Abstract:
:The exact sites at which a number of drugs inhibit the nick translation of DNA by E.coli DNA polymerase-I have been pinpointed. In order to do this, a method has been developed for sequencing double-stranded plasmid DNA from the site of a specifically induced nick. The initial experiments have concentrated on analysis of drug inhibition of nick translation in a 200 nucleotide region near the Eco Rl origin of pBR313. Many drugs were found to inhibit nick translation in a highly sequence specific manner. For actinomycin D, significant inhibition occurred at just four sites in the nucleotide sequence under test and only one sequence (pGpCpGpCpGpGp) gave really strong inhibition. Distamycin A gave a different pattern of inhibition with particularly strong stops in just two of the many A-T rich regions in the DNA. Experiments with caffeine suggest that factors in addition to primary sequence are important in determining where major inhibition occurs.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wilkins RJdoi
10.1093/nar/10.22.7273subject
Has Abstractpub_date
1982-11-25 00:00:00pages
7273-82issue
22eissn
0305-1048issn
1362-4962journal_volume
10pub_type
杂志文章abstract::Humans have two nearly identical copies of the survival motor neuron (SMN ) gene, SMN1 and SMN2. Homozygous loss of SMN1 causes spinal muscular atrophy (SMA). SMN2 is unable to prevent the disease due to skipping of exon 7. Using a systematic approach of in vivo selection, we have previously demonstrated that a weak 5...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1050
更新日期:2007-01-01 00:00:00
abstract::Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr017
更新日期:2011-05-01 00:00:00
abstract::The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks755
更新日期:2012-10-01 00:00:00
abstract::Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.10.3995
更新日期:1986-05-27 00:00:00
abstract::Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a sub...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw106
更新日期:2016-06-20 00:00:00
abstract::E. coli can be transformed to extremely high efficiencies by subjecting a mixture of cells and DNA to brief but intense electrical fields of exponential decay waveform (electroporation). We have obtained 10(9) to 10(10) transformants/micrograms with strains LE392 and DH5 alpha, and plasmids pUC18 and pBR329. The proce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.13.6127
更新日期:1988-07-11 00:00:00
abstract::The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.7.1859
更新日期:1990-04-11 00:00:00
abstract::We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.6.1052
更新日期:1994-03-25 00:00:00
abstract::Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed link...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1102
更新日期:2014-01-01 00:00:00
abstract::Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the stan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl773
更新日期:2006-01-01 00:00:00
abstract::Late SV40 16S and 19S mRNAs were found to contain an average of three m6A residues per mRNA molecule. The methylated residues of both the viral and cellular mRNAs occur in two sequences; Gpm6ApC and (Ap)nm6ApC, where n = 1-4. More than 60% of the m6A residues in SV40 16S and 19S mRNAs occur in Gpm6ApC even though ther...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2879
更新日期:1979-06-25 00:00:00
abstract::A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3753
更新日期:1992-07-25 00:00:00
abstract::Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.23.8645
更新日期:1985-12-09 00:00:00
abstract::The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp957
更新日期:2010-01-01 00:00:00
abstract::'Linker scanning' has been used as an efficient method for systematically surveying a segment of DNA for functional elements by mutagenesis. A three-step PCR method was developed to simplify this process. In this method, a set of 'mutation primers' was made with 6 to 8 base substitutions in the center of the primers. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.16.3745
更新日期:1993-08-11 00:00:00
abstract::Real-time PCR is being used increasingly as the method of choice for mRNA quantification, allowing rapid analysis of gene expression from low quantities of starting template. Despite a wide range of approaches, the same principles underlie all data analysis, with standard approaches broadly classified as either absolu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng073
更新日期:2003-07-15 00:00:00
abstract::While antibiotic selection has been routinely used for the selection of genetically modified cells, administration of cytotoxic drugs often leads to deleterious effects not only to inert cells but also to transfected or transduced ones. In this study, we propose an Antigen-MEdiated Genetically modified cell Amplificat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng032
更新日期:2003-04-01 00:00:00
abstract::The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1208
更新日期:2017-03-17 00:00:00
abstract::It is believed that depending on the thermodynamic stability of the 5'-strand and the 3'-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm641
更新日期:2007-01-01 00:00:00
abstract::The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr214
更新日期:2011-07-01 00:00:00
abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh236
更新日期:2004-02-11 00:00:00
abstract::The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq318
更新日期:2010-07-01 00:00:00
abstract::We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.17.5133
更新日期:1990-09-11 00:00:00
abstract::A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part1.101
更新日期:1984-01-11 00:00:00
abstract::DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1500
更新日期:2002-04-01 00:00:00
abstract::ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl880
更新日期:2007-01-01 00:00:00
abstract::The small nucleolar RNA U3 is essential for viability in yeast. We have previously shown that U3 can be cross-linked in vivo to the pre-rRNA in the 5' external transcribed spacer (ETS), at +470. This ETS region contains 10 nucleotides of perfect complementarity to U3. In a genetic background where the mutated rDNA is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.20.4057
更新日期:1994-10-11 00:00:00
abstract::Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.15.3567
更新日期:1998-08-01 00:00:00
abstract::Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku463
更新日期:2014-07-01 00:00:00
abstract::Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1031
更新日期:2013-01-07 00:00:00