• Several techniques have been developed aiming to produce high-density RNA microarrays suitable for quantitative RNA-binding assays. (nature.com)
  • RNA-targeting CRISPR-Cas systems - We use biochemical activity assays in conjunction with structural techniques and sequencing to investigate RNA-targeting CRISPR systems, such as the Type VI effector, Cas13a. (berkeley.edu)
  • In this study, by conducting high-throughput pri-miRNA cleavage assays for approximately 260,000 pri-miRNA sequences, we discovered and comprehensively characterized a noncanonical cleavage mechanism of MP. (bvsalud.org)
  • The detection assays need to be extremely sensitive and selective in small value of intricate RNA samples. (unboundmedicine.com)
  • In order to validate ribozymes, in vitro assays can be used to assess RNA cleavage. (biomedcentral.com)
  • In these assays, the ribozyme sequence is fused to a reporter gene which modulates its activity when expressed as RNA. (biomedcentral.com)
  • Finally, we describe the discovery of boceprevir, from the early chemistry studies, through the development of high-throughput assays, to the phase III clinical development program that ultimately provided the basis for approval of this drug. (xiahepublishing.com)
  • RNA catalytic and binding interactions with proteins and small molecules are fundamental elements of cellular life processes as well as the basis for RNA therapeutics and molecular engineering. (nature.com)
  • Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. (nyu.edu)
  • NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing. (ablife.cc)
  • Over 40 protocols to process DNA, RNA, and proteins have been optimized for use on the QIAsymphony, which incorporates continuous loading of sample racks, reagents, and consumables at the rate of 1 to 96 samples per run. (genengnews.com)
  • modern pathway proteins, highly 100 responsibilities also, showed Okazaki mitochondria are located on the RNA-DNA males other. (erik-mill.de)
  • The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. (asu.edu)
  • Nucleolytic ribozymes (hereafter referred to as ribozymes for short) are small RNAs (less than 200 nt) that function independently of proteins, of which nine classes are known to exist (hammerhead, hairpin, Varkud satellite, hepatitis delta virus (HDV), glmS , twister, twister-sister, pistol and hatchet) each with distinctive folding patterns. (biomedcentral.com)
  • RNA is not only a mediator of genomic information encoded in DNA to the final products, proteins. (amegroups.org)
  • The virally encoded non-structural serine protease (NS3) is required to process the HCV polyprotein and release the individual proteins that form the viral RNA replication machinery. (xiahepublishing.com)
  • 2 The non-structural 3 (NS3) serine protease cleaves the viral polyprotein to release the non-structural proteins, which then form the viral RNA replication machinery. (xiahepublishing.com)
  • At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)
  • Many of us intricate upon facts coming from virus-based RNA range of motion assay, grow grafting, RNA along with phosphorescent health proteins marking, as well as CRISPR/Cas9 gene-editing technological innovation, to signify that this Feet mRNA in addition to the Foot health proteins can easily move systemically and performance as an important Transbronchial forceps biopsy (TBFB) component of the particular florigenic transmission in flowering. (hormonessignaling.com)
  • A mammalian cell-based assay for screening inhibitors of RNA cleavage. (bcm.edu)
  • Identification of inhibitors of ribozyme self-cleavage in mammalian cells via high-throughput screening of chemical libraries. (bcm.edu)
  • Exogenous control of mammalian gene expression via modulation of RNA self-cleavage. (bcm.edu)
  • Sequence-specific cleavage of Huntington mRNA by catalytic DNA. (bcm.edu)
  • However, reporter activity can be confounded by phenomena unrelated to ribozyme-mediated cleavage of RNA. (biomedcentral.com)
  • They catalyze site-specific cleavage of RNA, and in some cases, the reverse ligation reaction via a concerted general acid-base mechanism [ 2 ]. (biomedcentral.com)
  • Despite differing in their biogenesis pathway (see below), both classes of art-sRNAs function similarly by associating with AGO1 to specifically silence target RNAs through endonucleolytic cleavage or translation repression (Figure 1). (encyclopedia.pub)
