Escherichia coli single-stranded DNA binding protein stimulates the DNA deoxyribophosphodiesterase activity of exonuclease I.

Abstract:

:The E. coli single-stranded binding protein (SSB) has been demonstrated in vitro to be involved in a number of replicative, DNA renaturation, and protective functions. It was shown previously that SSB can interact with exonuclease I to stimulate the hydrolysis of single-stranded DNA. We demonstrate here that E. coli SSB can also enhance the DNA deoxyribophosphodiesterase (dRpase) activity of exonuclease I by stimulating the release of 2-deoxyribose-5-phosphate from a DNA substrate containing AP endonuclease-incised AP sites, and the release of 4-hydroxy-2-pentenal-5-phosphate from a DNA substrate containing AP lyase-incised AP sites. E. coli SSB and exonuclease I form a protein complex as demonstrated by Superose 12 gel filtration chromatography. These results suggest that SSB may have an important role in the DNA base excision repair pathway.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Sandigursky M,Franklin WA

doi

10.1093/nar/22.2.247

subject

Has Abstract

pub_date

1994-01-25 00:00:00

pages

247-50

issue

2

eissn

0305-1048

issn

1362-4962

journal_volume

22

pub_type

杂志文章
  • Transcription regulation of caspase-1 by R393 of HIPPI and its molecular partner HIP-1.

    abstract::Earlier we have shown that exogenous expression of HIPPI, a molecular partner of Huntingtin interacting protein HIP-1, induces apoptosis and increases expression of caspases-1, -8 and -10 in HeLa and Neuro2A cells. The C-terminal pseudo death effector domain of HIPPI (pDED-HIPPI) specifically interacts with the putati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1011

    authors: Banerjee M,Datta M,Majumder P,Mukhopadhyay D,Bhattacharyya NP

    更新日期:2010-01-01 00:00:00

  • Deaminase-independent inhibition of HIV-1 reverse transcription by APOBEC3G.

    abstract::APOBEC3G (A3G), a host protein that inhibits HIV-1 reverse transcription and replication in the absence of Vif, displays cytidine deaminase and single-stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity, whic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm750

    authors: Iwatani Y,Chan DS,Wang F,Stewart-Maynard K,Sugiura W,Gronenborn AM,Rouzina I,Williams MC,Musier-Forsyth K,Levin JG

    更新日期:2007-01-01 00:00:00

  • Unlocking hidden genomic sequence.

    abstract::Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnh022

    authors: Keith JM,Cochran DA,Lala GH,Adams P,Bryant D,Mitchelson KR

    更新日期:2004-02-18 00:00:00

  • In vivo footprinting and functional analysis of the human c-sis/PDGF B gene promoter provides evidence for two binding sites for transcriptional activators.

    abstract::By in vivo DMS footprint and reporter gene analyses we identified two transcription factor binding sites in the human c-sis/PDGF B gene promoter. The low basal activity of the PDGF B promoter in HeLa and undifferentiated K562 cells, which express low PDGF B mRNA levels, and in PC3 cells, which express a high PDGF B mR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.7.1119

    authors: Dirks RP,Jansen HJ,van Gerven B,Onnekink C,Bloemers HP

    更新日期:1995-04-11 00:00:00

  • The interaction of ribonuclease T 1 with DNA.

    abstract::The interaction of RNase T1 with calf thymus DNA was studied using uv difference spectroscopy and the effect of the enzyme on DNA melting. There was no indication of RNase T1 binding with native DNA. A prominent difference spectrum for RNase T1 binding with denatured DNA (d-DNA) was observed at pH 5, 25 degrees and lo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.1.11

    authors: Walz FG,Biddlecome S,Hooverman L

    更新日期:1975-01-01 00:00:00

  • Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression.

    abstract::Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnh104

    authors: Mitta B,Weber CC,Rimann M,Fussenegger M

    更新日期:2004-07-16 00:00:00

  • Replication of proto-oncogenes early during the S phase in mammalian cell lines.

    abstract::Members of several classes of proto-oncogenes replicate during the first third of S-phase in two human (K562 erythroleukemia and HeLa), one Chinese hamster (CHO) and eight mouse cell lines. These cell lines exhibit a variety of specialized functions characteristic of pre-B and B cells, T cells and erythroid cells. The...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.1.87

    authors: Iqbal MA,Chinsky J,Didamo V,Schildkraut CL

    更新日期:1987-01-12 00:00:00

  • Benzpyrene groups bind preferentially to the DNA of active chromatin in human lung cells.

