Abstract：
:The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecules have been located. The majority of these occur in the first coordination shell of solvation. There are extensive networks of connected waters, both in the major and minor grooves. In particular, there are 21 water molecules associated with the minor-groove drug, via hydrogen bonds from the four charged nitrogen atoms. One cluster of four waters is situated in the groove itself; the majority are on the outer edge of the groove, and serve to bridge between the outward-directed drug nitrogen atoms and backbone phosphate oxygen atoms. These bridges are both intra- and inter-strand, with the net effect that the outer edge of the drug molecule is covered by ribbons of water molecules.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Guerri A,Simpson IJ,Neidle Sdoi
10.1093/nar/26.12.2873subject
Has Abstractpub_date
1998-06-15 00:00:00pages
2873-8issue
12eissn
0305-1048issn
1362-4962pii
gkb494journal_volume
26pub_type
杂志文章abstract：:E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.22.7153
更新日期：1982-11-25 00:00:00
abstract：:Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expres...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn744
更新日期：2009-01-01 00:00:00
abstract：:Equilibrium and kinetics of thermal melting of yeast 5S ribosomal RNA in aqueous NaCl with or without Mg2+ were investigated by differential thermal melting and temperature jump methods. Two peaks (1 and 2) and a shoulder were observed in each of melting curves at ionic strength I=0.002-0.5 and linearity between each ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3363
更新日期：1983-05-25 00:00:00
abstract：:Mitochondrial transcription factor A (TFAM) stimulates transcription from mitochondrial DNA (mtDNA) promoters in vitro and in organello. To investigate whether changes of TFAM levels also modulate transcription and replication in situ, the protein was transiently overexpressed in cultured cells. Mitochondrial mRNAs we...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh921
更新日期：2004-11-16 00:00:00
abstract：:CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR inter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1259
更新日期：2015-12-15 00:00:00
abstract：:Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku230
更新日期：2014-05-01 00:00:00
abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1081
更新日期：2011-04-01 00:00:00
abstract：:When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq353
更新日期：2010-10-01 00:00:00
abstract：:We have investigated the substrate specificity of the Ogg1 protein of Saccharomyces cerevisiae (yOgg1 protein) for excision of modified DNA bases from oxidatively damaged DNA substrates using gas chromatography/isotope dilution mass spectrometry. Four DNA substrates prepared by treatment with H2O2/Fe(III)-EDTA/ascorbi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.5.1228
更新日期：1998-03-01 00:00:00
abstract：:Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes witho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx572
更新日期：2017-08-21 00:00:00
abstract：:The role of the mRNA-binding protein human antigen R (HuR) in stabilization and translation of AU-rich elements (ARE) containing mRNAs is well established. However, the trafficking of HuR and bound mRNA cargo, which comprises a fundamental requirement for the aforementioned HuR functions is only poorly understood. By ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt663
更新日期：2013-10-01 00:00:00
abstract：:Naturally occurring hammerhead ribozymes are produced by rolling circle replication followed by self-cleavage. This results in monomer-length catalytic RNAs which have self-complementary sequences that can occupy their trans -binding domains and potentially block their ability to cleave other RNA strands. Here we show...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.3.776
更新日期：2000-02-01 00:00:00
abstract：:The transcription factor CHOP/GADD153 gene is induced by cellular stress and is involved in mediating apoptosis. We report the identification of a conserved region in the promoter of the CHOP gene responsible for its inducibility by endoplasmic reticulum (ER) stress. Deletion mutants of the human CHOP promoter identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.24.4987
更新日期：2000-12-15 00:00:00
abstract：:Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt718
更新日期：2013-11-01 00:00:00
abstract：:The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.5.1443
更新日期：1985-03-11 00:00:00
abstract：:Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.3.778
更新日期：1998-02-01 00:00:00
abstract：:The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1020
更新日期：2018-01-04 00:00:00
abstract：:In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr080
更新日期：2011-07-01 00:00:00
abstract：:We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq254
更新日期：2010-07-01 00:00:00
abstract：:Six 1',5'-anhydrohexitol uridine triphosphates were synthesized with aromatic substitutions appended via a carboxamide linker to the 5-position of their bases. An improved method for obtaining such 5-substituted hexitol nucleosides and nucleotides is described. The incorporation profile of the nucleotide analogues int...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz008
更新日期：2019-03-18 00:00:00
abstract：:The role of TATA elements in the expression of a mammalian promoter was investigated in the fission yeast Schizosaccharomyces pombe, by studying the human adenovirus E2-early promoter. This is a unique dual promoter with two nonconsensus TATA elements directing transcription from two cap sites, +1 and -26. A sequence ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.11.2737
更新日期：1993-06-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx407
更新日期：2017-07-03 00:00:00
abstract：:Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr467
更新日期：2011-07-01 00:00:00
abstract：:RNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4(+) T cell differentiation. CD4(+...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv752
更新日期：2015-09-18 00:00:00
abstract：:A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.19.7327
更新日期：1984-10-11 00:00:00
abstract：:RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks289
更新日期：2012-08-01 00:00:00
abstract：:Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2017-04-07 00:00:00
abstract：:The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations fas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa162
更新日期：2020-05-07 00:00:00
abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky977
更新日期：2019-01-08 00:00:00
abstract：:A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.18.7195
更新日期：1989-09-25 00:00:00
