• crRNA
  • Foreign DNA surveillance is performed by a complex of Cas proteins (Csy1-4) that assemble with a CRISPR RNA (crRNA) into a 350-kDa ribonucleoprotein called the Csy complex. (montana.edu)
  • Binding assays performed with G-C/G-C-rich competitor sequences indicate that the Csy complex interacts directly with this dinucleotide motif, and kinetic analyses reveal that recognition of a G-C/G-C motif is a prerequisite for crRNA-guided binding to a target sequence. (montana.edu)
  • Together, these data indicate that the Csy complex first interacts with G-C/G-C base pairs and then samples adjacent target sequences for complementarity to the crRNA guide. (montana.edu)
  • Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA(1)B(2)C(6)D(1)E(1)) and a 61-nucleotide CRISPR RNA (crRNA) with 5'-hydroxyl and 2',3'-cyclic phosphate termini. (ox.ac.uk)
  • The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. (ox.ac.uk)
  • In molecular biology, trans-activating crRNA (tracrRNA) is a small trans-encoded RNA. (wikipedia.org)
  • The crRNAs are then incorporated into effector complexes, where the crRNA guides the complex to the invading nucleic acid and the Cas proteins degrade this nucleic acid. (wikipedia.org)
  • TracrRNA is complementary to and base pairs with a pre-crRNA forming an RNA duplex. (wikipedia.org)
  • This is cleaved by RNase III, an RNA-specific ribonuclease, to form a crRNA/tracrRNA hybrid. (wikipedia.org)
  • 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)
  • deletion
  • Editing events may include the insertion, deletion, and base substitution of nucleotides within the edited RNA molecule. (wikipedia.org)
  • RNA editing through the addition and deletion of uracil has been found in kinetoplasts from the mitochondria of Trypanosoma brucei Because this may involve a large fraction of the sites in a gene, it is sometimes called "pan-editing" to distinguish it from topical editing of one or a few sites. (wikipedia.org)
  • nucleotide
  • Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. (biomedcentral.com)
  • RNA editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within a RNA molecule after it has been generated by RNA polymerase. (wikipedia.org)
  • The diversity of RNA editing phenomena includes nucleobase modifications such as cytidine (C) to uridine (U) and adenosine (A) to inosine (I) deaminations, as well as non-templated nucleotide additions and insertions. (wikipedia.org)
  • eukaryotes
  • This study provides unprecedented insight into the organization and function of pseudouridylation guide RNPs, and Dr. Terns indicates that "this is only the beginning of the gold mine of new information that this system will yield about a complex that is also involved in rRNA processing and the function of telomerase in eukaryotes. (brightsurf.com)
  • interference
  • Whole genome, non-coding transcripts from the maternal genome are compared with transcripts from the zygotic genome that are processed through an RNA interference (RNAi)-related process. (jcvi.org)
  • Using RNA interference, scientists have produced a cow whose milk contains increased amounts of casein, a protein used to make cheese and other foods, and almost no beta-lactoglobulin, a component in milk whey protein that causes allergies. (wikipedia.org)
  • sgRNA
  • Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. (biomedcentral.com)
  • enzymes
  • Adenosine deaminases acting on RNA (ADARs) are the RNA-editing enzymes involved in the hydrolytic deamination of Adenosine to Inosine (A-to-I editing). (wikipedia.org)
  • Early in her scientific career, Doudna worked to uncover the structure and biological function of RNA enzymes or ribozymes. (wikipedia.org)
  • genes
  • In this study, we report the development of a two-plasmid CRISPRi and the detail studies with single guide RNAs for single or double repression of target genes in C. glutamicum wild-type (Fig. 1 a). (biomedcentral.com)
  • The nuclear and maxicircle genomes have been sequenced and assembled for Trypanosoma cruzi , the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised. (biomedcentral.com)
  • Two maxicircle guide RNA genes were found. (biomedcentral.com)
  • molecules
  • Having the chemical properties intermediate between RNA and DNA, 2'-O-methylation is presumed to have one of the reactive group of RNA molecules on early earth that would have given rise to DNA 1. (wikipedia.org)
  • complex
  • Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA at 2.8 Å resolution. (shapeways.com)
  • Drs. Michael and Rebecca Terns and colleagues have effectively reconstituted the archaeal modification guide ribonucleoprotein complex that guides pseudouridylation in vitro in a site-specific manner. (brightsurf.com)
  • Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. (montana.edu)
  • The complex can act on only a single guide RNA at a time. (wikipedia.org)
  • Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex. (wikipedia.org)
  • dCas9
  • By fusing the DNMT3a catalytic domain with the dCas9 protein, dCas9-DNMT3a is capable of achieving targeted DNA methylation of a targeted region as specified by the present guide RNA. (wikipedia.org)
  • substrate
  • Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs. (wikipedia.org)
  • gene
  • For example, RNA-guided gene drives could potentially prevent the spread of disease, support agriculture by reversing pesticide and herbicide resistance in insects and weeds, and control damaging invasive species. (elifesciences.org)
  • A technology called GUIDE-Seq has been devised to assay off-target cleavages produced by such gene editing. (wikipedia.org)
  • Mechanism
  • The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited transcript. (wikipedia.org)
  • genome
  • JCVI: RNA-guided DNA Rearrangements In Ciliates: Is the Best Genome Defence a Good Offence? (jcvi.org)
  • thus, current genome editing protocols recommend [ 9 ] that researchers select guides carefully to minimize potential off-target effects and test several to optimize on-target activity. (biomedcentral.com)
  • We developed a novel web-based tool, CRISPOR ( http://crispor.org ), to assist with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. (biomedcentral.com)
  • Doudna
  • While in the Szostak lab, Doudna reengineered the self-splicing Group I catalytic intron into a true catalytic ribozyme that would copy RNA templates. (wikipedia.org)
  • occurs
  • Ribonucleic acid (RNA) occurs in different forms within organisms. (wikipedia.org)
  • RNA editing occurs in the cell nucleus and cytosol, as well as within mitochondria and plastids. (wikipedia.org)
  • modification
  • 2'-O-methylation is a common nucleoside modification of RNA, where a methyl group is added to the 2' hydroxyl of the ribose moiety of a nucleoside, producing a methoxy group. (wikipedia.org)
  • Currently, about 1210 2'-O-methylations (2'-O-Me) have been identified in mammals and yeast and deposited in RMBase (RNA Modification Base) database. (wikipedia.org)
  • target
  • Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. (biomedcentral.com)
  • PAM is not relevant for an RNA-targeting CRISPR, although a guanine flanking the target affects efficacy, and has been designated Protospacer Flanking Site (PFS). (wikipedia.org)
  • catalytic
  • Her Ph.D. thesis was on engineering a self-replicating catalytic RNA and was supervised by Jack W. Szostak. (wikipedia.org)