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 Resjournal_title
Nucleic acids researchauthors
Kim JH,Larson RGdoi
10.1093/nar/gkm332subject
Has Abstractpub_date
2007-01-01 00:00:00pages
3848-58issue
11eissn
0305-1048issn
1362-4962pii
gkm332journal_volume
35pub_type
杂志文章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
更新日期:2001-06-15 00:00:00
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
更新日期:1998-12-15 00:00:00
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
更新日期:2006-01-01 00:00:00
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
更新日期:2019-09-19 00:00:00
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
更新日期:2005-04-11 00:00:00
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
更新日期:1987-11-11 00:00:00
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
更新日期:2020-07-09 00:00:00
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
更新日期:2006-02-25 00:00:00
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
更新日期:2005-01-01 00:00:00
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
更新日期:1993-09-25 00:00:00
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
更新日期:2003-07-01 00:00:00
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
更新日期:2007-01-01 00:00:00
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
更新日期:1993-12-25 00:00:00
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
更新日期:1988-11-11 00:00:00
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
更新日期:2008-11-01 00:00:00
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
更新日期:1998-06-01 00:00:00
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
更新日期:2010-04-01 00:00:00
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
更新日期:2003-09-01 00:00:00
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
更新日期:2004-07-01 00:00:00
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
更新日期:2012-12-01 00:00:00
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
更新日期:1993-09-11 00:00:00
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
更新日期:2019-07-09 00:00:00
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
更新日期:2001-04-15 00:00:00
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
更新日期:2014-07-01 00:00:00
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
更新日期:2012-01-01 00:00:00
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
更新日期:2016-12-15 00:00:00
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
更新日期:2006-04-20 00:00:00
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
更新日期:1987-05-26 00:00:00
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
更新日期:2008-07-01 00:00:00
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
更新日期:1990-12-25 00:00:00