The miniF plasmid C protein: sequence, purification and DNA binding.


:The C (pifC) protein of miniF represses transcription of its own gene by binding to the pif operator (pifO); it is also needed for replication initiated from the miniF primary origin (ori-1). We have determined the nucleotide sequence of the C gene. The gene has been inserted into an expression vector under Ptrp control where it is expressed at high levels. The C protein has been purified from cells carrying the Ptrp-C plasmid, and a preliminary study of C protein-DNA binding properties has been carried out. C protein binds strongly to pifO, and weakly to sequences in the ori-1 region.


Nucleic Acids Res


Nucleic acids research


Caughey PA,de Feyter R,Lane HE




Has Abstract


1986-12-22 00:00:00












  • Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin.

    abstract::Invariance of temporal order of genome replication in eukaryotic cells and its correlation with gene activity has been well-documented. However, recent data suggest a relax control of replication timing. To evaluate replication schedule accuracy, we detailed the replicational organization of the developmentally regula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bénard M,Maric C,Pierron G

    更新日期:2007-01-01 00:00:00

  • PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.

    abstract::The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Böhlke K,Pisani FM,Vorgias CE,Frey B,Sobek H,Rossi M,Antranikian G

    更新日期:2000-10-15 00:00:00

  • The TP53 website: an integrative resource centre for the TP53 mutation database and TP53 mutant analysis.

    abstract::A novel resource centre for TP53 mutations and mutants has been developed ( TP53 gene dysfunction can be found in the majority of human cancer types. The potential use of TP53 mutation as a biomarker for clinical studies or exposome analysis has led to the publication of thousands of reports describing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Leroy B,Fournier JL,Ishioka C,Monti P,Inga A,Fronza G,Soussi T

    更新日期:2013-01-01 00:00:00

  • Temporal regulation of the Mus81-Mms4 endonuclease ensures cell survival under conditions of DNA damage.

    abstract::The structure-specific Mus81-Eme1/Mms4 endonuclease contributes importantly to DNA repair and genome integrity maintenance. Here, using budding yeast, we have studied its function and regulation during the cellular response to DNA damage and show that this endonuclease is necessary for successful chromosome replicatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saugar I,Vázquez MV,Gallo-Fernández M,Ortiz-Bazán MÁ,Segurado M,Calzada A,Tercero JA

    更新日期:2013-10-01 00:00:00

  • The human insulin receptor mRNA contains a functional internal ribosome entry segment.

    abstract::Regulation of mRNA translation is an important mechanism determining the level of expression of proteins in eukaryotic cells. Translation is most commonly initiated by cap-dependent scanning, but many eukaryotic mRNAs contain internal ribosome entry segments (IRESs), providing an alternative means of initiation capabl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Spriggs KA,Cobbold LC,Ridley SH,Coldwell M,Bottley A,Bushell M,Willis AE,Siddle K

    更新日期:2009-09-01 00:00:00

  • Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.

    abstract::The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wu W,Stupi BP,Litosh VA,Mansouri D,Farley D,Morris S,Metzker S,Metzker ML

    更新日期:2007-01-01 00:00:00

  • Recognition of native DNA methylation by the PvuII restriction endonuclease.

    abstract::Recognizing the methylation status of specific DNA sequences is central to the function of many systems in eukaryotes and prokaryotes. Restriction-modification systems have to distinguish between 'self' and 'non-self' DNA and depend on the inability of restriction endonucleases to cleave their DNA substrates when the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rice MR,Blumenthal RM

    更新日期:2000-08-15 00:00:00

  • A missense mutation in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase suppresses a mitochondrial tRNA(Asp) mutation.

    abstract::The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chiang CS,Liaw GJ

    更新日期:2000-04-01 00:00:00

  • Analysis of recombination in mammalian cells using SV40 genome segments having homologous overlapping termini.

    abstract::Segments of SV40 DNA having homologous overlapping termini recombine to produce viable genomes in monkey cells. Frequencies of recombination on either side of a deletion marker are non-random; replication and palindromes do not appear to be essential. Since recombination involves host enzymes, a suitable system has be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Upcroft P,Carter B,Kidson C

    更新日期:1980-06-25 00:00:00

  • Quantitation of DNA double-strand break resection intermediates in human cells.

    abstract::5' strand resection at DNA double strand breaks (DSBs) is critical for homologous recombination (HR) and genomic stability. Here we develop a novel method to quantitatively measure single-stranded DNA intermediates in human cells and find that the 5' strand at endonuclease-generated break sites is resected up to 3.5 k...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhou Y,Caron P,Legube G,Paull TT

    更新日期:2014-02-01 00:00:00

  • Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping.

    abstract::Many enzymes acting on DNA require Mg(2+) ions not only for catalysis but also to bind DNA. Binding studies often employ Ca(2+) as a substitute for Mg(2+), to promote DNA binding whilst disallowing catalysis. The SfiI endonuclease requires divalent metal ions to bind DNA but, in contrast to many systems where Ca(2+) m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bellamy SR,Kovacheva YS,Zulkipli IH,Halford SE

    更新日期:2009-09-01 00:00:00

  • Regulation of the Oct-4 gene by nuclear receptors.

    abstract::To unravel the network of transcription factors established during development it is important to understand how genes specifically expressed during embryogenesis are regulated. Oct-4 is a transcription factor whose expression is associated with an undifferentiated cell phenotype in the early mouse embryo and is downr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sylvester I,Schöler HR

