当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets.

PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets.

Abstract：

:We have developed a novel method of genetic library construction on magnetic microbeads based on solid-phase single-molecule PCR in a fine and robust water-phase compartment formed in water-in-oil (w/o) emulsions. In this method, critically diluted DNA fragments were distributed over the emulsion as templates, where beads crosslinked with multiple primers and other PCR components were encapsulated to form multiple reaction compartments. The delivered DNA was then amplified and covalently immobilized on the beads in parallel, within individual compartments, to construct a genetic library on beads (GLOBE), which was readily applicable to a genomewide global scanning of genetic elements recognized by a defined DNA-binding protein. We constructed a GLOBE of Paracoccus denitrificans and selected gene beads that were bound to the His-tagged transcription factor PhaR by flow cytometry. As a result of flow cytometry screening with an anti-His fluorescent antibody, the PhaR target fragments were enriched 1200-fold from this library with this system. Therefore, this system is a powerful tool for analyzing the transcription network on a genomewide scale.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kojima T,Takei Y,Ohtsuka M,Kawarasaki Y,Yamane T,Nakano H

doi

10.1093/nar/gni143

keywords:

subject

Has Abstract

pub_date

2005-10-06 00:00:00

pages

e150

issue

17

eissn

0305-1048

issn

1362-4962

pii

33/17/e150

journal_volume

33

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Protection of discrete DNA fragments by the complex H1-octamerhistones or H5-octamerhistones after micrococcal nuclease digestion.

    abstract：:Several authors, including ourselves, have reported the existence of chromatosomes with DNA size larger than 166 bp in bird erythrocyte chromatin. It was tempting to correlate this increased DNA size with the presence of histone H5. In order to substantiate this hypothesis, we performed a micrococcal nuclease digestio...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.15.3671

    authors： Muyldermans S,Lasters I,Wyns L,Hamers R

    更新日期：1981-08-11 00:00:00

  • Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development.

    abstract：:Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv514

    authors： Rockowitz S,Zheng D

    更新日期：2015-07-13 00:00:00

  • Nuclear speckles: molecular organization, biological function and role in disease.

    abstract：:The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, w...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/gkx759

    authors： Galganski L,Urbanek MO,Krzyzosiak WJ

    更新日期：2017-10-13 00:00:00

  • Determination of tumor necrosis factor receptor-associated factor trimerization in living cells by CFP->YFP->mRFP FRET detected by flow cytometry.

    abstract：:The availability of protein fluorophores with appropriate spectral properties has made it possible to employ fluorescence resonance energy transfer (FRET) to assess interactions between three proteins microscopically. Flow cytometry offers excellent sensitivity, effective signal separation and the capacity to assess a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gni057

    authors： He L,Wu X,Simone J,Hewgill D,Lipsky PE

    更新日期：2005-04-01 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

  • AdoMet-dependent methylation, DNA methyltransferases and base flipping.

    abstract：:Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/29.18.3784

    authors： Cheng X,Roberts RJ

    更新日期：2001-09-15 00:00:00

  • A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm.

    abstract：:Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioa...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx693

    authors： Taniguchi J,Pandian GN,Hidaka T,Hashiya K,Bando T,Kim KK,Sugiyama H

    更新日期：2017-09-19 00:00:00

  • Fail-safe genetic codes designed to intrinsically contain engineered organisms.

    abstract：:One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz745

    authors： Calles J,Justice I,Brinkley D,Garcia A,Endy D

    更新日期：2019-11-04 00:00:00

  • A revised secondary structure model for the 3'-end of hepatitis B virus pregenomic RNA.

    abstract：:The polymerase encoded by human hepatitis B virus, which has reverse transcriptase and RNase H activity, binds to its pregenomic RNA template in a two-step process involving a terminal redundancy. Both first strand and second strand DNA synthesis involve primer translocation and second strand synthesis involves a temp...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.17.3295

    authors： Kidd AH,Kidd-Ljunggren K

    更新日期：1996-09-01 00:00:00

  • PI2PE: protein interface/interior prediction engine.

