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  • Molecule
  • Almost nothing is known about the mechanism by which a monophosphate at the 5′ end of an RNA molecule is able to influence the rate of ribonuclease cleavage at an internal site that may be far downstream. (pnas.org)
  • Furthermore, the SHAPE reactivities that are the output of this pipeline are well established and can be immediately used in existing RNA folding algorithms to determine the structures for each RNA molecule ( 8 , 9 ). (pnas.org)
  • At the same time, bacterial non-coding RNAs are being found to function as small-molecule-sensing riboswitches and as elements of the CRISPR defense system. (keystonesymposia.org)
  • RNA was the first genetic molecule. (dnalc.org)
  • synthesis
  • Catalytic RNAs are involved in a number of biological processes, including RNA processing and protein synthesis. (nature.com)
  • During virus replication, PB1 initiates RNA synthesis and copy vRNA into complementary RNA (cRNA) which in turn serves as a template for the production of more vRNAs. (uniprot.org)
  • Deletion of both relA and spoT, the two genes that are responsible for synthesis of ppGpp, does not affect the rate of synthesis of either RNA species. (diva-portal.org)
  • These results suggest that if RNA was somehow incorporated into a primitive form of RNA-based thermophilic life, either it must be protected from random hydrolytic events, or the rate of synthesis must exceed the rate of hydrolysis. (springer.com)
  • Dr. Ferré-D'Amaré's second translational research focus is on the role of a catalytic RNA-glmS-in controlling the synthesis of the bacterial cell wall. (nih.gov)
  • Dr. Ferré-D'Amaré and colleagues elucidated the structural basis for fluorescence of several RNA-chromophore complexes, and are leveraging this knowledge to generate optimized tools to study the synthesis, maturation, targeting, localization and turnover of RNAs that play essential roles in metabolism, development and disease progression. (nih.gov)
  • enzymes
  • RNAPs (RNA polymerases) are key enzymes of the cellular gene expression machineries of all organisms. (biochemsoctrans.org)
  • Cech TR (1987) The chemistry of self-splicing RNA and RNA enzymes. (springer.com)
  • Although monomeric forms of RNase E and RNase G can cut RNA, the ability of these enzymes to discriminate between RNA substrates on the basis of their 5′ phosphorylation state requires the formation of protein multimers. (pnas.org)
  • The greater susceptibility of 5′-monophosphorylated RNAs to cleavage by these enzymes may help to ensure the rapid degradation of the downstream products of initial endonucleolyic cleavage, which differ from their primary-transcript precursors in being 5′-monophosphorylated rather than 5′-triphosphorylated. (pnas.org)
  • Within the catalytic domain of these enzymes, there presumably is a site that can interact productively with RNA 5′ ends that are monophosphorylated but not with those that bear a triphosphate or hydroxyl, yet the presence of such a 5′-end-binding site has not been verified empirically. (pnas.org)
  • Much of the mammalian genome is transcribed into long non-coding RNAs, but their biological roles -- such as transcriptional regulation via recruitment of histone-modifying enzymes - are only beginning to be discovered. (keystonesymposia.org)
  • group I intr
  • Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA. (biomedsearch.com)
  • Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. (biomedsearch.com)
  • high-throughput
  • SHAPE-Seq thus represents a powerful step toward making the study of RNA secondary and tertiary structures high throughput and accessible to a wide array of scientific pursuits, from fundamental biological investigations to engineering RNA for synthetic biological systems. (pnas.org)
  • Two techniques for high-throughput RNA structure characterization have recently been reported: parallel analysis of RNA structures (PARS) ( 3 ) and fragmentation sequencing (Frag-Seq) ( 4 ). (pnas.org)
  • protein
  • The catalytically active amino-terminal half of the protein (N-RNase E: residues 1-498) is alone sufficient for the enzyme's ribonuclease activity, whereas the carboxyl half of the protein (residues 499-1061) contains both an arginine-rich region and a carboxy-terminal domain that serves as a scaffold for the assembly of a multiprotein complex known as the RNA degradosome ( 4 , 5 ). (pnas.org)