    更新日期:1994-03-25 00:00:00

  • The germ line limited M element of Tetrahymena is targeted for elimination from the somatic genome by a homology-dependent mechanism.

    abstract::A RNA interference (RNAi) like mechanism is involved in elimination of thousands of DNA segments from the developing somatic macronucleus of Tetrahymena, yet how specific internal eliminated sequences (IESs) are recognized remains to be fully elucidated. To define requirements for DNA rearrangement, we performed mutag...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kowalczyk CA,Anderson AM,Arce-Larreta M,Chalker DL

    更新日期:2006-01-01 00:00:00

  • Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.

    abstract::The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mignon P,Loverix S,Steyaert J,Geerlings P

    更新日期:2005-03-23 00:00:00

  • AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species.

    abstract::Arabidopsis thaliana is a reference plant that has been studied intensively for several decades. Recent advances in high-throughput experimental technology have enabled the generation of an unprecedented amount of data from A. thaliana, which has facilitated data-driven approaches to unravel the genetic organization o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lee T,Yang S,Kim E,Ko Y,Hwang S,Shin J,Shim JE,Shim H,Kim H,Kim C,Lee I

    更新日期:2015-01-01 00:00:00

  • Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules.

    abstract::Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep)...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pastrana CL,Carrasco C,Akhtar P,Leuba SH,Khan SA,Moreno-Herrero F

    更新日期:2016-10-14 00:00:00

  • Structure of a (3+1) hybrid G-quadruplex in the PARP1 promoter.

    abstract::Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sengar A,Vandana JJ,Chambers VS,Di Antonio M,Winnerdy FR,Balasubramanian S,Phan AT

    更新日期:2019-02-20 00:00:00

  • The Reactome pathway knowledgebase.

    abstract::Reactome ( 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


    authors: Croft D,Mundo AF,Haw R,Milacic M,Weiser J,Wu G,Caudy M,Garapati P,Gillespie M,Kamdar MR,Jassal B,Jupe S,Matthews L,May B,Palatnik S,Rothfels K,Shamovsky V,Song H,Williams M,Birney E,Hermjakob H,Stein L,D'Eusta

    更新日期:2014-01-01 00:00:00

  • Phosphorylated (pT371)TRF1 is recruited to sites of DNA damage to facilitate homologous recombination and checkpoint activation.

    abstract::TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

    更新日期:2013-12-01 00:00:00

  • Nucleotide sequence of the genes III, VI and I of bacteriophage M13.

    abstract::A DNA region of 2750 base pairs encompassing the genes III, VI and I of bacteriophage M13 has been sequenced by the Maxam-Gilbert procedure. By establishing the nucleotide changes introduced by several amber mutations, the coding region and the regulatory signals of each gene have been deduced. The genes appear to spa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: van Wezenbeek P,Schoenmakers JG

    更新日期:1979-06-25 00:00:00

  • Quantitation of RNA editing substrates, products and potential intermediates: implications for developmental regulation.

    abstract::Kinetoplast mitochondrial RNA editing is the developmentally regulated post-transcriptional process of uridine insertion and deletion in mRNAs directed by short guide RNAs (gRNAs), which creates functional mRNAs. Two mechanisms are proposed: transesterification which predicts gRNA/mRNA chimeric intermediates, and enzy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Riley GR,Myler PJ,Stuart K

    更新日期:1995-02-25 00:00:00

  • Upstream box/TATA box order is the major determinant of the direction of transcription.

    abstract::Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of tran...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Xu LC,Thali M,Schaffner W

    更新日期:1991-12-25 00:00:00

  • The production of hybrid Ty:IFN virus-like particles in yeast.

    abstract::The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Malim MH,Adams SE,Gull K,Kingsman AJ,Kingsman SM

    更新日期:1987-09-25 00:00:00

  • Reversal of methylation-mediated repression with short-chain fatty acids: evidence for an additional mechanism to histone deacetylation.

    abstract::We have constructed a stable cell line, human embryonal kidney 293M+, containing a lacZ reporter gene controlled by an in vitro methylated hormone-responsive enhancer. Methylation of the enhancer-promoter abolishes lacZ expression controlled by ponasterone A (an analogue of ecdysone). Ponasterone A-induced expression ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Benjamin D,Jost JP

    更新日期:2001-09-01 00:00:00

  • Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape.

    abstract::The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pupov D,Kuzin I,Bass I,Kulbachinskiy A

    更新日期:2014-04-01 00:00:00

  • Cyber-T web server: differential analysis of high-throughput data.

    abstract::The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kayala MA,Baldi P

    更新日期:2012-07-01 00:00:00

  • Structural insights into NusG regulating transcription elongation.

    abstract::NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu B,Steitz TA

    更新日期:2017-01-25 00:00:00

  • Synergistic effects of ATP and RNA binding to human DEAD-box protein DDX1.

    abstract::RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kellner JN,Reinstein J,Meinhart A

    更新日期:2015-03-11 00:00:00

  • Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

    abstract::Interactive Tree Of Life ( is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Letunic I,Bork P

    更新日期:2011-07-01 00:00:00

  • Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events.

    abstract::Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gellert P,Teranishi M,Jenniches K,De Gaspari P,John D,Kreymborg Kg,Braun T,Uchida S

    更新日期:2012-03-01 00:00:00