Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules.

Abstract:

:Using total internal reflection fluorescence microscopy, we directly visualize in real-time, the 1D Brownian motion and transcription elongation of T7 RNA polymerase along aligned DNA molecules bound to substrates by molecular combing. We fluorescently label T7 RNA polymerase with antibodies and use flow to convect them orthogonally to the DNA alignment direction, permitting observation and estimation of the protein diffusivity along the DNA at the single-molecule level. Our observations suggest that the 1D diffusion coefficient varies from molecule to molecule over the range 6.1 x 10(-11) cm2/s to 4.3 x 10(-9) cm2/s. We also observe binding and transcription by T7 RNA polymerases on single combed T7 DNA molecules with an apparent association rate of 1.6 microM(-1)s(-1). From the measured dependence of the rate of transcription on concentration of nucleotide triphosphate, we infer that the combed DNA molecules capable of interacting with proteins are under an average tension of 25 pN.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kim JH,Larson RG

doi

10.1093/nar/gkm332

subject

Has Abstract

pub_date

2007-01-01 00:00:00

pages

3848-58

issue

11

eissn

0305-1048

issn

1362-4962

pii

gkm332

journal_volume

35

pub_type

杂志文章
  • The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine.

    abstract::The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.12.2522

    authors: Cubero E,Güimil-García R,Luque FJ,Eritja R,Orozco M

    更新日期:2001-06-15 00:00:00

  • Interaction of the resolving enzyme YDC2 with the four-way DNA junction.

    abstract::Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.24.5609

    authors: White MF,Lilley DM

    更新日期:1998-12-15 00:00:00

  • FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum.

    abstract::The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj026

    authors: Güldener U,Mannhaupt G,Münsterkötter M,Haase D,Oesterheld M,Stümpflen V,Mewes HW,Adam G

    更新日期:2006-01-01 00:00:00

  • Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes.

    abstract::G-quadruplexes (G4s) are stable secondary structures that can lead to the stalling of replication forks and cause genomic instability. Pif1 is a 5' to 3' helicase, localized to both the mitochondria and nucleus that can unwind G4s in vitro and prevent fork stalling at G4 forming sequences in vivo. Using in vitro prime...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz608

    authors: Sparks MA,Singh SP,Burgers PM,Galletto R

    更新日期:2019-09-19 00:00:00

  • Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities.

    abstract::An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki338

    authors: Nakahata S,Kawamoto S

    更新日期:2005-04-11 00:00:00

  • An alternative protein factor which binds the internal promoter of Xenopus 5S ribosomal RNA genes.

    abstract::In small oocytes of Xenopus species, two sets of 5S RNA genes, oocyte-type and somatic-type, are fully activated. The 5S RNA transcripts are temporarily stored, half in association with TFIIIA to form a 7S particle, the other half in association with tRNA and two proteins (p48 and p43) to form a 42S particle. It has b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.21.8679

    authors: Barrett P,Sommerville J

    更新日期:1987-11-11 00:00:00

  • The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans.

    abstract::Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa427

    authors: Binas O,Schamber T,Schwalbe H

    更新日期:2020-07-09 00:00:00

  • Alkylation of template strand of coding region causes effective gene silencing.

    abstract::We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific seq...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl005

    authors: Shinohara K,Sasaki S,Minoshima M,Bando T,Sugiyama H

    更新日期:2006-02-25 00:00:00

  • SpliceInfo: an information repository for mRNA alternative splicing in human genome.

    abstract::We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki129

    authors: Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

    更新日期:2005-01-01 00:00:00

  • Specific binding of MobA, a plasmid-encoded protein involved in the initiation and termination of conjugal DNA transfer, to single-stranded oriT DNA.

    abstract::MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.19.4563

    authors: Bhattacharjee MK,Meyer RJ

    更新日期:1993-09-25 00:00:00

  • REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.

    abstract::REDUCE is a motif-based regression method for microarray analysis. The only required inputs are (i) a single genome-wide set of absolute or relative mRNA abundances and (ii) the DNA sequence of the regulatory region associated with each gene that is probed. Currently supported organisms are yeast, worm and fly; it is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg630

    authors: Roven C,Bussemaker HJ

    更新日期:2003-07-01 00:00:00

  • Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde-hydrazine chemistry and protease-cleavable linkers.

    abstract::The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl1110

    authors: Pfander S,Fiammengo R,Kirin SI,Metzler-Nolte N,Jäschke A

    更新日期:2007-01-01 00:00:00

  • Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition.

    abstract::We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.25.5978

    authors: Kagawa TF,Howell ML,Tseng K,Ho PS

    更新日期:1993-12-25 00:00:00

  • An oligodeoxynucleotide affinity column for the isolation of sequence specific DNA binding proteins.

    abstract::A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand has been prepared as an example of a material which can be used for the rapid and effective isolation of sequence specific DNA binding proteins. Two complementary oligodeoxynucleotides have been employed, one of which contains a small 5'-spa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.21.10283

    authors: Blanks R,McLaughlin LW

    更新日期:1988-11-11 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

    doi:10.1093/nar/gkn629

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

    更新日期:2008-11-01 00:00:00

  • The influence of fluorescent dye structure on the electrophoretic mobility of end-labeled DNA.

