Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA.


:We have purified to near homogeneity a novel nuclear protein from HeLa cells, that specifically binds to scaffold or matrix attachment region DNA elements (S/MAR DNA). The protein, designated SAF-B for scaffold attachment factor B, is an abundant component of chromatin, but not of the nuclear matrix and is expressed in all human tissues investigated. Antibodies against the purified protein were raised in rabbit and used to isolate the complete cDNA encoding SAF-B by immunoscreening. As predicted from the cDNA sequence, SAF-B contains 849 amino acids (96 696 Da), without significant homology to any known protein. SAF-B is rich in charged residues, leading to an aberrant migration on SDS gels, and has two putative bipartite nuclear localisation signals.


Nucleic Acids Res


Nucleic acids research


Renz A,Fackelmayer FO




Has Abstract


1996-03-01 00:00:00














  • Heat effects on DNA repair after ionising radiation: hyperthermia commonly increases the number of non-repaired double-strand breaks and structural rearrangements.

    abstract::After ionising radiation double-strand breaks (dsb) are lethal if not repaired or misrepaired. Cell killing is greatly enhanced by hyperthermia and it is questioned here whether heat not only affects dsb repair capacity but also fidelity in a chromosomal context. dsb repair experiments were designed so as to mainly sc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: El-Awady RA,Dikomey E,Dahm-Daphi J

    更新日期:2001-05-01 00:00:00

  • The right hand copy of the nopaline Ti-plasmid 25 bp repeat is required for tumour formation.

    abstract::At either end of the nopaline Ti-plasmid T-region resides a copy of a 25 bp repeated element. The normal T-DNA endpoint is 1 bp internal of the right copy, with the transcription initiation site of the nopaline synthase (nos) gene being approximately 300 bp away in the same direction. Here we describe results which de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shaw CH,Watson MD,Carter GH,Shaw CH

    更新日期:1984-08-10 00:00:00

  • ASD: a comprehensive database of allosteric proteins and modulators.

    abstract::Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang J

    更新日期:2011-01-01 00:00:00

  • Polynucleotides. XL. Synthesis and properties of poly 2'-azido-2'-deoxyadenylic acid.

    abstract::Poly 2'-azido-2'-deoxyadenylic acid (Poly Az) was synthesized from 2'-azido-2'-deoxyadenosine diphosphate by polynucleotide phosphorylase. Poly (Az) has U.V. absorption properties similar to poly (A) and hypochromicity of 40% at 0.1 M Na+ and neutrality. CD curve also resembled to that of poly (A), but has smaller ell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ikehara M,Fukui T,Kakiuchi N

    更新日期:1976-08-01 00:00:00

  • OpenTein: a database of digital whole-slide images of stem cell-derived teratomas.

    abstract::Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Park SJ,Komiyama Y,Suemori H,Umezawa A,Nakai K

    更新日期:2016-01-04 00:00:00

  • Conformation transitions of eukaryotic polyribosomes during multi-round translation.

    abstract::Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformation...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Afonina ZA,Myasnikov AG,Shirokov VA,Klaholz BP,Spirin AS

    更新日期:2015-01-01 00:00:00

  • Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering.

    abstract::DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable 'scar' sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinato...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Taylor GM,Mordaka PM,Heap JT

    更新日期:2019-02-20 00:00:00

  • CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA.

    abstract::Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhou J,Wu R,Xue X,Qin Z

    更新日期:2016-08-19 00:00:00

  • Specificities of human, rat and E. coli O6-methylguanine-DNA methyltransferases towards the repair of O6-methyl and O6-ethylguanine in DNA.

    abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liem LK,Lim A,Li BF

    更新日期:1994-05-11 00:00:00

  • Mg2+ binding and structural stability of mature and in vitro synthesized unmodified Escherichia coli tRNAPhe.

    abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Serebrov V,Vassilenko K,Kholod N,Gross HJ,Kisselev L

    更新日期:1998-06-01 00:00:00

  • Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog.

    abstract::The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nagatsugi F,Sasaki S,Miller PS,Seidman MM

    更新日期:2003-03-15 00:00:00

  • End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining.

    abstract::DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Davis BJ,Havener JM,Ramsden DA

    更新日期:2008-05-01 00:00:00

  • Photosnesitization of DNA by gold.

    abstract::Au (III) reacts with DNA at pH 5.6 to form a complex which is sensitive to mid-UV radiation. Cyclobutane pyrimidine dimers are produced at some 15 to 30 times the rate that they are in untreated DNA. The mechanism of photosensitization appears to involve energy absorption by Au-urine and Au-cytosine adducts which can ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wilkins RJ

