27Hunter S.E. Spremulli L.L. RNA Biol. (ncsu.edu)
Site2
  • The erm genes codes for methylase enzyme which methylates and alters the target site of MLS B antibiotics i.e. the 23S ribosomal RNA [ 4 ]. (biomedcentral.com)
  • Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. (embl.de)
Domain1
  • the E-value for the Ribosomal_L31e domain shown below is 3.1e-43. (embl.de)
Chain1
  • The transcription of the beta-globin genes in mouse erythroleukemia cells has been examined by hybridizing labeled RNA obtained from isolated nuclei after chain elongation in the presence of [alpha-32P]UTP. (shengsci.com)
TRNA4
  • The amino group of an aminoacyl-tRNA (binds to A site) attacks the carbon of a carbonyl group of a peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site and a deacylated tRNA in the P site. (wikipedia.org)
  • Originally, RNA was understood to participate in protein expression as a carrier of genetic information (mRNA) and as an adapter molecule (tRNA) for reading the code. (rochester.edu)
  • Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-codon stem loop. (wikipedia.org)
  • The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. (lookformedical.com)
Bacterial2
  • Moreover, mouse TLR13 recognizes bacterial 23S ribosomal RNA. (medscape.com)
  • New findings have identified RNA as a potential target in multitude of diseases including bacterial/viral infections and cancer. (fortuneonline.org)
Molecules7
  • LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules. (rochester.edu)
  • Therefore, much work is required in this field to identify the RNA that can act as drug target and to design smaller molecules that can act on them. (fortuneonline.org)
  • Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. (wikipedia.org)
  • Ribosomes assemble polymeric protein molecules whose sequence is controlled by the sequence of messenger RNA molecules. (wikipedia.org)
  • Ribonucleic acid (RNA) molecules are extremely versatile polymers fulfilling numerous roles essential for life, including gene regulation and catalytic functions [ 1 , 2 ]. (biorxiv.org)
  • The contrast in the difficulty of determining sequence versus structure has created a sequence-structure gap, where there are vast amounts of sequenced RNA molecules without any known corresponding structure. (biorxiv.org)
  • 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). (lookformedical.com)
NcRNAs3
  • It is well established that these folded configurations are of importance to the function of non-coding RNAs (ncRNAs) [ 4 ]. (biorxiv.org)
  • These approaches are not dependent on the identification of conserved RNA sequences or secondary structures, and therefore are well-suited for the discovery of unstructured or poorly-conserved ncRNAs. (biomedcentral.com)
  • While there have been surveys conducted with the marine metagenome to discover additional examples of known ncRNAs [ 6 , 7 ], there have been no studies explicitly examining these data for novel RNA motifs, in part due to unique computational challenges inherent to metagenomic datasets. (biomedcentral.com)
Peptide bond formation2
  • Then RNA was discovered to catalyze reactions, including self-splicing, phosphodiester bond cleavage, and peptide bond formation. (rochester.edu)
  • Now it has been shown that RNA has an important role in the transcription regulation, regulation of the translation, catalysis, protein function, protein transport, peptide bond formation and RNA splicing [1]. (fortuneonline.org)
MRNA1
  • 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. (lookformedical.com)
Subunits2
  • Ribosomes consist of two major components: the small and large ribosomal subunits. (wikipedia.org)
  • They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits. (lookformedical.com)
Nucleic1
  • The most frequently reported mechanisms of linezolid resistance include the mutation in 23S ribosomal nucleic acid and presence of cfr gene. (cambridge.org)
Nucleotides1
Protein6
  • Targeting these RNAs offers opportunities to therapeutically modulate numerous cellular processes, including those linked to 'undruggable' protein targets. (fortuneonline.org)
  • The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain. (wikipedia.org)
  • Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. (wikipedia.org)
  • They differ in their size, sequence, structure, and the ratio of protein to RNA. (wikipedia.org)
  • It inhibits protein synthesis by binding to RNA. (lookformedical.com)
  • Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. (biomedcentral.com)
Ribosomes1
  • Ribosomes are ribozymes , because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. (wikipedia.org)
Sequences1
  • RNA sequences can be evolved in vitro to catalyze many reactions that are not part of the natural repertoire. (rochester.edu)
Gene1
  • RNA is now known to play functions in diverse cellular processes, such as development, immunity, RNA editing and modification, and post-transcriptional gene regulation. (rochester.edu)
Linezolid1
  • Currently, only linezolid antibiotics that target RNA are being used clinically [4]. (fortuneonline.org)
Polypeptide1
  • For each coding triplet ( codon ) in the messenger RNA, there is a unique transfer RNA that must have the exact anti-codon match, and carries the correct amino acid for incorporating into a growing polypeptide chain. (wikipedia.org)
Functional2
  • The recent advancement in the knowledge about diversity, structural and functional information related to RNAs has put them in the lime light as a drug target. (fortuneonline.org)
  • This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task. (biomedcentral.com)
Mathews1
  • We are interested in predicting RNA structure and we develop computational tools for targeting RNA with pharmaceuticals and for using RNA as a pharmaceutical (Mathews et al. (rochester.edu)
Structural diversity2
  • Compared to DNA, RNA is being considered to be a better therapeutic since RNA displays a greater structural diversity and lacks repair mechanisms. (fortuneonline.org)
  • Part of this versatility can be attributed to the structural diversity of RNA [ 3 ]. (biorxiv.org)
Genomic1
  • To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of ' Cand . (biomedcentral.com)
Roles2
  • However, with advancement, now it is well established that RNA performs a number of vital roles in the cell, and its malfunction may lead to a disease. (fortuneonline.org)
  • However, with discovery of new RNA classes and their sequencing, disease related roles of RNA in mammals also are being explored [3]. (fortuneonline.org)
Role1
  • The results identify a proteomic map of SDC1 nuclear interactors in a mesothelioma cell line and suggest a previously unknown role for SDC1 in RNA biogenesis. (scilifelab.se)
Form1
Diseases1
  • RNA is also an important player in many diseases, including Prader-Willi, b-thalassemia, and myotonic dystrophy. (rochester.edu)
Identify1
  • To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from ' Cand . (biomedcentral.com)
Potential2
  • Here, in this mini-review, discussion has been done that coding as well as non-coding RNA regions have potential as a drug target. (fortuneonline.org)
  • We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. (biomedcentral.com)
Cells1
  • Further loss- and gain-of-function experiments showed that SDC1 influences RNA levels in mesothelioma cells. (scilifelab.se)
Data1
  • Availability Source code and data is available at https://github.com/marcellszi/dl-rna . (biorxiv.org)
Tools1
  • Besides, a few databases and tools used for the RNA target prediction have also been discussed. (fortuneonline.org)
Includes1