DNA unwinding and protein displacement by superfamily 1 and superfamily 2 helicases.

Abstract:

:DNA helicases are required for virtually every aspect of DNA metabolism, including replication, repair, recombination and transcription. A comprehensive description of these essential biochemical processes requires detailed understanding of helicase mechanisms. These enzymes are ubiquitous, having been identified in viruses, prokaryotes and eukaryotes. Disease states, such as xeroderma pigmentosum, Cockayne's syndrome, Bloom's syndrome and Werner's syndrome, have been linked to defects in specific genes coding for DNA helicases. Helicases have been placed into different subfamilies based on sequence comparison. The largest subgroups are termed superfamily 1 and superfamily 2. A proposed mechanism for helicases in these classes has been described in terms of an 'inchworm model'. The inchworm model includes conformational changes driven by ATP binding and hydrolysis that allow unidirectional translocation along DNA. A monomeric form of the enzyme is proposed to have two DNA-binding sites that enable sequential steps of DNA binding and release. Significant differences exist between helicases in important aspects of the models such as the oligomerization state of the enzyme with some helicases functioning as monomers, some as dimers and others as higher-order oligomers.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Mackintosh SG,Raney KD

doi

10.1093/nar/gkl501

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

4154-9

issue

15

eissn

0305-1048

issn

1362-4962

pii

gkl501

journal_volume

34

pub_type

杂志文章,评审
  • Archaebacterial reverse gyrase cleavage-site specificity is similar to that of eubacterial DNA topoisomerases I.

    abstract::ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.9.2801

    authors: Kovalsky OI,Kozyavkin SA,Slesarev AI

    更新日期:1990-05-11 00:00:00

  • Highly recurring sequence elements identified in eukaryotic DNAs by computer analysis are often homologous to regulatory sequences or protein binding sites.

    abstract::We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.4.1835

    authors: Bodnar JW,Ward DC

    更新日期:1987-02-25 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

  • Direct sequencing of polymerase chain reaction amplified DNA fragments through the incorporation of deoxynucleoside alpha-thiotriphosphates.

    abstract::The direct sequencing of DNA generated by the polynucleotide chain reaction, via the incorporation of phosphorothioate nucleotides and followed by treatment with an alkylating reagent that cleaves specifically at the phosphorothioate positions, is described. The Taq polymerase used in the amplification reaction incorp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.21.9947

    authors: Nakamaye KL,Gish G,Eckstein F,Vosberg HP

    更新日期:1988-11-11 00:00:00

  • Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): unpaired nucleotides can be stabilizing or destabilizing.

    abstract::Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.12.2212

    authors: Kadrmas JL,Ravin AJ,Leontis NB

    更新日期:1995-06-25 00:00:00

  • Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex.

    abstract::Initial steps in the synthesis of functional tRNAs require 5'- and 3'-processing of precursor tRNAs (pre-tRNAs), which in yeast mitochondria are achieved by two endonucleases, RNase P and RNase Z. In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr941

    authors: Daoud R,Forget L,Lang BF

    更新日期:2012-02-01 00:00:00

  • Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

    abstract::Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky033

    authors: Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

    更新日期:2018-03-16 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

  • Regulation of estrogen receptor alpha gene mediated by promoter B responsible for its enhanced expressionin human breast cancer.

    abstract::We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.3.903

    authors: Tanimoto K,Eguchi H,Yoshida T,Hajiro-Nakanishi K,Hayashi S

    更新日期:1999-02-01 00:00:00

  • Selection and some properties of recombinant clones of lambda bacteriophage containing genes of Drosophila melanogaster.

    abstract::The lambdagt clones containing fragments of the Drosophila melanogaster genome were prepared and characterized by hybridization of their DNA with (I) lambdagt-cRNA; (2) lambdaC-cRNA; (3) Dm-cRNA; (4) the mRNA of D.melanogaster culture cells and (5) the stable cytoplasmic poly (A) RNA from the same source. The techniqu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.8.2115

    authors: Ilyin YV,Tchurikov NA,Georgiev

    更新日期:1976-08-01 00:00:00

  • Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.

    abstract::The DNA repair enzyme human uracil DNA glycosylase (UNG) scans short stretches of genomic DNA and captures rare uracil bases as they transiently emerge from the DNA duplex via spontaneous base pair breathing motions. The process of DNA scanning requires that the enzyme transiently loosen its grip on DNA to allow stoch...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp161

    authors: Friedman JI,Majumdar A,Stivers JT

    更新日期:2009-06-01 00:00:00

  • Complex formation between ribosomal protein S1, oligo-and polynucleotides: chain length dependence and base specificity.

    abstract::In order to examine the nature of the complex formation between the ribosomal protein S1 and nucleic acids three methods were used: Inhibition of the reaction of n-ethyl[2.3 14C]-maleimide with S1 by the addition of oligonucleotides; adsorption of the complexes to nitrocellulose filters; and equilibrium dialysis. The ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.10.3627

    authors: Lipecky R,Kohlschein J,Gassen HG

    更新日期:1977-10-01 00:00:00

  • HIV-1 Tat directly binds to NFkappaB enhancer sequence: role in viral and cellular gene expression.