    更新日期:1978-10-01 00:00:00

  • Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer.

    abstract::A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA-U placed in position U3,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pasternak A,Hernandez FJ,Rasmussen LM,Vester B,Wengel J

    更新日期:2011-02-01 00:00:00

  • MGView: an alignment and visualization tool to enhance gap closure of microbial genomes.

    abstract::Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conserv...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Herron-Olson L,Freeman J,Zhang Q,Retzel EF,Kapur V

    更新日期:2003-09-01 00:00:00

  • Conserved thermochemistry of guanosine nucleophile binding for structurally distinct group I ribozymes.

    abstract::We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kuo LY,Cech TR

    更新日期:1996-10-01 00:00:00

  • The Wilms' tumor suppressor gene (wt1) product represses different functional classes of transcriptional activation domains.

    abstract::We have studied the ability of the wt1 tumor suppressor gene product to repress different classes of activation domains previously shown to stimulate the initiation and elongation steps of RNA polymerase II transcription in vivo. Repression assays revealed that WT1 represses all three classes of activation domains: Sp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lee TH,Moffett P,Pelletier J

    更新日期:1999-07-15 00:00:00

  • Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.

    abstract::The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Komatsu S,Kojima K,Suzuki K,Ozaki K,Higo K

    更新日期:2004-01-01 00:00:00

  • Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA.

    abstract::The satellite RNA of tobacco ringspot virus (STobRV RNA) replicates and becomes encapsidated in association with tobacco ringspot virus. Previous results show that the infected tissue produces multimeric STobRV RNAs of both polarities. RNA that is complementary to encapsidated STobRV RNA, designated as having the (-) ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Buzayan JM,Hampel A,Bruening G

    更新日期:1986-12-22 00:00:00

  • State changes of the HORMA protein ASY1 are mediated by an interplay between its closure motif and PCH2.

    abstract::HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yang C,Hu B,Portheine SM,Chuenban P,Schnittger A

    更新日期:2020-11-18 00:00:00

  • Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis.

    abstract::Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ahmed I,Sarazin A,Bowler C,Colot V,Quesneville H

    更新日期:2011-09-01 00:00:00

  • Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts.

    abstract::The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu WM,Chu WM,Choudary PV,Schmid CW

    更新日期:1995-05-25 00:00:00

  • Predicted structure and phyletic distribution of the RNA-binding protein Hfq.

    abstract::Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sun X,Zhulin I,Wartell RM

    更新日期:2002-09-01 00:00:00

  • Amino acid sequence variations in Nicotiana CRR4 orthologs determine the species-specific efficiency of RNA editing in plastids.

    abstract::In flowering plants, RNA editing is a posttranscriptional process that converts specific C to U in organelle mRNAs. Nicotiana tabacum is an allotetraploid species derived from the progenitors of Nicotiana sylvestris and Nicotiana tomentosiformis. These Nicotiana species have been used as a model for understanding the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Okuda K,Habata Y,Kobayashi Y,Shikanai T

    更新日期:2008-11-01 00:00:00

  • The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis.

    abstract::We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Cur...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rampp M,Soddemann T,Lederer H

    更新日期:2006-07-01 00:00:00

  • Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition.

    abstract::The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in exp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bailly C,Chessari G,Carrasco C,Joubert A,Mann J,Wilson WD,Neidle S

    更新日期:2003-03-01 00:00:00

  • All Tcf HMG box transcription factors interact with Groucho-related co-repressors.

    abstract::Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brantjes H,Roose J,van De Wetering M,Clevers H

    更新日期:2001-04-01 00:00:00

  • rQuant.web: a tool for RNA-Seq-based transcript quantitation.

    abstract::We provide a novel web service, called rQuant.web, allowing convenient access to tools for quantitative analysis of RNA sequencing data. The underlying quantitation technique rQuant is based on quadratic programming and estimates different biases induced by library preparation, sequencing and read mapping. It can tack...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bohnert R,Rätsch G

    更新日期:2010-07-01 00:00:00

  • Site-directed integration of the cre gene mediated by Cre recombinase using a combination of mutant lox sites.

    abstract::The Cre-lox system is an important tool for genetic manipulation. To promote integrative reactions, two strategies using mutant lox sites have been developed. One is the left element/right element (LE/RE)-mutant strategy and the other is the cassette exchange strategy using heterospecific lox sites such as lox511 or l...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Araki K,Araki M,Yamamura K

    更新日期:2002-10-01 00:00:00

  • EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.

    abstract::The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool desig...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang H,Ramanathan Y,Soteropoulos P,Recce ML,Tolias PP

    更新日期:2002-11-01 00:00:00