Abstract:
:An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucleotide and its neighbours as they are defined by the tertiary structure of the molecule. Informational content of each tile is calculated as its probability to occur exclusively in a set of cognate tRNAs. Based on this algorithm the identity sites of E. coli tRNA(Ala) and tRNA(Gln) were determined. The results are in a good agreement with the biochemical data and provide new information about identity sites of these tRNAs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Steinberg SV,Kisselev LLdoi
10.1093/nar/21.8.1941subject
Has Abstractpub_date
1993-04-25 00:00:00pages
1941-7issue
8eissn
0305-1048issn
1362-4962journal_volume
21pub_type
杂志文章abstract::Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally deter...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg757
更新日期:2003-10-01 00:00:00
abstract::Near-UV difference spectral analysis of the triplex formed from d(C-T)6 and d(A-G)6.d(C-T)6 in neutral and acidic solution shows that the third strand dC residues are protonated at pH 7.0, far above their intrinsic pKa. Additional support for ion-dipole interactions between the third strand dC residues and the G.C tar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.14.2692
更新日期:1995-07-25 00:00:00
abstract::In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA-eEF1A-GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv376
更新日期:2015-05-19 00:00:00
abstract::The poly(A) signal and downstream elements with transcriptional pausing activity play an important role in termination of RNA polymerase II transcription. We show that an intronic sequence derived from the plant seed protein gene (AmA1) specifically acts as a transcriptional terminator in the fission yeast, Schizosacc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf334
更新日期:2002-07-01 00:00:00
abstract::We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laborato...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg397
更新日期:2003-06-01 00:00:00
abstract::The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku836
更新日期:2014-11-10 00:00:00
abstract::The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 repre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.206
更新日期:1996-01-01 00:00:00
abstract::PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa971
更新日期:2021-01-08 00:00:00
abstract::Studying the intricate folding of rRNA within the ribosome remains a complex problem. Phenanthroline-Cu(II) complexes cleave phosphodiester bonds in rRNA in specific regions, apparently especially where the rRNA structure is constrained in some fashion. We have introduced phenanthroline-copper complexes into 50S Esche...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.8.1906
更新日期:1999-04-15 00:00:00
abstract::The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm279
更新日期:2007-07-01 00:00:00
abstract::The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.10.1935
更新日期:1997-05-15 00:00:00
abstract::DAP-like kinase (Dlk, also termed ZIP kinase) is a leucine zipper-containing serine/threonine-specific protein kinase with as yet unknown biological function(s). Interaction partners so far identified are either transcription factors or proteins that can support or counteract apoptosis. Thus, Dlk might be involved in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.6.1408
更新日期:2002-03-15 00:00:00
abstract::During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw172
更新日期:2016-05-19 00:00:00
abstract::5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx473
更新日期:2017-06-20 00:00:00
abstract::Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1225
更新日期:2021-01-25 00:00:00
abstract::Mouse globin messenger ribonucleoprotein (mRNP) has been isolated from reticulocyte polysomes by affinity chromatography to oligo(T)-cellulose, using a procedure modified from that of Lindberg and Sundquist. The messenger RNA and protein moieties fo the mRNP are indistinguishable from those isolated by less rapid tech...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.12.2251
更新日期:1975-12-01 00:00:00
abstract::The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks152
更新日期:2012-07-01 00:00:00
abstract::Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt416
更新日期:2013-07-01 00:00:00
abstract::Spectroscopic studies of the complexes of double-stranded (ds) DNA with the polymethylene-amine linked heterodimers thiazole orange-thiazole blue, thiazole orange-ethidium, and fluorescein-ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson, S.C., Singh, P. and Glazer, A.N...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5720
更新日期:1993-12-11 00:00:00
abstract::RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp388
更新日期:2009-07-01 00:00:00
abstract::The hexanucleoside pentaphosphate d(m5CpGpm5CpGpm5CpG) has been studied in solution by ultra-violet absorption, circular dichroism and 31P nuclear magnetic resonance under various experimental conditions. In 0.2 M NaClO4 at low temperature, an hexamer duplex is formed which has a B or B-like conformation. As the salt ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.13.4453
更新日期:1983-07-11 00:00:00
abstract::As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the fam...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq626
更新日期:2010-11-01 00:00:00
abstract::Transcript of the rbpA1 gene in Anabaena variabilis accumulates significantly at low growth temperatures below 28 degreesC. This accumulation was maximal at 16 degreesC. Accumulation of the rbpA1 transcript was completely abolished by rifampicin, but not by chloramphenicol. Photosynthesis was not required for this col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.9.2192
更新日期:1998-05-01 00:00:00
abstract::The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.13.2999
更新日期:1980-07-11 00:00:00
abstract::Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1079
更新日期:2010-03-01 00:00:00
abstract::Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv657
更新日期:2015-08-18 00:00:00
abstract::Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki430
更新日期:2005-07-01 00:00:00
abstract::The direct sequencing of DNA generated by the polynucleotide chain reaction, via the incorporation of phosphorothioate nucleotides and followed by treatment with an alkylating reagent that cleaves specifically at the phosphorothioate positions, is described. The Taq polymerase used in the amplification reaction incorp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.9947
更新日期:1988-11-11 00:00:00
abstract::RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv444
更新日期:2015-06-23 00:00:00
abstract::Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9471
更新日期:1987-11-25 00:00:00