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  • assay
  • Since the development of these synthetic catalytic oligonucleotides, the main way of determining their cleavage kinetics has been through the use of a laborious and error prone gel assay to quantify substrate and product at different time-points. (diva-portal.org)
  • catalytic
  • The discovery of catalytic RNA was a surprise, as RNA at first pass seems ill-suited to be a catalyst. (stanford.edu)
  • Today RNA is recognized as an active catalyst in biology, in self-splicing of group I and group II introns, in various small ribozymes, and also as the catalytic center of the ribosome and spliceosome. (stanford.edu)
  • These studies also define the unique properties of RNA and proteins lead to catalytic and behavioral distinctions. (stanford.edu)
  • We currently focus on the group I ribozyme, the most well-studied catalytic RNA in both structure and function. (stanford.edu)
  • We harness previous studies, including multiple crystal structures, a robust phylogeny model, and a defined kinetic and thermodynamic framework for the Tetrahymena group I ribozyme, to delve more deeply into questions about catalytic RNA and, in particular, how an RNA scaffold can be used to sculpt an active site and how RNA achieves specific and strong molecular recognition. (stanford.edu)
  • Structure-function Analysis from the Outside In: Long-range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles. (stanford.edu)
  • bind
  • 1999) SELEX: Systematic evolution of ligands by exponential amplification What can RNA bind / catalyze? (coursehero.com)
  • However, even 4 mu M C20 was not able to fully bind the same concentration of 40-mer RNA. (bjmu.edu.cn)
  • In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. (wikipedia.org)
  • enzymes
  • Much has been learned from comparing catalysts constructed from RNA versus proteins, and the study of RNA enzymes, or ribozymes, continues to reveal basic properties and behaviors of RNA, which in turn will help us understand RNA's roles in biology. (stanford.edu)
  • Energy from binding interactions can be used to facilitate reactions of bond substrates, a fundamental precept of enzymology posited by Jencks for protein enzymes and demonstrated in our studies of RNA enzymes. (stanford.edu)
  • World
  • These findings, and the fundamental ability of RNA to act both as an efficient information carrier and functional macromolecule led to proposal of an RNA World early in evolution. (stanford.edu)
  • simple
  • By simple adjustment of ring size of caged asODNs, we could successfully photoregulate their hybridization with mRNA and target RNA hydrolysis by RNase H with light activation. (bjmu.edu.cn)
  • messenger
  • The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. (wikipedia.org)
  • multiple
  • Cleavage at the 5´ end is by ribonuclease P. Multiple exonucleases can participate in the processing of the 3´ end of tmRNA, although RNase T and RNase PH are most effective. (wikipedia.org)

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  • protein
  • The psiRNA-Cmr protein complexes cleave complementary target RNAs at a fixed distance from the 3' end of the integral psiRNAs. (pubmedcentralcanada.ca)
  • One strand of the small RNA duplex is subsequently loaded onto the Argonaute protein to yield an active RNA-induced silencing complex. (mskcc.org)
  • Our study showed that prodigiosin (500 μM) (extracted from Serratia marcescens culture) and a prodigiosin/copper(II) (100 μM each) complex have strong RNA and dsDNA cleaving properties while they have no pronounced effect on protein. (frontiersin.org)
  • Inhibitors of protein-RNA complexation that target the RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. (nih.gov)
  • This cleavage can be influenced by ribosomal protein presence. (wikipedia.org)
  • The exosome complex (or PM/Scl complex, often just called the exosome) is a multi-protein intracellular complex capable of degrading various types of RNA (ribonucleic acid) molecules. (wikipedia.org)
  • In the case of PNPase, which is a phosphorolytic RNA-degrading protein found in bacteria and the chloroplasts and mitochondria of some eukaryotic organisms, two RNase PH domains, and both an S1 and KH RNA binding domain are part of a single protein, which forms a trimeric complex that adopts a structure almost identical to that of the exosome. (wikipedia.org)