  • Both amiRNA and syn-tasiRNA guide strands associated with AGO1 to silence viral RNAs through endonucleolytic cleavage or translational inhibition. (encyclopedia.pub)
  • High-throughput sequencing-RNA affinity profiling (HiTS-RAP) 22 is conceptually similar to RNA-MaP, but uses the E. coli replication terminator protein Tus to stall the RNA polymerase after transcribing the variable section of the DNA library. (nature.com)
  • These systems can be extremely divergent mechanistically and provide a rich area to research RNA:protein interactions, including novel protein folds. (berkeley.edu)
  • In this platform, catalytically inactive Cas9 serves as an RNA-guided DNA binding protein to silence gene expression in a sequence-specific manner. (berkeley.edu)
  • In collaboration with the laboratory of David Savage , we have also developed a series of high-throughput mutant library construction, screening, and sequencing pipelines to probe CRISPR-Cas protein function and to isolate engineered variants with novel properties. (berkeley.edu)
  • Aberrant chimeric RNA GOLM1-MAK10 encoding a secreted fusion protein as a molecular signature for human esophageal squamous cell carcinoma. (bcm.edu)
  • Mechanisms of regulation of gene expression by structured RNA molecules and RNA-protein complexes. (nyu.edu)
  • We have recombinantly expressed Schistosoma mansoni cytochrome P450, screened a preliminary series of cytochrome P450 inhibitors, and found that RNA interference silencing of cytochrome P450 in larval worms is lethal, indicating that cytochrome P450 is an essential and druggable protein. (rush.edu)
  • Thermo Fisher Scientific introduced the KingFisher Flex magnetic particle processor for DNA/RNA, protein, and cell purification from virtually any source. (genengnews.com)
  • Because alternative RNA splicing allows different types of mRNA molecules to be created from a single gene, it generates the diversity of protein function and structure that is essential to complex organisms. (genomicglossaries.com)
  • Interestingly, a protein-coding splice variant of SETD2 lacks the extended N-terminus but contains the catalytic SET domain as per the ENSEMBL database. (frontiersin.org)
  • The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. (asu.edu)
  • Distinct classes of RNA catalyse biochemical reactions (ribozymes), although the large subunit rRNA and RNaseP ribozymes common to all organisms require protein partners to function [ 1 ]. (biomedcentral.com)
  • A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (nih.gov)
  • One of the strands of the duplex is preferentially loaded into an ARGONAUTE (AGO) protein, and the resulting complex termed RNA-induced silencing complex (RISC) recognizes and silences complementary target RNA through diverse mechanisms [ 3 ] [ 4 ] . (encyclopedia.pub)
  • The emergence of non-protein-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and more recent long non-coding RNAs (lncRNAs), has shed a light on further dissecting the gene regulatory networks of the heart ( 3 , 4 ). (amegroups.org)
  • The deduced amino series regarding LsTAT1 revealed the phylogenetic romantic relationship (43% identity) together with that relating to sterol O-acyltransferase (AtSAT1) of Arabidopsis thaliana coupled with catalytic protein elements (Asn and his awesome) which can be typically preserved in membrane-bound O-acyltransferase (MBOAT) household protein. (hormonessignaling.com)
  • The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes. (boisestate.edu)
  • SARS-CoV-2 (SARS2) and highly pathogenic arenaviruses, including Lassa virus (LASV), Junin virus, and Machupo virus, share structurally and functionally related enzymes that are capable of degrading an RNA strand. (umn.edu)
  • These enzymes, called exoribonuclease (ExoN), play essential roles in proofreading viral RNA and suppressing antiviral responses. (umn.edu)
  • Our team has contributed extensively to understanding these viral ExoN enzymes, including shedding light on their atomic structures and catalytic mechanisms. (umn.edu)
  • The lifecycle of RNA is more dynamic, where they can be modified by a variety of enzymes. (amegroups.org)
  • This new field of study extends further understanding of epigenetics from the perspective of RNA, where the terminologies are adopted from epigenetics, including writers, readers, and erasers to categorize epitranscriptomic enzymes. (amegroups.org)
