New photoactivatable structural and affinity probes of RNAs: specific features and applications for mapping of spermine binding sites in yeast tRNA(Asp) and interaction of this tRNA with yeast aspartyl-tRNA synthetase.

Abstract:

:Aryldiazonium salts are shown to be useful as phototriggered structural probes for RNA mapping as well as for footprinting of RNA/protein interaction. In particular the yeast tRNA(Asp)/aspartyl-tRNA synthetase complex is shown to involve the variable loop face and the concave side of the L-shaped nucleic acid bound to a lipophilic area of the enzyme. When chemically linked to spermine, the photoactive group cleaves RNA at polyamine binding sites; 3-4 spermines have been located in the tRNA(Asp), stabilizing the central part of the molecule in regions where two ribose-phosphate strands are close to each other.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Garcia A,Giegé R,Behr JP

doi

10.1093/nar/18.1.89

subject

Has Abstract

pub_date

1990-01-11 00:00:00

pages

89-95

issue

1

eissn

0305-1048

issn

1362-4962

journal_volume

18

pub_type

杂志文章
  • Calf lens crystallin messenger RNA's contain polynucleotide sequences rich in adenylic acid.

    abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/1.2.245

    authors: Piperno G,Bertazzoni U,Berns AJ,Bloemendal H

    更新日期:1974-02-01 00:00:00

  • RegulonDB: a database on transcriptional regulation in Escherichia coli.

    abstract::RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli , as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. The operon is the basic structure used in RegulonDB to describe th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.1.55

    authors: Huerta AM,Salgado H,Thieffry D,Collado-Vides J

    更新日期:1998-01-01 00:00:00

  • The FALC-Loop web server for protein loop modeling.

    abstract::The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr352

    authors: Ko J,Lee D,Park H,Coutsias EA,Lee J,Seok C

    更新日期:2011-07-01 00:00:00

  • Preparation and properties of poly 2'-O-ethylcytidylic acid.

    abstract::Poly 2'0-ethylcytidylic acid (poly (Ce)) was prepared by polymerization of 2'-0-ethylcytidine-5'-pyrophosphate with Escherichia coli polynucleotide phosphorylase in the presence of Mn++, and its properties compared with those of poly (rC), poly (Cm) and poly (dC). The neutral form of pOLY (Ce) exhibits properties simi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.3.817

    authors: Kielanowska M,Shugar D

    更新日期:1976-03-01 00:00:00

  • Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus.

    abstract::Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.8.1714

    authors: Figlerowicz M

    更新日期:2000-04-15 00:00:00

  • Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.

    abstract::In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku249

    authors: Neumann P,Lakomek K,Naumann PT,Erwin WM,Lauhon CT,Ficner R

    更新日期:2014-06-01 00:00:00

  • In vivo and in vitro studies of Mgs1 suggest a link between genome instability and Okazaki fragment processing.

    abstract::The non-essential MGS1 gene of Saccharomyces cerevisiae is highly conserved in eukaryotes and encodes an enzyme containing both DNA-dependent ATPase and DNA annealing activities. MGS1 appears to function in post-replicational repair processes that contribute to genome stability. In this study, we identified MGS1 as a ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki900

    authors: Kim JH,Kang YH,Kang HJ,Kim DH,Ryu GH,Kang MJ,Seo YS

    更新日期:2005-10-26 00:00:00

  • The nucleotide sequence of 5.8S rRNA from the posterior silk gland of the silkworm Philosamia cynthia ricini.

    abstract::The nucleotide sequence of 5.8S rRNA from the Chinese silkworm Philosamia cynthia ricini has been determined by gel sequencing and mobility shift methods. The complete primary structure is (sequence in text). This is one of the largest known 5.8S rRNAs. As compared to Bombyx 5.8S rRNA, it is two nucleotides longer; t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.20.6383

    authors: Feng YX,Krupp G,Gross HJ

    更新日期:1982-10-25 00:00:00

  • An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA.

    abstract::It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.14.6839

    authors: Kitts PA,Nash HA

    更新日期:1988-07-25 00:00:00

  • Functional characterization of C. elegans Y-box-binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes.

    abstract::The cold shock domain is one of the most highly conserved motifs between bacteria and higher eukaryotes. Y-box-binding proteins represent a subfamily of cold shock domain proteins with pleiotropic functions, ranging from transcription in the nucleus to translation in the cytoplasm. These proteins have been investigate...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1077

    authors: Arnold A,Rahman MM,Lee MC,Muehlhaeusser S,Katic I,Gaidatzis D,Hess D,Scheckel C,Wright JE,Stetak A,Boag PR,Ciosk R

    更新日期:2014-12-01 00:00:00

  • Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control.

    abstract::SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1277

    authors: Danilenko M,Dalgliesh C,Pagliarini V,Naro C,Ehrmann I,Feracci M,Kheirollahi-Chadegani M,Tyson-Capper A,Clowry GJ,Fort P,Dominguez C,Sette C,Elliott DJ

    更新日期:2017-04-20 00:00:00

  • The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications.

    abstract::The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis gr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa411

    authors: Rose S,Auxilien S,Havelund JF,Kirpekar F,Huber H,Grosjean H,Douthwaite S

    更新日期:2020-07-09 00:00:00

  • HCAD, closing the gap between breakpoints and genes.

    abstract::Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information sy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki061

    authors: Hoffmann R,Dopazo J,Cigudosa JC,Valencia A

    更新日期:2005-01-01 00:00:00

  • MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes.