  • In bacteria, a separate RNase PH protein exists that is involved in transfer RNA processing, which has been shown to adopt a similar six-membered ring structure, but in this case consisting of 6 identical protein subunits. (wikipedia.org)
  • Messenger RNA (mRNA) is RNA that has a coding region that acts as a template for protein synthesis (translation). (wikipedia.org)
  • Cleavage also involves the protein CFII, though it is unknown how. (wikipedia.org)
  • The Argonaute protein family plays a central role in RNA silencing processes, as essential components of the RNA-induced silencing complex (RISC). (wikipedia.org)
  • RNA strand separation and incorporation into the Argonaute protein are guided by the strength of the hydrogen bond interaction at the 5'-ends of the RNA duplex, known as the asymmetry rule. (wikipedia.org)
  • Cleavage and polyadenylation specificity factor subunit 6 is a protein that in humans is encoded by the CPSF6 gene. (wikipedia.org)
  • The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitement of other processing factors. (wikipedia.org)
  • In RNA, regulation may occur at the level of protein biosynthesis (translation), RNA cleavage, RNA splicing, or transcriptional termination. (wikipedia.org)
  • mRNAs
  • Rnc (UniProtKB P0A7Y0) - E.Coli - this RNase III is involved in the processing of viral transcripts and some mRNAs through the cleavage of multiple areas on the dsRNA. (wikipedia.org)
  • The targeting of these RNA motifs by lead in mRNAs and other RNAs may explain lead-mediated toxicity resulting in cell death. (wikipedia.org)
  • These are the only mRNAs in eukaryotes that lack a poly(A) tail, ending instead in a stem-loop structure followed by a purine-rich sequence, termed histone downstream element, that directs where the RNA is cut so that the 3' end of the histone mRNA is formed. (wikipedia.org)
  • dsRNA
  • The basic dsRNA cleavage function of Class 1 RNase III is similar in most of the organisms in which it is present. (wikipedia.org)
  • Dicer enzymes process dsRNA subtrates into small RNA fragments of individual size ranging from 21-27 nucleotides in length. (wikipedia.org)
  • Whereas rde-4 deficiency can be rescued by high concentrations of trigger dsRNA, and secondary Argonaute exhibit functional redundancy, there has been no evidence that RNA-mediated silencing can be reinstated in rde-1 deficient mutants. (wikipedia.org)
  • MDA5, an RNA helicase, is known to be activated by long dsRNA transcribed from the viral genome. (wikipedia.org)
  • In addition, cyclin E dsRNA only diminished cyclin E RNA - a similar result was also shown using dsRNA corresponding to cyclin A which acts in S, G2 and M phases of the cell cycle. (wikipedia.org)
  • The dsRNA is then separated into two single-stranded RNAs (ssRNA) - the passenger strand and the guide strand. (wikipedia.org)
  • mediates
  • But, for many long noncoding RNAs - a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which mediates X chromosome inactivation - a poly(A) tail is part of the mature RNA. (wikipedia.org)
  • RISC
  • Primary siRNA binding to RDE-1 then promotes the formation of the RNA-induced silencing complex (RISC). (wikipedia.org)
  • The single strand acts as a template for RISC to recognize complementary messenger RNA (mRNA) transcript. (wikipedia.org)
  • These single-stranded RNAs, referred to as guide strands, are incorporated into RNA silencing effectors complexes such as the RNA-induced silencing complex (RISC). (wikipedia.org)
  • Consequently, the passenger strand is degraded, while the guide strand is incorporated into the RNA-induced silencing complex (RISC). (wikipedia.org)
  • nucleotide
  • Note that the complete sequence of our molecular clones may differ from the sequence published for this corresponding reference, e.g., by representing an alternative RNA splicing form or single nucleotide polymorphism (SNP). (origene.com)
  • The cleavage site of leadzyme is located within a four-nucleotide long asymmetric internal loop that also consists of RNA helices on its both sides. (wikipedia.org)
