Abstract:
:Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of (1)H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO(6)CACTG)/d(CAGTGX(17)GTCAC), X = C or T]. (1)H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C(17) 4-amino proton of the O:C duplex and of T(17) imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30 °C, although the melting temperatures were >50 °C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C(17) toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T(17) toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Pack SP,Morimoto H,Makino K,Tajima K,Kanaori Kdoi
10.1093/nar/gkr872subject
Has Abstractpub_date
2012-02-01 00:00:00pages
1841-55issue
4eissn
0305-1048issn
1362-4962pii
gkr872journal_volume
40pub_type
杂志文章abstract::Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw963
更新日期:2017-02-28 00:00:00
abstract::The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.7.1535
更新日期:1980-04-11 00:00:00
abstract::The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Prote...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt887
更新日期:2014-01-01 00:00:00
abstract::Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1157
更新日期:2014-01-01 00:00:00
abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx037
更新日期:2017-05-05 00:00:00
abstract::Although mobility of the phylogenetically widespread group I introns appears to be mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of the td and sunY introns are different from their eukaryotic counterparts. Most notably, they cleave at a distance from the intron insertion site...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.13.3763
更新日期:1990-07-11 00:00:00
abstract::MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1239
更新日期:2011-04-01 00:00:00
abstract::This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw256
更新日期:2016-07-08 00:00:00
abstract::The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm874
更新日期:2008-02-01 00:00:00
abstract::A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg130
更新日期:2003-01-15 00:00:00
abstract::ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1022
更新日期:2012-01-01 00:00:00
abstract::Two enzymatic pathways are involved in the inhibitory effects of double-stranded (ds)RNA on protein synthesis in cell extracts derived from interferon-treated human fibroblasts or HeLa cells, an oligonucleotide polymerase that synthesizes (2'-5')An from ATP and a protein kinase that phosphorylates the alpha subunit of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.19.4939
更新日期:1981-10-10 00:00:00
abstract::The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.15.3467
更新日期:1980-08-11 00:00:00
abstract::Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.9.3061
更新日期:1979-07-11 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::Electrophoretic mobility shift assays (EMSA) were used to define the regions of the INO1 promoter that interact with factors present in extracts prepared from the yeast, Saccharomyces cerevisae. These experiments identified three different types of protein:DNA complexes that assemble with the INO1 promoter. Formation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.14.3987
更新日期:1991-07-25 00:00:00
abstract::The binding of anti poly(I). poly (C) Fab fragments to double or triple stranded polynucletides has been studied by fluorescence. Association constants were deduced from competition experiments. The comparison of the association constants leads to the conclusion that several atoms of the base residues do not interact ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.12.3337
更新日期:1976-12-01 00:00:00
abstract::Restriction fragments of T7 DNA which selectively bind E. coli RNA polymerase have been identified. These include fragments located close to the beginning of gene 1 where according to Minkley and Pribnow (1973) there is a promoter called C. The smallest fragment from this region which binds RNA polymerase has been seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.2.525
更新日期:1979-02-01 00:00:00
abstract::The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achiev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1311
更新日期:2016-01-04 00:00:00
abstract::In nematodes, the 22 nucleotide (nt) spliced leader (SL) is normally encoded by a multi-copy, tandemly reiterated SL gene and is trans-spliced from SL-RNA onto the 5' end of a subset of mRNAs. We have found that the SL is also encoded at multiple (> 100) orphon genomic sites in the parasitic nematode Angiostrongylus c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.6.1030
更新日期:1995-03-25 00:00:00
abstract::Decay of (125)I produces a shower of low energy electrons (Auger electrons) that cause strand breaks in DNA in a distance-dependent manner with 90% of the breaks located within 10 bp from the decay site. We studied strand breaks in RNA molecules produced by decay of (125)I incorporated into complementary DNA oligonucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf622
更新日期:2002-11-15 00:00:00
abstract::The 279-bp major breakpoint region (mbr) within the 3'-untranslated region (3'-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr023
更新日期:2011-06-01 00:00:00
abstract::The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1068
更新日期:2015-01-01 00:00:00
abstract::We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh363
更新日期:2004-07-01 00:00:00
abstract::Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Span...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx338
更新日期:2017-07-27 00:00:00
abstract::Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz474
更新日期:2019-09-05 00:00:00
abstract::The apolipoprotein AI (apoAI) promoter/enhancer contains multiple cis -acting elements on which a variety of hepatocyte-enriched and ubiquitous transcription factors function synergistically to regulate liver-specific transcription. Adenovirus E1A proteins repress tissue-specific gene expression and disrupt the differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.7.1761
更新日期:1998-04-01 00:00:00
abstract::Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1064
更新日期:2012-01-01 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::Labeling of a covalently closed circular double-stranded DNA was achieved using a so-called 'padlock oligonucleotide'. The oligonucleotide was targeted to a sequence which is present in the replication origin of phage f1 and thus in numerous commonly used plasmids. After winding around the double-stranded target DNA s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.e12
更新日期:2002-02-01 00:00:00