    abstract::The cells of the bronchial epithelium of man are targets for benzo(a)pyrene carcinogenesis. When cultures of these cells, and of non-target fibroblasts, are exposed to [3H]-benzo(a)pyrene, we find that the epithelial cells metabolise and bind to DNA far greater amounts of benzpyrene than do fibroblasts. By analysis of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.5.1547

    authors: Arrand JE,Murray AM

    更新日期:1982-03-11 00:00:00

  • The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

    abstract::We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl959

    authors: Greene LH,Lewis TE,Addou S,Cuff A,Dallman T,Dibley M,Redfern O,Pearl F,Nambudiry R,Reid A,Sillitoe I,Yeats C,Thornton JM,Orengo CA

    更新日期:2007-01-01 00:00:00

  • Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays.

    abstract::Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally deter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg757

    authors: Pe'er I,Arbili N,Liu Y,Enck C,Gelfand CA,Shamir R

    更新日期:2003-10-01 00:00:00

  • Fine structure mapping of an avian tumor virus RNA by immunoelectron microscopy.

    abstract::The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.19.4485

    authors: Castleman H,Meredith RD,Erlanger BF

    更新日期:1980-10-10 00:00:00

  • A mathematical model and a computerized simulation of PCR using complex templates.

    abstract::A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.18.3538

    authors: Rubin E,Levy AA

    更新日期:1996-09-15 00:00:00

  • In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important.

    abstract::Small interfering RNAs (siRNAs) are promising new active compounds in gene medicine but the induction of non-specific immune responses following their delivery continues to be a serious problem. With the purpose of avoiding such effects chemically modified siRNAs are tested in screening assay but often only examining ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks033

    authors: Schyth BD,Bramsen JB,Pakula MM,Larashati S,Kjems J,Wengel J,Lorenzen N

    更新日期:2012-05-01 00:00:00

  • Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.

    abstract::Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw077

    authors: Voltz K,Léonard J,Touceda PT,Conyard J,Chaker Z,Dejaegere A,Godet J,Mély Y,Haacke S,Stote RH

    更新日期:2016-04-20 00:00:00

  • Two step binding of HIV-1 reverse transcriptase to nucleic acid substrates.

    abstract::The interactions of HIV-1 reverse transcriptase (HIV-1 RT) with a synthetic 53/19-mer DNA substrate was investigated. For this template-primer HIV-1 RT displayed a Km value of 20 nM. The 53/19-mer competitively inhibited DNA synthesis performed on poly (rC).oligo(dG) with Ki value of 260 nM. This corresponded well to ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.17.3943

    authors: Kruhøffer M,Urbanke C,Grosse F

    更新日期:1993-08-25 00:00:00

  • DNA repair of pyrimidine dimers and 6-4 photoproducts in the ribosomal DNA.

    abstract::The nucleolus is a unique structural component of interphase nuclei where the ribosomal genes, trans-cribed by RNA polymerase I (RNA pol I), are organized. In the present study, the repair of UV-induced photolesions was investigated in the ribosomal DNA (rDNA) in relation to RNA pol I transcription. We used hamster ce...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.12.2511

    authors: Balajee AS,May A,Bohr VA

    更新日期:1999-06-15 00:00:00

  • Nucleotide excision repair efficiency in quiescent human fibroblasts is modulated by circadian clock.

    abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv081

    authors: Bee L,Marini S,Pontarin G,Ferraro P,Costa R,Albrecht U,Celotti L

    更新日期:2015-02-27 00:00:00

  • Invariant amino acids essential for decoding function of polypeptide release factor eRF1.

    abstract::In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki927

    authors: Kolosov P,Frolova L,Seit-Nebi A,Dubovaya V,Kononenko A,Oparina N,Justesen J,Efimov A,Kisselev L

    更新日期:2005-11-10 00:00:00

  • ChIP-Enrich: gene set enrichment testing for ChIP-seq data.