  • The name poly(A) tail (for polyadenylic acid tail) reflects the way RNA nucleotides are abbreviated, with a letter for the base the nucleotide contains (A for adenine, C for cytosine, G for guanine and U for uracil). (wikipedia.org)
  • complexes
  • The effects of donor groups of dizinc complexes, formed from a 2:1 mixture of Zn(II) and a dinucleating ligand, on adenylyl(3′-5′)adenosine (ApA) cleavage have been studied. (springer.com)
  • complementary
  • The other three (C20, C30 and C40) without stable secondary structures have the middle 20 deoxynucleotides complementary to 40-mer RNA. (bjmu.edu.cn)
  • termination
  • Since the cleavages occurred proximally downstream of the premature termination codons, these cleavages could depend on translation termination. (genetics.org)
  • The Rpc11p subunit of Pol III shows homology with the zinc ribbon of TFIIS and is known to mediate RNA 3′ cleavage and to be important for termination. (pubmedcentralcanada.ca)
  • The role of dT n extends beyond termination, since it provides a means to link Pol III transcripts to La, an abundant and ubiquitous nuclear phosphoprotein that binds these RNAs in a 3′-oligo(U) length-dependent manner and promotes their posttranscriptional processing ( 27 , 32 , 37 ). (pubmedcentralcanada.ca)
  • The first stage involves pre-termination cleavage (PTC) of the nascent transcript downstream of the poly(A) site. (wikipedia.org)
  • motif
  • A simple search for this RNA motif in the genomes of humans, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana revealed that on average this motif is present with the frequency of 2-9 motifs for 1 Mbp of DNA sequence. (wikipedia.org)
  • Silencing
  • Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs. (pubmedcentralcanada.ca)
  • Structural biology of RNA silencing and its functional implications. (mskcc.org)
  • It may interact with dicer1 and play a role in short-interfering-RNA-mediated gene silencing. (wikipedia.org)
  • RNA silencing pathways process long RNAs into small RNAs that direct the repression of transcription or translation of nucleic acid targets with sequence corresponding to the small RNAs. (wikipedia.org)
  • 2002
  • RIBONUCLEASE LS ( l ate-gene s ilencing in bacteriophage T4) plays a role in Escherichia coli RNA metabolism ( O tsuka and Y onesaki 2005 ), although its effect seems modest in comparison to that of RNase E ( K ushner 2002 ). (genetics.org)
  • Indeed, some cleavages by RNase LS are introduced only when the target is translatable, while others are independent of translation ( K ai and Y onesaki 2002 ). (genetics.org)
  • During characterization of RNase LS activity after infection of a T4 dmd mutant, we found cleavages in T4 soc mRNA when two successive ochre codons were introduced into the open reading frame ( K ai and Y onesaki 2002 ). (genetics.org)
  • Isolation of total RNA from T4-infected cells, primer-extension analysis of soc RNA, and analysis of cDNA products with polyacrylamide gel electrophoresis were performed as described previously ( K ai and Y onesaki 2002 ). (genetics.org)
  • small
  • Substrates of the exosome include messenger RNA, ribosomal RNA, and many species of small RNAs. (wikipedia.org)
  • A category of ribozymes called small ribonucleolytic ribozymes enhances the spontaneity of the cleavage of their own RNA using acid-base catalysis. (wikipedia.org)
  • There are small RNAs where the poly(A) tail is seen only in intermediary forms and not in the mature RNA as the ends are removed during processing, the notable ones being microRNAs. (wikipedia.org)
  • fragments
  • Some of the resulting RNA fragments can also further induce the production of IFN-β as noted in the Significance section. (wikipedia.org)
  • pathway
  • The data indicate that Rpc11p limits RNA 3′-U length and that this significantly restricts pre-tRNAs to a La-independent pathway of maturation in fission yeast. (pubmedcentralcanada.ca)
  • viral
  • Ribonuclease L or RNase L (for latent), known sometimes as ribonuclease 4 or 2'-5' oligoadenylate synthetase-dependent ribonuclease - is an interferon (IFN)-induced ribonuclease which, upon activation, destroys all RNA within the cell (both cellular and viral). (wikipedia.org)
  • residues
  • Surprisingly, RNase L and Ire1p showed mutually exclusive RNA substrate specificity and partially overlapping but not identical requirements for phylogenetically conserved amino acid residues in their nuclease domains. (ucsf.edu)
