Identification of proteins interacting with newly replicated DNA in SV40-infected cells by UV-induced DNA-protein cross-linking.

Abstract:

:Protein species interacting with newly replicated DNA were analyzed using a photo cross-linking technique. Nascent DNA was labeled in vitro with [alpha-32P]dCTP and BrdUTP in SV40-infected CV-1 cells made permeable with saponin. The labeled cells were then irradiated with UV light (254 nm) and were treated extensively with DNase I. Proteins with radioactive DNA tags were separated by SDS-PAGE and visualized by autoradiography. Among 10-15 proteins which were cross-linked, the proteins with apparent molecular weights of 16.5 K, 44 K, 82 K and those in the 94-140 K region appeared to be associated with newly replicated SV40 DNA. A pulse-chase experiment showed that the 82 K and 94-140 K proteins interacted with new DNA in a relatively localized region close to the replication fork. The 44 K protein was identified as the major viral capsid protein, VP1, using antiserum to SV40 capsid proteins. It was suggested that VP1 binds to nascent DNA shortly after DNA synthesis and migrates into chromatin maturation regions.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Tsutsui K,Watanabe S,Katagiri M,Oda T

doi

10.1093/nar/11.14.4793

subject

Has Abstract

pub_date

1983-07-25 00:00:00

pages

4793-807

issue

14

eissn

0305-1048

issn

1362-4962

journal_volume

11

pub_type

杂志文章
  • PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

    abstract::The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1089

    authors: Urban M,Cuzick A,Rutherford K,Irvine A,Pedro H,Pant R,Sadanadan V,Khamari L,Billal S,Mohanty S,Hammond-Kosack KE

    更新日期:2017-01-04 00:00:00

  • A search for base analogs to enhance third-strand binding to 'inverted' target base pairs of triplexes in the pyrimidine/parallel motif.

    abstract::Eight base analogs were tested as third strand residues in otherwise homopyrimidine strands opposite each of the 'direct' (A.T and G.C) and 'inverted' (T.A and C.G) Watson-Crick base pairs, using UV melting profiles to assess triplex stability. The target duplexes contained 20 A.T base pairs and a central test base pa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.23.4632

    authors: Amosova OA,Fresco JR

    更新日期:1999-12-01 00:00:00

  • Complete nucleotide sequence of the Escherichia coli recB gene.

    abstract::The complete nucleotide sequence of the Escherichia coli recB gene which encodes a subunit of the ATP-dependent DNase, Exonuclease V, has been determined. The proposed coding region for the RecB protein is 3543 nucleotides long and would encode a polypeptide of 1180 amino acids with a calculated molecular weight of 13...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.21.8573

    authors: Finch PW,Storey A,Chapman KE,Brown K,Hickson ID,Emmerson PT

    更新日期:1986-11-11 00:00:00

  • Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines.

    abstract::By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky209

    authors: Dong Z,Yu J,Li H,Huang W,Xu L,Zhao Y,Zhang T,Xu W,Jiang J,Su Z,Jin W

    更新日期:2018-06-01 00:00:00

  • Antisense-induced ribosomal frameshifting.

    abstract::Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl531

    authors: Henderson CM,Anderson CB,Howard MT

    更新日期:2006-01-01 00:00:00

  • The active site residue Valine 867 in human telomerase reverse transcriptase influences nucleotide incorporation and fidelity.

    abstract::Human telomerase reverse transcriptase (hTERT), the catalytic subunit of human telomerase, contains conserved motifs common to retroviral reverse transcriptases and telomerases. Within the C motif of hTERT is the Leu866-Val867-Asp868-Asp869 tetrapeptide that includes a catalytically essential aspartate dyad. Site-dire...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm002

    authors: Drosopoulos WC,Prasad VR

    更新日期:2007-01-01 00:00:00

  • 2'-O-methyl-modified phosphorothioate antisense oligonucleotides have reduced non-specific effects in vitro.

    abstract::Antisense oligodeoxynucleotides (ODNs) have biological activity in treating various forms of cancer. The antisense effects of two types of 20mer ODNs, phosphorothioate-modified ODNs (S-ODNs) and S-ODNs with 12 2'-O-methyl groups (Me-S-ODNs), targeted to sites 109 and 277 of bcl-2 mRNA, were compared. Both types were a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh516

    authors: Yoo BH,Bochkareva E,Bochkarev A,Mou TC,Gray DM

    更新日期:2004-04-02 00:00:00

  • Y box-binding protein-1 binds preferentially to single-stranded nucleic acids and exhibits 3'-->5' exonuclease activity.