    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

    authors: Welch RP,Lee C,Imbriano PM,Patil S,Weymouth TE,Smith RA,Scott LJ,Sartor MA

    更新日期:2014-07-01 00:00:00

  • The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

    abstract::The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map po...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm956

    authors: Sprague J,Bayraktaroglu L,Bradford Y,Conlin T,Dunn N,Fashena D,Frazer K,Haendel M,Howe DG,Knight J,Mani P,Moxon SA,Pich C,Ramachandran S,Schaper K,Segerdell E,Shao X,Singer A,Song P,Sprunger B,Van Slyke CE,Weste

    更新日期:2008-01-01 00:00:00

  • Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications.

    abstract::RNA molecules of > 20 nucleotides have been the focus of numerous recent NMR structural studies. Several investigators have used the UNCG family of hairpins to ensure proper folding. We show that th UUCG hairpin has a minimum requirement of a two base-pair stem. Hairpins with a CG loop closing base pair and an initial...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.15.3056

    authors: Molinaro M,Tinoco I Jr

    更新日期:1995-08-11 00:00:00

  • Specific isolation of 3'-terminal exons of human genes by exon trapping.

    abstract::Exon trapping is a method to functionally clone expressed sequences from genomic DNA. We have previously developed the vector system pETV-SD2, which contains only a splice donor site (SD) followed by a LacZ gene, allowing trapping of internal exons of human genes by blue-white selection. We now describe the adaptation...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.20.4148

    authors: Datson NA,Duyk GM,Van Ommen JB,Den Dunnen JT

    更新日期:1994-10-11 00:00:00

  • Molecular dynamics simulations of sarcin-ricin rRNA motif.

    abstract::Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj470

    authors: Spacková N,Sponer J

    更新日期:2006-02-02 00:00:00

  • Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites.

    abstract::MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky306

    authors: Sheng P,Fields C,Aadland K,Wei T,Kolaczkowski O,Gu T,Kolaczkowski B,Xie M

    更新日期:2018-06-20 00:00:00

  • Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions.

    abstract::Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz368

    authors: Roy AA,Dhawanjewar AS,Sharma P,Singh G,Madhusudhan MS

    更新日期:2019-07-02 00:00:00

  • Tumor suppressor p53: from engaging DNA to target gene regulation.

    abstract::The p53 transcription factor confers its potent tumor suppressor functions primarily through the regulation of a large network of target genes. The recent explosion of next generation sequencing protocols has enabled the study of the p53 gene regulatory network (GRN) and underlying mechanisms at an unprecedented depth...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa666

    authors: Sammons MA,Nguyen TT,McDade SS,Fischer M

    更新日期:2020-09-18 00:00:00

  • High resolution deletion breakpoint mapping in the DMD gene by whole cosmid hybridization.

    abstract::The locus DXS269 (P20) defines a deletion hotspot in the distal part of the Duchenne Muscular Dystrophy gene. We have cloned over 90 kilobase-pairs of genomic DNA from this region in overlapping cosmids. The use of whole cosmids as probes in a competitive DNA hybridization analysis proves a fast and convenient method ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.14.5611

    authors: Blonden LA,den Dunnen JT,van Paassen HM,Wapenaar MC,Grootscholten PM,Ginjaar HB,Bakker E,Pearson PL,van Ommen GJ

    更新日期:1989-07-25 00:00:00

  • The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells.

    abstract::Previous studies have established a critical role of both TFIIB and RNA polymerase II (RNAPII) in start site selection in the yeast Saccharomyces cerevisiae. However, it remains unclear how the TFIIB-RNAPII interaction impacts on this process since such an interaction can potentially influence both preinitiation compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf422

    authors: Zhang DY,Carson DJ,Ma J

    更新日期:2002-07-15 00:00:00

  • CAG*CTG repeat instability in cultured human astrocytes.

    abstract::Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl614

    authors: Farrell BT,Lahue RS

    更新日期:2006-01-01 00:00:00

  • Transcription regulation in vitro by an E. coli promoter containing a DNA cruciform in the '-35' region.

    abstract::A promoter with the potential to adopt a 50 basepair (bp) cruciform spanning from -19 to -69 has been constructed in the plasmid pBR322 tetracycline resistance gene (tet) by forming an inverted repeat from '-35' sequences. Compared to a control promoter, the sequence of this cruciform promoter differs only by a 22 bp ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.14.5537

    authors: Horwitz MS

    更新日期:1989-07-25 00:00:00