  • These epitranscriptomic enzymes mark all kinds of RNA species, including mRNAs and ncRNAs, such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), miRNAs, and lncRNAs ( 11 ). (amegroups.org)
  • We are interested in understanding and harnessing RNA-mediated control of the genome, including CRISPR-Cas bacterial adaptive immunity and related systems. (berkeley.edu)
  • The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
  • 1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. (asu.edu)
  • It is possible to isolate novel ribozymes encoded in a genome by a high-throughput, iterative in vitro ribozyme assay. (biomedcentral.com)
  • Quantitative analysis of RNA on a massively parallel array (RNA-MaP) 21 , 23 starts with ssDNA sequencing libraries including an RNA polymerase promoter region, a stall sequence, and a variable region complementary to the desired RNA. (nature.com)
  • 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
  • Unlike DNA, which mostly exists as double-stranded structures that are well defined and exhibit low structural and binding diversity, RNA is typically single-stranded and naturally assumes complex three-dimensional structures. (nature.com)
  • HCV belongs to the Flaviviridae family of single-stranded RNA viruses. (xiahepublishing.com)
  • The COVID-19 etiologic agent is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded positive-sense RNA virus. (figshare.com)
  • Cellix' VenaFlux™ platform, reported to be the first semiautomated, high-throughput microfluidic cell-based assay system, measures cells' adhesion to antibody-coated or endothelial cell cultured microchannels, mimicking physiological flow. (genengnews.com)
  • We developed a novel fluorescence resonance energy transfer-based strand displacement assay for monitoring SARS-CoV-2 RdRp activity suitable for a high-throughput format. (figshare.com)
  • High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay. (cdc.gov)
  • RNA molecules are uniquely capable of encoding and controlling the expression of genetic information, often as a consequence of their three-dimensional structures. (berkeley.edu)
  • Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. (boisestate.edu)
  • Genetic exchange leading to self-assembling RNA species upon encapsulation in artificial protocells. (boisestate.edu)
  • CDK9 promotes RNA synthesis in genetic programs for cell growth, differentiation, and viral pathogenesis. (thermofisher.com)
  • Ribozymes were first discovered in viral-like RNA pathogens of plants (hammerhead and hairpin) or of humans (HDV), and sporadically in metazoan genomes [ 3 ]. (biomedcentral.com)
  • In plants, RNAi tools based on the expression of dsRNAs of viral sequence have been extensively used to confer antiviral resistance, despite their lack of high specificity. (encyclopedia.pub)
  • The amiRNA transgene expresses a monocistronic MIRNA precursor sequentially processed into an amiRNA targeting a single site in a single viral RNA. (encyclopedia.pub)
  • The syn-tasiRNA transgene expresses a polycistronic TAS precursor sequentially processed into four different syn-tasiRNAs targeting multiple sites in multiple viral RNAs. (encyclopedia.pub)
  • Sequential processing by DCL1 produces the pre-amiRNA followed by the amiRNA duplex, and the amiRNA guide strand is incorporated into AGO1 to target complementary viral RNA, typically in a single site (Figure 1a). (encyclopedia.pub)
  • The RdRp is one of the key druggable targets for CoVs due to its essential role in viral replication, high degree of sequence and structural conservation and the lack of homologues in human cells. (figshare.com)
  • miRNAs are a large family of non-coding RNAs which play important roles in translational and post-transcriptional regulation of gene expression and biological processes. (unboundmedicine.com)
  • M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. (beds.ac.uk)
  • Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. (genomicglossaries.com)
  • Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. (biomedcentral.com)
  • With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. (beds.ac.uk)
  • Epigenetics refers to heritable changes in gene expression without changing the nucleotide sequence of the gene, including DNA methylation, histone modifications, and RNA modifications. (beds.ac.uk)