  • complex
  • The dizinc complex with 2 [(Zn 2+ ) 2 - 2 ] showed higher activities toward ApA cleavage than the dizinc complex using an analogous dinucleating ligand having four 2-pyridylmethyl donor moieties [(Zn 2+ ) 2 - 1 ] at pH 5-8. (springer.com)
  • P. aeruginosa cell surface hydrophobicity and biofilm integrity were significantly altered due to the cleavage of nucleic acids by prodigiosin or the prodigiosin/copper(II) complex. (frontiersin.org)
  • The cleavage factor complex is composed of four polypeptides. (wikipedia.org)
  • species
  • The differences in the pH-rate constant profile are attributable to the various distributions of the monohydroxo-dizinc species, i.e. dideprotonated species, which are responsible for ApA cleavage. (springer.com)
  • In contrast, (Zn 2+ ) 2 - 3 2− showed lower activity toward ApA cleavage at pH 7.0, which can be ascribed to the absence of the monohydroxo-dizinc species under these conditions. (springer.com)
  • Further, it was demonstrated that reactive oxygen species scavengers significantly reduced the DNA and RNA cleaving property of prodigiosin. (frontiersin.org)
  • ribozyme
  • Cotranscriptional cleavage mediated by a hammerhead ribozyme can affect alternative splicing if interposed between an exon and its intronic regulatory elements. (ox.ac.uk)
  • Our results suggest that targeted hammerhead ribozyme cleavage within introns can be used as a tool to define splicing regulatory elements. (ox.ac.uk)
  • Splicing
  • Splicing ribozymes catalyze RNA splicing, removing a section of RNA that contains a mutation and replacing it with well-functioning RNA. (wikipedia.org)
  • regulatory
  • Cold Spring Harbor Laboratory Symposium on Regulatory RNAs 71, 81-93. (mskcc.org)
  • Like the untranslated regions, many of these non-coding RNAs have regulatory roles. (wikipedia.org)
  • Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to control mRNA biogenesis or translation. (wikipedia.org)
  • tRNA
  • Consistent with this suggestion, the cleavage dependency on an amber codon was considerably reduced in the presence of amber-codon-suppressing tRNA. (genetics.org)
  • assay
  • Since the development of these synthetic catalytic oligonucleotides, the main way of determining their cleavage kinetics has been through the use of a laborious and error prone gel assay to quantify substrate and product at different time-points. (diva-portal.org)
  • catalytic
  • The discovery of catalytic RNA was a surprise, as RNA at first pass seems ill-suited to be a catalyst. (stanford.edu)
  • Today RNA is recognized as an active catalyst in biology, in self-splicing of group I and group II introns, in various small ribozymes, and also as the catalytic center of the ribosome and spliceosome. (stanford.edu)
  • These studies also define the unique properties of RNA and proteins lead to catalytic and behavioral distinctions. (stanford.edu)
  • We currently focus on the group I ribozyme, the most well-studied catalytic RNA in both structure and function. (stanford.edu)
  • We harness previous studies, including multiple crystal structures, a robust phylogeny model, and a defined kinetic and thermodynamic framework for the Tetrahymena group I ribozyme, to delve more deeply into questions about catalytic RNA and, in particular, how an RNA scaffold can be used to sculpt an active site and how RNA achieves specific and strong molecular recognition. (stanford.edu)
  • Structure-function Analysis from the Outside In: Long-range Tertiary Contacts in RNA Exhibit Distinct Catalytic Roles. (stanford.edu)
  • bind
  • 1999) SELEX: Systematic evolution of ligands by exponential amplification What can RNA bind / catalyze? (coursehero.com)
  • However, even 4 mu M C20 was not able to fully bind the same concentration of 40-mer RNA. (bjmu.edu.cn)
  • In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. (wikipedia.org)
  • enzymes
  • Much has been learned from comparing catalysts constructed from RNA versus proteins, and the study of RNA enzymes, or ribozymes, continues to reveal basic properties and behaviors of RNA, which in turn will help us understand RNA's roles in biology. (stanford.edu)