    abstract::Over the past 10 years, fluorescent end-labeling of DNA fragments has evolved into the preferred method of DNA detection for a wide variety of applications, including DNA sequencing and PCR fragment analysis. One of the advantages inherent in fluorescent detection methods is the ability to perform multi-color analyses...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.11.2797

    authors: Tu O,Knott T,Marsh M,Bechtol K,Harris D,Barker D,Bashkin J

    更新日期:1998-06-01 00:00:00

  • Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

    abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1239

    authors: Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

    更新日期:2010-04-01 00:00:00

  • Analysis of the DNA joining repertoire of Chlorella virus DNA ligase and a new crystal structure of the ligase-adenylate intermediate.

    abstract::Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent DNA ligase known; it suffices for yeast cell growth in lieu of the essential yeast DNA ligase Cdc9. The Chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its DNA footprint extends 8-9 nt on the 3'-hydroxyl (3'-OH...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg665

    authors: Odell M,Malinina L,Sriskanda V,Teplova M,Shuman S

    更新日期:2003-09-01 00:00:00

  • The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

    abstract::In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. Ther...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh367

    authors: Huynh T,Rigoutsos I

    更新日期:2004-07-01 00:00:00

  • CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA.

    abstract::Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks906

    authors: Liu WH,Roemer SC,Port AM,Churchill ME

    更新日期:2012-12-01 00:00:00

  • Cloning and characterization of the C. elegans histidyl-tRNA synthetase gene.

    abstract::In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.18.4344

    authors: Amaar YG,Baillie DL

    更新日期:1993-09-11 00:00:00

  • Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species.

    abstract::G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz463

    authors: Puig Lombardi E,Holmes A,Verga D,Teulade-Fichou MP,Nicolas A,Londoño-Vallejo A

    更新日期:2019-07-09 00:00:00

  • Identification of the yeast cytidine deaminase CDD1 as an orphan C-->U RNA editase.

    abstract::Yeast co-expressing rat APOBEC-1 and a fragment of human apolipoprotein B (apoB) mRNA assembled functional editosomes and deaminated C6666 to U in a mooring sequence-dependent fashion. The occurrence of APOBEC-1-complementing proteins suggested a naturally occurring mRNA editing mechanism in yeast. Previously, a hidde...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.8.1772

    authors: Dance GS,Beemiller P,Yang Y,Mater DV,Mian IS,Smith HC

    更新日期:2001-04-15 00:00:00

  • WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans.

    abstract::High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku367

    authors: Cho A,Shin J,Hwang S,Kim C,Shim H,Kim H,Kim H,Lee I

    更新日期:2014-07-01 00:00:00

  • The Pfam protein families database.

    abstract::Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that ha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr1065

    authors: Punta M,Coggill PC,Eberhardt RY,Mistry J,Tate J,Boursnell C,Pang N,Forslund K,Ceric G,Clements J,Heger A,Holm L,Sonnhammer EL,Eddy SR,Bateman A,Finn RD

    更新日期:2012-01-01 00:00:00

  • Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection.

    abstract::To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw782

    authors: Bouttier M,Laperriere D,Memari B,Mangiapane J,Fiore A,Mitchell E,Verway M,Behr MA,Sladek R,Barreiro LB,Mader S,White JH

    更新日期:2016-12-15 00:00:00

  • Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates.

    abstract::Array based DNA pooling techniques facilitate genome-wide scale genotyping of large samples. We describe a structured analysis method for pooled data using internal replication information in large scale genotyping sets. The method takes advantage of information from single nucleotide polymorphisms (SNPs) typed in par...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl136

    authors: Macgregor S,Visscher PM,Montgomery G

    更新日期:2006-04-20 00:00:00

  • Molecular relationships between U snRNP proteins as investigated by rabbit antisera and peptide mapping.

    abstract::Each of the major U snRNP polypeptides from human cells was purified by electroelution from SDS-polyacrylamide gels. Rabbit antisera could be obtained against the individual proteins 70K, A, B', B and D, although rabbits failed to elicit antibodies against E, F and G. A strong structural homology was found between pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.10.4021

    authors: Reuter R,Rothe S,Lührmann R

    更新日期:1987-05-26 00:00:00

  • GeneCAT--novel webtools that combine BLAST and co-expression analyses.

    abstract::The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughpu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn292

    authors: Mutwil M,Obro J,Willats WG,Persson S

    更新日期:2008-07-01 00:00:00

  • Processing of complementary sense RNAs of Digitaria streak virus in its host and in transgenic tobacco.

    abstract::We have used a polymerase chain reaction (PCR) procedure to analyse low abundance complementary sense RNAs of Digitaria streak virus (DSV) from infected leaves of Digitaria setigera. This study has confirmed that both spliced and unspliced RNAs are synthesised by the same transcription unit. The position of the intron...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.24.7259

    authors: Mullineaux PM,Guerineau F,Accotto GP

    更新日期:1990-12-25 00:00:00