    abstract::HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh289

    authors: Dandekar DH,Ganesh KN,Mitra D

    更新日期:2004-02-23 00:00:00

  • Differential transcription of the orphan receptor RORbeta in nuclear extracts derived from Neuro2A and HeLa cells.

    abstract::An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.16.3424

    authors: Gawlas K,Stunnenberg HG

    更新日期:2001-08-15 00:00:00

  • Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx).

    abstract::Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn358

    authors: Baldwin AJ,Busse K,Simm AM,Jones DD

    更新日期:2008-08-01 00:00:00

  • CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

    abstract::The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt462

    authors: Blaszczyk M,Jamroz M,Kmiecik S,Kolinski A

    更新日期:2013-07-01 00:00:00

  • Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer.

    abstract::The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.15.3155

    authors: Ghosh SS,Eis PS,Blumeyer K,Fearon K,Millar DP

    更新日期:1994-08-11 00:00:00

  • Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells.

    abstract::When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.19.3951

    authors: Homann M,Tabler M,Tzortzakaki S,Sczakiel G

    更新日期:1994-09-25 00:00:00

  • CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli.

    abstract::Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1285

    authors: Beloglazova N,Kuznedelov K,Flick R,Datsenko KA,Brown G,Popovic A,Lemak S,Semenova E,Severinov K,Yakunin AF

    更新日期:2015-01-01 00:00:00

  • Characterization of the DNA-binding site repertoire for the Epstein-Barr virus transcription factor R.

    abstract::The Epstein-Barr virus gene BRLF1 encodes the transcription factor R, which is a sequence-specific DNA-binding protein important for the switch from latency to a productive cycle. We have defined a repertoire of specific R-binding sites using a GST-R fusion protein and a pool of 23 bp random DNA sequences. The R-bound...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.7.1172

    authors: Gruffat H,Sergeant A

    更新日期:1994-04-11 00:00:00

  • Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain.

    abstract::Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku107

    authors: Barrow JJ,Li Y,Hossain M,Huang S,Bungert J

    更新日期:2014-04-01 00:00:00

  • Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA.

    abstract::Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh634

    authors: Wanrooij S,Luoma P,van Goethem G,van Broeckhoven C,Suomalainen A,Spelbrink JN

    更新日期:2004-06-04 00:00:00

  • The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor.

    abstract::Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku225

    authors: Gossan NC,Zhang F,Guo B,Jin D,Yoshitane H,Yao A,Glossop N,Zhang YQ,Fukada Y,Meng QJ

    更新日期:2014-05-01 00:00:00

  • Allegro: analyzing expression and sequence in concert to discover regulatory programs.

    abstract::A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn1064

    authors: Halperin Y,Linhart C,Ulitsky I,Shamir R

    更新日期:2009-04-01 00:00:00

  • Chromosome size polymorphism in Plasmodium falciparum can involve deletions of the subtelomeric pPFrep20 sequence.

    abstract::The P. falciparum pPFrep20 repetitive element from the Palo Alto Uganda strain has been isolated and sequenced. The Palo Alto pPFrep20 repeat (pPFPArep20) has a clustered subtelomeric location and on chromosome 1 has been deleted from one end. Analysis of chromosome 1 from 5 other strains has revealed that pPFrep20 se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.10.4331

    authors: Patarapotikul J,Langsley G

    更新日期:1988-05-25 00:00:00

  • The nucleotide sequence of the initiator tRNA from Drosophila melanogaster.

    abstract::The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.2.421

    authors: Silverman S,Heckman J,Cowling GJ,Delaney AD,Dunn RJ,Gillam IC,Tener GM,Söll D,RajBhandary UL

    更新日期:1979-02-01 00:00:00

  • The TP53 website: an integrative resource centre for the TP53 mutation database and TP53 mutant analysis.

    abstract::A novel resource centre for TP53 mutations and mutants has been developed (http://p53.fr). TP53 gene dysfunction can be found in the majority of human cancer types. The potential use of TP53 mutation as a biomarker for clinical studies or exposome analysis has led to the publication of thousands of reports describing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1033

    authors: Leroy B,Fournier JL,Ishioka C,Monti P,Inga A,Fronza G,Soussi T

    更新日期:2013-01-01 00:00:00

  • The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

    abstract::Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the functio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1337

    authors: Wiegand S,Meier D,Seehafer C,Malicki M,Hofmann P,Schmith A,Winckler T,Földesi B,Boesler B,Nellen W,Reimegård J,Käller M,Hällman J,Emanuelsson O,Avesson L,Söderbom F,Hammann C

    更新日期:2014-03-01 00:00:00

  • MutSβ and histone deacetylase complexes promote expansions of trinucleotide repeats in human cells.

    abstract::Trinucleotide repeat (TNR) expansions cause at least 17 heritable neurological diseases, including Huntington's disease. Expansions are thought to arise from abnormal processing of TNR DNA by specific trans-acting proteins. For example, the DNA repair complex MutSβ (MSH2-MSH3 heterodimer) is required in mice for on-go...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks810

    authors: Gannon AM,Frizzell A,Healy E,Lahue RS

    更新日期:2012-11-01 00:00:00

  • Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination.

    abstract::Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp814

    authors: Basenko EY,Cesare AJ,Iyer S,Griffith JD,McEachern MJ

    更新日期:2010-01-01 00:00:00