  • The detection of RNA modifications is fundamental to the study of m7G modifications in the regulation of gene expression. (beds.ac.uk)
  • Enzyme catalysis of chemical reactions occur with high selectivity and rate. (wikipedia.org)
  • RNA which contains an intron sequence that has an enzyme- like catalytic activity. (genomicglossaries.com)
  • 2022. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function . (cardiff.ac.uk)
  • It is possible to create similar catalysts from small molecules by combining substrate-binding with catalytic functional groups. (wikipedia.org)
  • Testing regulatory RNAs and small-molecules as novel therapeutic agents. (nyu.edu)
  • RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. (nyu.edu)
  • Using Analytical Ultra Centrifugation to measure global structural changes during equilibrium folding of RNA molecules. (nyu.edu)
  • My research involves the design and laboratory evolution of RNA in order to discover molecules with potential biomedical and biotechnical applications. (boisestate.edu)
  • RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
  • The two main classes of plant art-sRNAs are artificial microRNAs (amiRNAs) and artificial/synthetic trans-acting small interfering RNAs (atasiRNAs/syn-tasiRNAs, hereafter syn-tasiRNAs) [ 5 ] . (encyclopedia.pub)
  • Three classes of small RNAs (smRNAs) have been described, microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs) [ 5 ]. (biomedcentral.com)
  • Hayden, E. J. (2016) Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions. (boisestate.edu)
  • Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs designed to recognize and silence complementary target RNAs with high specificity. (encyclopedia.pub)
  • They consist in 21-nucleotide sRNAs expressed in planta from endogenous sRNA precursors and computationally designed to silence target RNAs with high specificity [ 5 ] . (encyclopedia.pub)
  • Mainly, it focuses on newly emerged enhanced SPR biosensors towards high-throughput and ultrasensitive screening of miRNAs using labeling processes with focusing on the future application in biomedical research and clinical diagnosis. (unboundmedicine.com)
  • miRNAs are the most common and best understood class of non-coding RNAs, but with ongoing research in the field of RNAi, differences and similarities in biogenesis and functionality of the different smRNA classes are becoming clearer [ 6 ]. (biomedcentral.com)
  • Here we report on a simple and highly accessible approach to convert commercially available customized DNA microarrays of any complexity and density to RNA microarrays via a T7 RNA polymerase-mediated extension of photocrosslinked methyl RNA primers and subsequent degradation of the DNA templates. (nature.com)
  • RNA interference (RNAi) is a biological process conserved in most eukaryotes and characterized by the sequence-specific degradation of target RNA by complementary small RNAs (sRNAs) [ 1 ] . (encyclopedia.pub)
  • I have contributed to the basic understanding of the catalytic mechanisms and structures of flavoenzymes and peroxiredoxins. (rush.edu)
  • Prokaryotes have evolved a nucleic acid-based immune system that shares some functional similarities with RNA interference in eukaryotes. (berkeley.edu)
  • Ribozymes are modular and functional in different RNA contexts. (biomedcentral.com)
  • Although RNA modifications have been reported in many tissues and disease contexts, detailed functional studies in the heart and cardiovascular disease are only beginning to be reported. (amegroups.org)
  • In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. (nature.com)
  • The combination of this conformational heterogeneity of RNA and the composite of ionic and hydrogen bonding, hydrophobic effects, π interactions, and van der Waals forces acting on binding targets, puts predictions of these interactions outside of our current reach and requires experimental approaches 8 . (nature.com)
  • Environmental change exposes beneficial epistatic interactions in a catalytic RNA. (boisestate.edu)
  • This complex facilitates the transition from abortive to productive elongation by phosphorylating the CTD of the large subunit of RNA polymerase II, POLR2A, SUPT5H, and RDBP. (thermofisher.com)
  • Recent work has demonstrated the role of CRISPRs in adaptive immunity and shown that small RNAs derived from CRISPRs (crRNAs) are implemented as homing oligos for the targeted interference of foreign DNA. (berkeley.edu)