    abstract：:The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm231

    authors： Tjong H,Qin S,Zhou HX

    更新日期：2007-07-01 00:00:00

  • The telomere resolvase of the Lyme disease spirochete, Borrelia burgdorferi, promotes DNA single-strand annealing and strand exchange.

    abstract：:Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt832

    authors： Mir T,Huang SH,Kobryn K

    更新日期：2013-12-01 00:00:00

  • TRDB--the Tandem Repeats Database.

    abstract：:Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of informati...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl1013

    authors： Gelfand Y,Rodriguez A,Benson G

    更新日期：2007-01-01 00:00:00

  • The complete nucleotide sequence of the I-E alpha d immune response gene.

    abstract：:We have isolated and sequenced the complete murine I-E alpha immune response gene of the H-2db haplotype. The I-E alpha d gene consists of 5300 basepairs and is organized into five or possibly six exons that correspond to different domains of the alpha chain. The amino acid sequence deduced from the I-E alpha gene sho...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.15.5055

    authors： Hyldig-Nielsen JJ,Schenning L,Hammerling U,Widmark E,Heldin E,Lind P,Servenius B,Lund T,Flavell R,Lee JS,Trowsdale J,Schreier PH,Zablitzky F,Larhammar D,Peterson PA,Rask L

    更新日期：1983-08-11 00:00:00

  • Chiral metallohelices enantioselectively target hybrid human telomeric G-quadruplex DNA.

    abstract：:The design and synthesis of metal complexes that can specifically target DNA secondary structure has attracted considerable attention. Chiral metallosupramolecular complexes (e.g. helicates) in particular display unique DNA-binding behavior, however until recently few examples which are both water-compatible and enant...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx244

    authors： Zhao A,Howson SE,Zhao C,Ren J,Scott P,Wang C,Qu X

    更新日期：2017-05-19 00:00:00

  • An on-bead tailing/ligation approach for sequencing resin-bound RNA libraries.

    abstract：:Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks004

    authors： Wiesmayr A,Fournier P,Jäschke A

    更新日期：2012-05-01 00:00:00

  • A test of 'polymerase handover' as a mechanism for stimulating initiation by RNA polymerase I.

    abstract：:On the tandemly linked ribosomal genes of Xenopus laevis, the RNA polymerase transcribes past the 3' end of the 40S coding region and terminates at T3 just upstream of the gene promoter. The close proximity of T3 to the gene promoter, and the functional interdependence of these two elements, has led to the suggestion ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.1.373

    authors： Lucchini R,Reeder RH

    更新日期：1989-01-11 00:00:00

  • miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.

    abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1258

    authors： Chou CH,Chang NW,Shrestha S,Hsu SD,Lin YL,Lee WH,Yang CD,Hong HC,Wei TY,Tu SJ,Tsai TR,Ho SY,Jian TY,Wu HY,Chen PR,Lin NC,Huang HT,Yang TL,Pai CY,Tai CS,Chen WL,Huang CY,Liu CC,Weng SL,Liao KW,Hsu WL,Hu

    更新日期：2016-01-04 00:00:00

  • Activation of interferon-regulated, dsRNA-dependent enzymes by human immunodeficiency virus-1 leader RNA.

    abstract：:Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.3.969

    authors： SenGupta DN,Silverman RH

    更新日期：1989-02-11 00:00:00

  • Identification of dynamic sequences in the central domain of 7SL RNA.

    abstract：:The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.11.4639

    authors： Zwieb C,Ullu E

    更新日期：1986-06-11 00:00:00

  • Polymers of random short oligonucleotides detect polymorphic loci in the human genome.

    abstract：:Polymers of random 14 mer oligonucleotides are shown to detect discrete loci in the human genome. Eighteen different synthetic tandem repeats of random 14 base-pair units (STRs) have been generated and all of them turn out to detect polymorphic loci on southern blots of human DNA samples, presumably corresponding to a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.19.7623

    authors： Vergnaud G

    更新日期：1989-10-11 00:00:00

  • Mobile dispersed genetic element MDG1 of Drosophila melanogaster: transcription pattern.

