Abstract:
:The bZip proteins GCN4 and C/EBP differ in their DNA binding specificities: GCN4 binds well to the pseudopalindromic AP1 site 5'-A4T3G2A1C0T1C2'A3'T4'-3' and to the palindromic ATF/CREB sequence 5'-A4T3G2A1-C0*G0'T1'C2'A3'T4'-3'; C/EBP preferentially recognizes the palindromic sequence 5'-A4T3T2G1C0*G0'C1'A2'-A3'T4'-3'. According to the X-ray structures of GCN4-DNA complexes, five residues of the basic region of GCN4 are involved in specific base contacts: asparagine -18, alanine -15, alanine -14, serine -11 and arginine -10 (numbered relative to the start point of the leucine zipper, which we define as +1). In the basic region of C/EBP position -14 is occupied by valine instead of alanine, the other four residues being identical. Here we analyse the role of valine -14 in C/EBP-DNA complex formation. Starting from a C/EBP-GCN4 chimeric bZip peptide which displays C/EBP specificity, we systematically mutated position -14 of its basic region and characterized the DNA binding specificities of the 20 possible different peptides by gel mobility shift assays with various target sites. We present evidence that valine -14 of C/EBP interacts more strongly with thymine 2 than with cytosine 1' of the C/EBP binding site, unlike the corresponding alanine -14 of GCN4, which exclusively contacts thymine 1' of the GCN4 binding sites.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Koldin B,Suckow M,Seydel A,von Wilcken-Bergmann B,Müller-Hill Bdoi
10.1093/nar/23.20.4162subject
Has Abstractpub_date
1995-10-25 00:00:00pages
4162-9issue
20eissn
0305-1048issn
1362-4962pii
5c0098journal_volume
23pub_type
杂志文章abstract::G-quadruplexes are dynamic structures folded in G-rich single-stranded DNA regions. These structures have been recognized as a potential nucleic acid based mechanism for regulating multiple cellular processes such as replication, transcription and genomic maintenance. So far, their transcriptional role in vivo during ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw011
更新日期:2016-05-19 00:00:00
abstract::The chemical reactivity of matched T and C bases to osmium tetroxide and hydroxylamine near mismatched and unmatched bases in a heteroduplex between two strands of DNA with multiple differences was examined. Data was available for matched bases one or two positions away from 24 mismatches. Reactive bases were found ne...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4223
更新日期:1989-06-12 00:00:00
abstract:T:Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄- GAG CA-3΄ or 5΄- GAG CA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx057
更新日期:2017-03-17 00:00:00
abstract::PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.22.10669
更新日期:1988-11-25 00:00:00
abstract::A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.4.689
更新日期:1995-02-25 00:00:00
abstract::The design of a family shuffling strategy (CLERY: Combinatorial Libraries Enhanced by Recombination in Yeast) associating PCR-based and in vivo recombination and expression in yeast is described. This strategy was tested using human cytochrome P450 CYP1A1 and CYP1A2 as templates, which share 74% nucleotide sequence id...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.20.e88
更新日期:2000-10-15 00:00:00
abstract::The Mouse Genome Database (MGD) (http://www.informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and oth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1225
更新日期:2014-01-01 00:00:00
abstract::DNA polymerases of the A and B families, and reverse transcriptases, share a common mechanism for preventing incorporation of ribonucleotides: a highly conserved active site residue obstructing the position that would be occupied by a 2' hydroxyl group on the incoming nucleotide. In the family Y (lesion bypass) polyme...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg417
更新日期:2003-07-15 00:00:00
abstract::A repeated sequence element which is located about 200 nucleotides upstream from the protein-coding portion of the muscle actin gene (probably within a large 5' intron) in the genome of the sea urchin, Strongylocentrotus purpuratus has been characterized, and shown to contain the sequence features which indicate that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.4.1431
更新日期:1988-02-25 00:00:00
abstract::SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz528
更新日期:2019-09-05 00:00:00
abstract::Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks742
更新日期:2012-10-01 00:00:00
abstract::In apurinic acid, a single-stranded polydeoxyribonucleotide easily obtained upon depurination of DNA, the proton resonances arising from thymine and cytosine are readily observable in aqueous solution of 25 degrees C. Two methyl thymine resonances, centered at 1.88 ppm and separated by 0.045 ppm, are observed. We attr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.8.999
更新日期:1974-08-01 00:00:00
abstract::Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of the phosphates of the DNA backbone. Whereas the phosphates of the pyrimidine strand are at least as accessible as in dou...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2735
更新日期:1992-06-11 00:00:00
abstract::Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng066
更新日期:2003-06-01 00:00:00
abstract::We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are carried out simultaneously in the reaction chamber: on or within gel elements, and in bulk solution over the gel element array. M...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh184
更新日期:2005-01-20 00:00:00
abstract::Various strategies employed in genomic DNA cloning by subtractive hybridization have been examined by computer simulations, with the comparison between the predictions and the published results. The result shows that the efficiency of target sequence enrichment and the sensitivity to experimental conditions depend str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.6.1440
更新日期:1998-03-15 00:00:00
abstract::A screening for human proteins capable of interacting with influenza virus NS1 has been carried out using the two-hybrid genetic trap in yeast. A cDNA corresponding to the human homologue of Drosophila melanogaster Staufen protein (hStaufen) was isolated that fulfilled all genetic controls of the two-hybrid protocol. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.11.2241
更新日期:1999-06-01 00:00:00
abstract::Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1187
更新日期:2012-01-01 00:00:00
abstract::With discovery of diverse roles for RNA, its centrality in cellular functions has become increasingly apparent. A number of algorithms have been developed to predict RNA secondary structure. Their performance has been benchmarked by comparing structure predictions to reference secondary structures. Generally, algorith...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1081
更新日期:2012-02-01 00:00:00
abstract::Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1253
更新日期:2014-12-16 00:00:00
abstract::The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigated by Me3 psoralen photoreaction of mitochondria isolated from embryos. After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.4.1991
更新日期:1984-02-24 00:00:00
abstract::SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg535
更新日期:2003-07-01 00:00:00
abstract::Circular DNA can arise from all parts of eukaryotic chromosomes. In yeast, circular ribosomal DNA (rDNA) accumulates dramatically as cells age, however little is known about the accumulation of other chromosome-derived circles or the contribution of such circles to genetic variation in aged cells. We profiled circular...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa545
更新日期:2020-08-20 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::Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1198
更新日期:2020-12-16 00:00:00
abstract::Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.24.5609
更新日期:1998-12-15 00:00:00
abstract::We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.4.1835
更新日期:1987-02-25 00:00:00
abstract::DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, whic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks229
更新日期:2012-07-01 00:00:00
abstract::Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh159
更新日期:2004-01-09 00:00:00
abstract::Pre-mRNA splicing is catalyzed by the spliceosome, a multi-megadalton ribonucleoprotein machine. Previous work from our laboratory revealed the splicing factor SRSF1 as a regulator of the SUMO pathway, leading us to explore a connection between this pathway and the splicing machinery. We show here that addition of a r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx213
更新日期:2017-06-20 00:00:00