    abstract::We have previously shown that Y box-binding protein-1 (YB-1) binds preferentially to cisplatin-modified Y box sequences. Based on structural and biochemical data, we predicted that this protein binds single-stranded nucleic acids. In the present study we confirmed the prediction and also discovered some unexpected fun...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.5.1200

    authors: Izumi H,Imamura T,Nagatani G,Ise T,Murakami T,Uramoto H,Torigoe T,Ishiguchi H,Yoshida Y,Nomoto M,Okamoto T,Uchiumi T,Kuwano M,Funa K,Kohno K

    更新日期:2001-03-01 00:00:00

  • The nature of the interaction of nucleosomes with a eukaryotic RNA polymerase II.

    abstract::The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.2.377

    authors: Lilley DM,Jacobs MF,Houghton M

    更新日期:1979-09-25 00:00:00

  • Two zinc finger proteins from Xenopus laevis bind the same region of 5S RNA but with different nuclease protection patterns.

    abstract::Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.8.1797

    authors: Sands MS,Bogenhagen DF

    更新日期:1991-04-25 00:00:00

  • Multiple isoform recovery (MIR)-PCR: a simple method for the isolation of related mRNA isoforms.

    abstract::We present a rapid and efficient method for the detection of related transcripts with different expression levels. This approach combines the rapid amplification of cDNA ends (RACE) method with a cDNA subtractive technique. The strategy is based on successive subtractions of prevalent isoforms resulting in enrichment ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.8.2031

    authors: Fagotti A,Gabbiani G,Pascolini R,Neuville P

    更新日期:1998-04-15 00:00:00

  • Sequence preference and structural heterogeneity of BZ junctions.

    abstract::BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We dete...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky784

    authors: Kim D,Hur J,Han JH,Ha SC,Shin D,Lee S,Park S,Sugiyama H,Kim KK

    更新日期:2018-11-02 00:00:00

  • Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC.

    abstract::Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular microRNAs. In addition, specific siRNA sequences can potentially hinder incorporation of other siRNAs when used in a co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm543

    authors: Castanotto D,Sakurai K,Lingeman R,Li H,Shively L,Aagaard L,Soifer H,Gatignol A,Riggs A,Rossi JJ

    更新日期:2007-01-01 00:00:00

  • Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs.

    abstract::siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq961

    authors: Vaish N,Chen F,Seth S,Fosnaugh K,Liu Y,Adami R,Brown T,Chen Y,Harvie P,Johns R,Severson G,Granger B,Charmley P,Houston M,Templin MV,Polisky B

    更新日期:2011-03-01 00:00:00

  • Human N-ras: cDNA cloning and gene structure.

    abstract::The structure and organisation of the human N-ras gene has been determined by analysing cDNA clones derived from the two main mRNA transcripts. One clone in particular is 4.1 Kb long and originates from the larger (4.3 Kb) message. Sequence analysis of this clone has revealed that the N-ras gene consists of seven exon...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.14.5255

    authors: Hall A,Brown R

    更新日期:1985-07-25 00:00:00

  • Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.

    abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt713

    authors: El Omari K,Meier C,Kainov D,Sutton G,Grimes JM,Poranen MM,Bamford DH,Tuma R,Stuart DI,Mancini EJ

    更新日期:2013-11-01 00:00:00

  • Transcription in vivo directed by consensus sequences of E.coli promoters: their context heavily affects efficiencies and start sites.

    abstract::We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer l...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.5.1137

    authors: Jacquet MA,Reiss C

    更新日期:1990-03-11 00:00:00

  • A group II intron in the Neurospora mitochondrial coI gene: nucleotide sequence and implications for splicing and molecular evolution.

    abstract::The temperature-sensitive Neurospora nuclear mutant cyt18-1 is deficient in splicing many Group I mitochondrial introns when grown at its non-permissive temperature; however, splicing of intron 1 in the coI gene of the Adiopodoume (formerly called North Africa) strain is unaffected (R.A. Collins and A.M. Lambowitz, J....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.22.9087

    authors: Field DJ,Sommerfield A,Saville BJ,Collins RA

    更新日期:1989-11-25 00:00:00

  • A conserved heptamer upstream of the IgH promoter region octamer can be the site of a coordinate protein-DNA interaction.