    abstract：:Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/8.22.5347

    authors： Ilyin Y,Chmeliauskaite VG,Kulguskin VV,Georgiev GP

    更新日期：1980-11-25 00:00:00

  • Sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex DNA containing a 5-bromo-2'-deoxyuridine or 5-bromo-2'-deoxycytidine.

    abstract：:The replacement of thymidine with 5-bromo-2'-deoxyuridine (BrdU) is well-known to sensitize cells to ionizing radiation and photoirradiation. We reported here the sequence-dependent formation of intrastrand crosslink products from the UVB irradiation of duplex oligodeoxynucleotides harboring a BrdU or its closely rela...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl892

    authors： Zeng Y,Wang Y

    更新日期：2006-01-01 00:00:00

  • 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl]-modified oligonucleotides inhibit expression of mRNA in vitro and in vivo.

    abstract：:Synthesis and antisense activity of oligonucleotides modified with 2'-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2'-O-DMAOE) are described. The 2'-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide 'gapmers', with 2'-O-DMAOE- modified nucleoside residues at t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkh220

    authors： Prakash TP,Johnston JF,Graham MJ,Condon TP,Manoharan M

    更新日期：2004-02-03 00:00:00

  • CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.

    abstract：:CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn305

    authors： Wishart DS,Arndt D,Berjanskii M,Tang P,Zhou J,Lin G

    更新日期：2008-07-01 00:00:00

  • Experimental approaches to identify non-coding RNAs.

    abstract：:Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/gkj469

    authors： Hüttenhofer A,Vogel J

    更新日期：2006-01-25 00:00:00

  • Fine structure analyses of the Drosophila and Saccharomyces heat shock factor--heat shock element interactions.

    abstract：:Heat shock genes are activated by the binding of the heat shock transcription factor (HSF) to heat shock elements (HSEs), consisting of arrays of the 5-bp unit NGAAN arranged as inverted repeats. Here, we have investigated the interaction of the 5-bp unit with HSFs of Drosophila and Saccharomyces. Mutations within the...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/22.2.167

    authors： Fernandes M,Xiao H,Lis JT

    更新日期：1994-01-25 00:00:00

  • The regulatory region of MS2 phage RNA replicase cistron. IV. Functional activity of specific MS2 RNA fragments in formation of the 70 S initiation complex of protein biosynthesis.

    abstract：:The initiation region of the MS2 replicase cistron can be isolated as a fragment 59 bases in length protected from RNAase by the binding of the coat protein which serves as a translational repressor. This fragment MS2 R(-53 leads to 6) starts 53 bases before the initiation codon and retains full activity in binding ri...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/6.5.1761

    authors： Borisova GP,Volkova TM,Berzin V,Rosenthal G,Gren EJ

    更新日期：1979-01-01 00:00:00

  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.

    abstract：:The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic program...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl480

    authors： Chivian D,Baker D

    更新日期：2006-01-01 00:00:00

  • Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.

    abstract：:Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here,...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa676

    authors： Hör J,Di Giorgio S,Gerovac M,Venturini E,Förstner KU,Vogel J

    更新日期：2020-09-18 00:00:00

  • Structural repeat units of Chinese hamster ovary chromatin. Evidence for variations in repeat unit DNA size in higher eukaryotes.

    abstract：:DNA lengths in the structural repeat units of Chinese hamster ovary (CHO) and chicken erythrocyte chromatin were compared by analyzing the sizes of DNA fragments produced after treatment of nuclei with staphylococcal nuclease. The repeat length of CHO chromatin (173 +- 4 BP) is about 20 base pairs (BP) smaller than th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/4.4.771

    authors： Rill RL,Nelson DA,Oosterhof DK,Hozier JC

    更新日期：1977-04-01 00:00:00