  • Much like green fluorescent protein (GFP) and its variants transformed the study of proteins, fluorescent RNAs have the potential to revolutionize the in vivo study of the tens of thousands of non-coding RNAs that have been discovered in the human transcriptome. (nih.gov)
  • Immunodetection of grapevine fanleaf virus satellite RNA-encoded protein in infected Chenopodium quinoa. (semanticscholar.org)
  • COMPLEX
  • Both techniques couple classic in vitro nuclease probing techniques that are traditionally performed one RNA at a time, with deep sequencing of RNA fragments to simultaneously probe a complex mixture of RNAs sampled from transcriptomes. (pnas.org)
  • Roles
  • New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. (pnas.org)
  • Over the past several years, there has been an explosion in the discovery of noncoding, but functional RNAs that play central roles in maintaining, regulating, and defending the genome ( 1 ). (pnas.org)
  • ribozyme
  • The function of a ribozyme depends upon the primary sequence of the RNA which folds into a 3-D structure. (sciencebuddies.org)
  • In a previous contribution, we discovered a variant of the Azoarcus group I ribozyme that represents a local peak in the RNA fitness landscape. (royalsocietypublishing.org)
  • By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca 2+ ion as a sign for the more catalytically useful Mg 2+ ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. (biomedcentral.com)
  • The glmS ribozyme is being studied as a potentially valuable target for novel antibiotics, and also an experimental platform with which to understand how RNA targets can evolve antibiotic resistance. (nih.gov)
  • In vitro activity of the hairpin ribozyme derived from the negative strand of arabis mosaic virus satellite RNA. (semanticscholar.org)
  • genomic
  • This study provides the strong position for future development of highly selective RNA-targeting agents that can potentially be used for disease-selective treatment at the level of messenger, micro, and genomic viral RNA. (novelconjugates.com)
  • viral
  • In turn, these short capped RNAs are used as primers by PB1 for transcription of viral mRNAs. (uniprot.org)
  • motifs
  • We report a novel class of catalytic biomaterials, comprising amphipathic RNA-cleaving peptides placed between two RNA recognition motifs, here demonstrated to target the TΨC loop and 3′- acceptor stem of tRNAPhe. (novelconjugates.com)
  • Hydrolysis
  • The minerals had little or no effect in promoting hydrolysis of RNA (24mer of polyadenylic acid) at 80°C over a pH range from 4.2 to 9.3. (springer.com)
  • intron
  • Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. (elifesciences.org)
  • Group I introns may also insert into the natural intron insertion site at the RNA level, and subsequently become stably integrated into the host genome. (biomedsearch.com)
  • enzymatic
  • The direct physical contacts between all these key players immediately suggest that conformational changes in any of them (especially in the bridge-helix) can be 'sensed' by numerous active elements within the catalytic site and thus directly influence many enzymatic parameters of the nucleotide addition cycle (and other chemistries) in a co-ordinated manner. (biochemsoctrans.org)
  • catalysis
  • Ferris JP (2006) Montmorillonite catalyzed formation of RNA oligomers: the possible role of catalysis in the origins of life. (springer.com)
  • acids
  • Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. (bookdepository.com)
  • antibiotics
  • Finally, RNA's central role in life suggests that its potential therapeutic value is barely tapped but already clinically validated: approximately 80 percent of antibiotics in use today target a single type of RNA-containing enzyme, the ribosome, and most do so by targeting its non-coding RNA component. (nih.gov)
  • transcriptional
  • Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. (elifesciences.org)
  • We propose that ubiquinitation of RNAPII is induced by RNA processing events and linked to transcriptional pausing, which is released by Bre5-Ubp3 associated with the nascent transcript. (elifesciences.org)