  • Energy from binding interactions can be used to facilitate reactions of bond substrates, a fundamental precept of enzymology posited by Jencks for protein enzymes and demonstrated in our studies of RNA enzymes. (stanford.edu)
  • World
  • These findings, and the fundamental ability of RNA to act both as an efficient information carrier and functional macromolecule led to proposal of an RNA World early in evolution. (stanford.edu)
  • simple
  • By simple adjustment of ring size of caged asODNs, we could successfully photoregulate their hybridization with mRNA and target RNA hydrolysis by RNase H with light activation. (bjmu.edu.cn)
  • messenger
  • The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. (wikipedia.org)
  • multiple
  • Cleavage at the 5´ end is by ribonuclease P. Multiple exonucleases can participate in the processing of the 3´ end of tmRNA, although RNase T and RNase PH are most effective. (wikipedia.org)
  • gene
  • The enzyme encoded by this gene is a member of the conserved DNA/RNA non-specific ββα-Me-finger nuclease family and possesses a unique site selectivity of poly(dG).poly(dC) sequences in double-stranded DNA. (wikipedia.org)
  • This in turn silences the particular gene by RNA interference. (wikipedia.org)
  • 2001
  • Dicer was given its name in 2001 by Emily Bernstein, a graduate student in Greg Hannon's lab at Cold Spring Harbor Laboratory, who sought to discover the enzyme responsible for generating small RNA fragments from double-stranded RNA. (wikipedia.org)
  • strands
  • Current research suggests the PAZ domain is capable of binding the 2 nucleotide 3' overhang of dsRNA while the RNaseIII catalytic domains form a pseudo-dimer around the dsRNA to initiate cleavage of the strands. (wikipedia.org)
  • Sequence
  • This precursor is activated by proteolytic cleavage of the mitochondrial targeting sequence, thus producing a mature 28-kDa enzyme that is translocated to the mitochondrial intermembrane space, where it forms an active homodimer. (wikipedia.org)
  • rnase
  • Subsequent experiments testing RNase III family enzymes abilities to create RNA fragments narrowed the search to Drosophila CG4792, now named Dicer. (wikipedia.org)
  • viral
  • The viral genome is around 2500 nm in length so we can therefore conclude that it must be tightly packaged within the capsid along with substances such as sodium ions in order to cancel out the negative charges on the RNA caused by the phosphate groups. (wikipedia.org)
  • although substantially less virulent than if contained within the viral particle, the RNA can have increased infectivity when transfected into cells. (wikipedia.org)
  • enzyme
  • Dicer's ability to generate ~22 nucleotide RNA fragments was discovered by separating it from the RISC enzyme complex after initiating the RNAi pathway with dsRNA transfection. (wikipedia.org)
  • initiate
  • Cas endonucleases are able to initiate double strand breaks within these foreign DNAs that are complement to the transcribed CRISPR RNAs (crRNA, or "protospacers"), thus degrading them. (wikipedia.org)
  • specific
  • While we cannot exclude entirely the possibility of off target modifications in addition to on target cleavage, we believe it represents a relatively low and controllable risk, as a number of recent publications have demonstrated that the CRISPR-Cas9 system is to be highly specific (e.g. (horizondiscovery.com)
  • JACUSA: site-specific identification of RNA editing events from replicate sequencing data. (mdc-berlin.de)
  • functional
  • In addition to these domains, hsDicer contains four other functional domains: two RNaseIII domains and two double stranded RNA binding domains (DUF283 and dsRBD). (wikipedia.org)
  • Product
  • The distance between the PAZ and RNaseIII domains is determined by the angle of the connector helix and influences the length of the micro RNA product. (wikipedia.org)
  • small
  • GlmZ (formally known as SraJ) is a small non-coding RNA (ncRNA). (wikipedia.org)
  • Small interfering RNA (siRNA) are produced and function in a similar manner to miRNA by cleaving double-stranded RNA with Dicer into smaller fragments, 21 to 23 nucleotides in length. (wikipedia.org)
  • complex
  • Dicer facilitates the activation of the RNA-induced silencing complex (RISC), which is essential for RNA interference. (wikipedia.org)