    abstract::Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.12.5503

    authors: Landolfi NF,Yin XM,Capra JD,Tucker PW

    更新日期:1988-06-24 00:00:00

  • Physical properties of inner histone-DNA complexes.

    abstract::Chicken-erythrocyte inner histone tetramer has been complexed with several natural and synthetic DNA duplexes by salt-gradient dialysis at various protein/DNA ratios. The resulting complexes, in low-ionic-strength buffer, have been examined by electron microscopy, circular dichroism, and thermal denaturation. Electron...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.10.3603

    authors: Bryan PN,Wright EB,Hsie MH,Olins AL,Olins DE

    更新日期:1978-10-01 00:00:00

  • The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.

    abstract::We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz905

    authors: Dans PD,Balaceanu A,Pasi M,Patelli AS,Petkevičiūtė D,Walther J,Hospital A,Bayarri G,Lavery R,Maddocks JH,Orozco M

    更新日期:2019-12-02 00:00:00

  • Specific ribosomal RNA recognition by a fragment of E. coli ribosomal protein S4 missing the C-terminal 36 amino acid residues.

    abstract::We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.17.6343

    authors: Changchien LM,Craven GR

    更新日期:1985-09-11 00:00:00

  • Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis.

    abstract::Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (-SCH(3)). Members of two of the four known subgroups of MTTases...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq364

    authors: Anton BP,Russell SP,Vertrees J,Kasif S,Raleigh EA,Limbach PA,Roberts RJ

    更新日期:2010-10-01 00:00:00

  • Genome engineering of isogenic human ES cells to model autism disorders.

    abstract::Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic suc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv164

    authors: Martinez RA,Stein JL,Krostag AR,Nelson AM,Marken JS,Menon V,May RC,Yao Z,Kaykas A,Geschwind DH,Grimley JS

    更新日期:2015-05-26 00:00:00

  • Discover 1: a new program to search for unusually represented DNA motifs.

    abstract::DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.22.5152

    authors: Valle G

    更新日期:1993-11-11 00:00:00

  • Evolutionarily conserved elements in the 5' untranslated region of beta globin mRNA mediate site-specific priming of a unique hairpin structure during cDNA synthesis.

    abstract::Generation of double-stranded cDNA during reverse transcription of a variety of mRNA molecules is well known to involve the formation of covalently linked antisense and sense strands in a hairpin configuration. In the present study we have examined the sequence of molecular events which occurs during cDNA synthesis fr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.24.5302

    authors: Volloch VZ,Schweitzer B,Rits S

    更新日期:1994-12-11 00:00:00

  • SplicePort--an interactive splice-site analysis tool.

    abstract::SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm407

    authors: Dogan RI,Getoor L,Wilbur WJ,Mount SM

    更新日期:2007-07-01 00:00:00

  • A new efficient gene disruption cassette for repeated use in budding yeast.

    abstract::The dominant kanr marker gene plays an important role in gene disruption experiments in budding yeast, as this marker can be used in a variety of yeast strains lacking the conventional yeast markers. We have developed a loxP-kanMX-loxP gene disruption cassette, which combines the advantages of the heterologous kanr ma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.13.2519

    authors: Güldener U,Heck S,Fielder T,Beinhauer J,Hegemann JH

    更新日期:1996-07-01 00:00:00

  • Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.

    abstract::The presence of a homing endonuclease gene (HEG) within a microbial intron or intein empowers the entire element with the ability to invade genomic targets. The persistence of a homing endonuclease lineage depends in part on conservation of its DNA target site. One such rDNA sequence has been invaded both in archaea a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn846

    authors: Nomura N,Nomura Y,Sussman D,Klein D,Stoddard BL

    更新日期:2008-12-01 00:00:00

  • Esc2 promotes telomere stability in response to DNA replication stress.

    abstract::Telomeric regions of the genome are inherently difficult-to-replicate due to their propensity to generate DNA secondary structures and form nucleoprotein complexes that can impede DNA replication fork progression. Precisely how cells respond to DNA replication stalling within a telomere remains poorly characterized, l...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz158

    authors: Jørgensen SW,Liberti SE,Larsen NB,Lisby M,Mankouri HW,Hickson ID

    更新日期:2019-05-21 00:00:00