  • Targeted Metabolomics and High-Throughput RNA Sequencing-Based Transcriptomics Reveal Massive Changes in the Streptomyces venezuelae NRRL B-65442 Metabolism Caused by Ethanol Shock. (univie.ac.at)
  • Not only is m7G involved in the normal physiological metabolism of RNA, but recent research also shows that m7G and related regulators appear to be considerably dysregulated in tumors [ 12 ]. (beds.ac.uk)
  • High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. (nyu.edu)
  • We have also developed robust fluorescence-based tests to analyze ExoN activities, including a novel method that enables a gain-of-function readout in ultra-high-throughput screening (uHTS) of small molecule inhibitors. (umn.edu)
  • Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp12/7/8 RNA-dependent RNA polymerase. (figshare.com)
  • Mitra, S. ( 2014 ) Methods in Molecular Biology, Vol. 1086 (RNA Folding - Methods and Protocols), Chapter 16: 265-288. (nyu.edu)
  • The molecular functions of ribonucleic acid (RNA) are diverse and essential in all organisms. (biomedcentral.com)
  • We propose a single to immediate further research for the molecular mechanism underlying the actual long-distance movements with this essential portable signaling RNA within plants.Vegetation is often mauled by various infections in their expansion, that might result in environmental pollution, food shortages, or fiscal loss in a certain location. (hormonessignaling.com)
  • Molecular formula of common RNA modifications. (beds.ac.uk)
  • Art-sRNAi tools have been broadly used in plants to confer antiviral resistance against multiple RNA and DNA viruses, and to viroids as well, however there are still important limitations to overcome. (encyclopedia.pub)
  • Actually, label-based signal amplification strategies of SPR platforms including nanoparticle enhancement, supersandwich assembly, streptavidin/biotin complex, antibody amplification, enzymatic reactions, triplex structure formation and catalytic hairpin assembly are discussed. (unboundmedicine.com)
  • The transporter of negative transcription results in throughput amino in economic aspects develops the I of intracellular acids. (erik-mill.de)
  • They also noted that scientists are expanding from high-throughput screening into secondary screening. (genengnews.com)
  • Combinatorial Chemistry and High Throughput Screening, 5 (2). (whiterose.ac.uk)
  • Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes. (genomicglossaries.com)
  • HCV is a positive-strand RNA virus of the Flaviviridae family that contains 9.6 kb of RNA. (nature.com)
  • In particular, numerous studies have reported the successful application of art-sRNAi tools to induce resistance against a large number of RNA and DNA viruses in model and crop species. (encyclopedia.pub)
  • Indeed, more than 170 RNA modifications have been identified across species ( 6 ). (amegroups.org)
  • Engineering high speed allosteric hammerhead ribozymes. (bcm.edu)
  • The main methods include quantitative detection and high-throughput sequencing (Table 1 ). (beds.ac.uk)
  • functions serve a catalytic non-muscle of folded, 18-21 wide scavenger sequence VDACs. (erik-mill.de)
  • With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
  • The length limitation for this technique could prevent the isolation of novel ribozymes that may reside among the numerous long non-coding RNAs (greater than 200 nt) encoded in bacterial genomes [ 17 ]. (biomedcentral.com)
  • RNAi pathways are triggered by double-stranded RNA (dsRNA) processed into sRNA duplexes by Dicer ribonucleases [ 1 ] [ 2 ] . (encyclopedia.pub)
  • A Statistical Method for the Detection of Alternative Splicing Using RNA-seq. (bcm.edu)
  • The recent emergence of epitranscriptomics provides an avenue for identifying RNA modifications implicated in the pathophysiology of human disease. (amegroups.org)
  • The recent discoveries of RNA modifications and their importance in normal and pathophysiological conditions have led to the emergence of new field of study called, epitranscriptomics ( 7 , 8 ). (amegroups.org)
  • Biochemical characterization of Dimocarpus longan polyphenol oxidase provides insights into its catalytic efficiency. (univie.ac.at)
  • Predicted to be involved in negative regulation of catalytic activity. (nih.gov)