Abstract:
:Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditions where little or no non-specific DNA degradation was observed, all three nucleases were able to generate double-strand breaks when the bistranded abasic sites were 1 and 3 base pairs apart. However, when the abasic sites were further apart, the enzymes again failed to cleave the DNA. These results indicate that single abasic sites do not cause sufficient denaturation of the DNA to allow incision by these single-strand specific endonucleases. The reactivity of these enzymes was also investigated on DNA substrates that were nicked by DNasel or more site-specifically by endonuclease III incision at the discrete abasic sites. The three nucleases readily induced a strand break opposite such nicks.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chaudhry MA,Weinfeld Mdoi
10.1093/nar/23.19.3805subject
Has Abstractpub_date
1995-10-11 00:00:00pages
3805-9issue
19eissn
0305-1048issn
1362-4962pii
5a0515journal_volume
23pub_type
杂志文章abstract::PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.220
更新日期:1998-01-01 00:00:00
abstract::The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx244
更新日期:2017-05-19 00:00:00
abstract::Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1149
更新日期:2020-12-16 00:00:00
abstract::In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seem...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq215
更新日期:2010-08-01 00:00:00
abstract::Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx755
更新日期:2017-11-02 00:00:00
abstract::A method is described to simultaneously amplify and sequence DNA using a new class of nucleotides containing boron. During the polymerase chain reaction, boron-modified nucleotides, i.e. 2'-deoxynucleoside 5'-alpha-[P-borano]-triphosphates, are incorporated into the product DNA. The boranophosphate linkages are resist...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.8.1611
更新日期:1997-04-15 00:00:00
abstract::The ability to integrate 'omics' (i.e. transcriptomics and proteomics) is becoming increasingly important to the understanding of regulatory mechanisms. There are currently no tools available to identify differentially expressed genes (DEGs) across different 'omics' data types or multi-dimensional data including time ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw157
更新日期:2016-06-02 00:00:00
abstract::The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.279
更新日期:1991-01-25 00:00:00
abstract::Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx985
更新日期:2018-01-04 00:00:00
abstract::Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl582
更新日期:2006-01-01 00:00:00
abstract::WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki421
更新日期:2005-07-01 00:00:00
abstract::The 5' and 3' untranslated regions of eukaryotic mRNAs (UTRs) play crucial roles in the post-transcriptional regulation of gene expression through the modulation of nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and message stability. UTRdb is a curated database of 5' and 3' untran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp902
更新日期:2010-01-01 00:00:00
abstract::In mammalian cells, DNA damage induces robust changes in gene expression and these changes contribute to the proper execution of cellular responses to DNA damage, including DNA repair, cell cycle arrest and apoptosis. The transcription factor E2F-1 has been suggested to play a key role in the regulation of cell cycle-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.491
更新日期:1999-01-15 00:00:00
abstract::Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky313
更新日期:2018-06-20 00:00:00
abstract::TGGCA-binding proteins are nuclear proteins with high affinity for double-stranded DNA homologous to the prototype recognition sequence 5'YTGGCANNNTGCCAR 3'. Their ubiquitous tissue distribution in higher vertebrates characterizes them as a class of highly conserved proteins which may exert a basic function. To obtain...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.6.2045
更新日期:1985-03-25 00:00:00
abstract::Release of RNA polymerase II (Pol II) from promoter-proximal pausing has emerged as a critical step regulating gene expression in multicellular organisms. The transition of Pol II into productive elongation requires the kinase activity of positive transcription elongation factor b (P-TEFb), which is itself under a str...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw585
更新日期:2016-09-19 00:00:00
abstract::A number of different protecting groups were compared with respect to their usefulness for protection of 2'-hydroxyl functions during synthesis of oligoribonucleotides using the H-phosphonate approach. The comparison was between the t-butyldimethylsilyl (t-BDMSi), the o-chlorobenzoyl (o-CIBz), the tetrahydropyranyl (T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.1.94
更新日期:1994-01-11 00:00:00
abstract::RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1047
更新日期:2020-01-10 00:00:00
abstract::Infrared and UV spectroscopies have been used to study the assembly of a hairpin nucleotide sequence (nucleotides 3-30) of the 5' non-coding region of the hepatitis C virus RNA (5'-GGCGGGGAUUAUCCCCGCUGUGAGGCGG-3') with a RNA 20mer ligand (5'-CCGCCUCACAAAGGUGGGGU-3') in the presence of magnesium ion and spermidine. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.6.1333
更新日期:2002-03-15 00:00:00
abstract::Guanine-rich DNA sequences can form G-quadruplexes stabilized by stacked G-G-G-G tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent so...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkm711
更新日期:2007-01-01 00:00:00
abstract::By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.14.3257
更新日期:1993-07-11 00:00:00
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
更新日期:2010-06-01 00:00:00
abstract::The DNA damage checkpoint halts cell cycle progression in G2 in response to genotoxic insults. Central to the execution of cell cycle arrest is the checkpoint-induced stabilization of securin-separase complex (yeast Pds1-Esp1). The checkpoint kinases Chk1 and Chk2 (yeast Chk1 and Rad53) are thought to critically contr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa355
更新日期:2020-06-19 00:00:00
abstract::A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.4.779
更新日期:1990-02-25 00:00:00
abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5533
更新日期:1988-06-24 00:00:00
abstract::In order to characterize structure-function relationships, the kinetic behavior of chimeric RNA/DNA ribozyme was compared with that of all RNA ribozyme. Determined kcat values were proven to represent the chemical-cleavage step and not the product-dissociation step. In agreement with the finding by Dahm and Uhlenbeck ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5656
更新日期:1993-12-11 00:00:00
abstract::Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1343
更新日期:2017-05-05 00:00:00
abstract::Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the alpha-subunit. The epsilon-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to alpha via a segment of 57 addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn489
更新日期:2008-09-01 00:00:00
abstract::A new method of representing DNA sequences has been devised which is termed stave projection. Compared with other formats for showing the base sequences of DNA, this method greatly enhances the ease of visual analysis of the sequences of bases and it is also in a machine readable form. Using this method it is possible...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.1.509
更新日期:1986-01-10 00:00:00
abstract::A novel, site-specific, DNA backbone S-modification (phosphorothioation) has been discovered, but its in vivo function(s) have remained obscure. Here, we report that the enteropathogenic Salmonella enterica serovar Cerro 87, which possesses S-modified DNA, restricts DNA isolated from Escherichia coli, while protecting...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq610
更新日期:2010-11-01 00:00:00