    abstract::MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm266

    authors: Kumar N,Mohanty D

    更新日期:2007-07-01 00:00:00

  • Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis.

    abstract::Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.18.3631

    authors: Ibba M,Sever S,Praetorius-Ibba M,Söll D

    更新日期:1999-09-15 00:00:00

  • Database resources of the National Center for Biotechnology Information.

    abstract::In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Ut...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1172

    authors: Sayers EW,Barrett T,Benson DA,Bolton E,Bryant SH,Canese K,Chetvernin V,Church DM,DiCuccio M,Federhen S,Feolo M,Fingerman IM,Geer LY,Helmberg W,Kapustin Y,Landsman D,Lipman DJ,Lu Z,Madden TL,Madej T,Maglott DR,Ma

    更新日期:2011-01-01 00:00:00

  • Direct analysis of the mini-exon donor RNA of Trypanosoma brucei: detection of a novel cap structure also present in messenger RNA.

    abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.23.9861

    authors: Freistadt MS,Cross GA,Branch AD,Robertson HD

    更新日期:1987-12-10 00:00:00

  • Salt-and histone H1-induced structural changes of reconstituted minichromosomes.

    abstract::Structural changes of reconstituted SV 40 minichromosomes have been studied in relation to the salt concentration and addition of histone H1 by sedimentation and electron microscopy. Sedimentation data are represented as functions of the NaCl concentration and the Debye-Hückel electrostatic screening radius 1/alpha. T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.11.3581

    authors: Böttger M,Scherneck S,von Mickwitz CU,Fenske H,Lindigkeit R

    更新日期:1979-08-10 00:00:00

  • Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.

    abstract::This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with ov...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa417

    authors: Poppleton E,Bohlin J,Matthies M,Sharma S,Zhang F,Šulc P

    更新日期:2020-07-09 00:00:00

  • Promoter chromatin remodeling of immediate-early genes is mediated through H3 phosphorylation at either serine 28 or 10 by the MSK1 multi-protein complex.

    abstract::Upon activation of the ERK and p38 MAPK pathways, the MSK1/2-mediated nucleosomal response, including H3 phosphorylation at serine 28 or 10, is coupled with the induction of immediate-early (IE) gene transcription. The outcome of this response, varying with the stimuli and cellular contexts, ranges from neoplastic tra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq030

    authors: Drobic B,Pérez-Cadahía B,Yu J,Kung SK,Davie JR

    更新日期:2010-06-01 00:00:00

  • LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.

    abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh441

    authors: Nair R,Rost B

    更新日期:2004-07-01 00:00:00

  • EMAGE--Edinburgh Mouse Atlas of Gene Expression: 2008 update.

    abstract::EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm938

    authors: Venkataraman S,Stevenson P,Yang Y,Richardson L,Burton N,Perry TP,Smith P,Baldock RA,Davidson DR,Christiansen JH

    更新日期:2008-01-01 00:00:00

  • Engineering of temperature- and light-switchable Cas9 variants.

    abstract::Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw930

    authors: Richter F,Fonfara I,Bouazza B,Schumacher CH,Bratovič M,Charpentier E,Möglich A

    更新日期:2016-11-16 00:00:00

  • A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.

    abstract::We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa015

    authors: Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco M

    更新日期:2020-03-18 00:00:00

  • Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit.

    abstract::More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1079

    authors: Braun CM,Hackert P,Schmid CE,Bohnsack MT,Bohnsack KE,Perez-Fernandez J

    更新日期:2020-01-10 00:00:00

  • MEIOK21: a new component of meiotic recombination bridges required for spermatogenesis.

    abstract::Repair of DNA double-strand breaks (DSBs) with homologous chromosomes is a hallmark of meiosis that is mediated by recombination 'bridges' between homolog axes. This process requires cooperation of DMC1 and RAD51 to promote homology search and strand exchange. The mechanism(s) regulating DMC1/RAD51-ssDNA nucleoprotein...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa406

    authors: Shang Y,Huang T,Liu H,Liu Y,Liang H,Yu X,Li M,Zhai B,Yang X,Wei Y,Wang G,Chen Z,Wang S,Zhang L

    更新日期:2020-07-09 00:00:00

  • Structural insights into NusG regulating transcription elongation.

    abstract::NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1159

    authors: Liu B,Steitz TA

    更新日期:2017-01-25 00:00:00

  • Contacts between the growing peptide chain and the 23S RNA in the 50S ribosomal subunit.

    abstract::Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Pepti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.8.1394

    authors: Stade K,Riens S,Bochkariov D,Brimacombe R

    更新日期:1994-04-25 00:00:00

  • A sigma factor toolbox for orthogonal gene expression in Escherichia coli.

    abstract::Synthetic genetic sensors and circuits enable programmable control over timing and conditions of gene expression and, as a result, are increasingly incorporated into the control of complex and multi-gene pathways. Size and complexity of genetic circuits are growing, but stay limited by a shortage of regulatory parts t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky010

    authors: Bervoets I,Van Brempt M,Van Nerom K,Van Hove B,Maertens J,De Mey M,Charlier D

    更新日期:2018-02-28 00:00:00

  • Coding capacity of complementary DNA strands.

    abstract::A Fortran computer algorithm has been used to analyze the nucleotide sequence of several structural genes. The analysis performed on both coding and complementary DNA strands shows that whereas open reading frames shorter than 100 codons are randomly distributed on both DNA strands, open reading frames longer than 100...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.6.1499

    authors: Casino A,Cipollaro M,Guerrini AM,Mastrocinque G,Spena A,Scarlato V

    更新日期:1981-03-25 00:00:00