Literature DB >> 19665592

Single-molecule studies of DNA replisome function.

Senthil K Perumal1, Hongjun Yue, Zhenxin Hu, Michelle M Spiering, Stephen J Benkovic.   

Abstract

Fast and accurate replication of DNA is accomplished by the interactions of multiple proteins in the dynamic DNA replisome. The DNA replisome effectively coordinates the leading and lagging strand synthesis of DNA. These complex, yet elegantly organized, molecular machines have been studied extensively by kinetic and structural methods to provide an in-depth understanding of the mechanism of DNA replication. Owing to averaging of observables, unique dynamic information of the biochemical pathways and reactions is concealed in conventional ensemble methods. However, recent advances in the rapidly expanding field of single-molecule analyses to study single biomolecules offer opportunities to probe and understand the dynamic processes involved in large biomolecular complexes such as replisomes. This review will focus on the recent developments in the biochemistry and biophysics of DNA replication employing single-molecule techniques and the insights provided by these methods towards a better understanding of the intricate mechanisms of DNA replication. Copyright (c) 2010 Elsevier B.V. All rights reserved.

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Year:  2009        PMID: 19665592      PMCID: PMC3020669          DOI: 10.1016/j.bbapap.2009.07.022

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  108 in total

1.  The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate.

Authors:  M Mok; K J Marians
Journal:  J Biol Chem       Date:  1987-12-05       Impact factor: 5.157

2.  Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation.

Authors:  R Derike Smiley; Zhihao Zhuang; Stephen J Benkovic; Gordon G Hammes
Journal:  Biochemistry       Date:  2006-07-04       Impact factor: 3.162

3.  The C-terminal residues of bacteriophage T7 gene 4 helicase-primase coordinate helicase and DNA polymerase activities.

Authors:  Seung-Joo Lee; Boriana Marintcheva; Samir M Hamdan; Charles C Richardson
Journal:  J Biol Chem       Date:  2006-06-28       Impact factor: 5.157

4.  DNA primase acts as a molecular brake in DNA replication.

Authors:  Jong-Bong Lee; Richard K Hite; Samir M Hamdan; X Sunney Xie; Charles C Richardson; Antoine M van Oijen
Journal:  Nature       Date:  2006-02-02       Impact factor: 49.962

5.  Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.

Authors:  Daniel S Johnson; Lu Bai; Benjamin Y Smith; Smita S Patel; Michelle D Wang
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

6.  A sequencing method based on real-time pyrophosphate.

Authors:  M Ronaghi; M Uhlén; P Nyrén
Journal:  Science       Date:  1998-07-17       Impact factor: 47.728

7.  Template recognition and ribonucleotide specificity of the DNA primase of bacteriophage T7.

Authors:  T Kusakabe; C C Richardson
Journal:  J Biol Chem       Date:  1997-02-28       Impact factor: 5.157

8.  Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.

Authors:  J Wang; A K Sattar; C C Wang; J D Karam; W H Konigsberg; T A Steitz
Journal:  Cell       Date:  1997-06-27       Impact factor: 41.582

9.  Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis.

Authors:  Atanaska V Mitkova; Sujata M Khopde; Subhasis B Biswas
Journal:  J Biol Chem       Date:  2003-10-13       Impact factor: 5.157

10.  Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.

Authors:  H Huang; R Chopra; G L Verdine; S C Harrison
Journal:  Science       Date:  1998-11-27       Impact factor: 47.728

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  9 in total

Review 1.  Organization of DNA replication.

Authors:  Vadim O Chagin; Jeffrey H Stear; M Cristina Cardoso
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-04       Impact factor: 10.005

2.  Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies.

Authors:  Ilya J Finkelstein; Eric C Greene
Journal:  Methods Mol Biol       Date:  2011

3.  Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis.

Authors:  Huidong Zhang; Seung-Joo Lee; Bin Zhu; Ngoc Q Tran; Stanley Tabor; Charles C Richardson
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-23       Impact factor: 11.205

Review 4.  Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork.

Authors:  Divya Nandakumar; Smita S Patel
Journal:  Methods       Date:  2016-05-09       Impact factor: 3.608

Review 5.  New insights into replisome fluidity during chromosome replication.

Authors:  Isabel Kurth; Mike O'Donnell
Journal:  Trends Biochem Sci       Date:  2012-11-12       Impact factor: 13.807

6.  Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures.

Authors:  Qian Peter Su; Ziqing Winston Zhao; Luming Meng; Miao Ding; Weiwei Zhang; Yongzheng Li; Mengzhu Liu; Rongqin Li; Yi-Qin Gao; Xiaoliang Sunney Xie; Yujie Sun
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-15       Impact factor: 11.205

Review 7.  Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging.

Authors:  Sheng-Wen Chiu; Mark C Leake
Journal:  Int J Mol Sci       Date:  2011-04-15       Impact factor: 5.923

8.  5'CAG and 5'CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs.

Authors:  Emmanuelle Delagoutte; Giuseppe Baldacci
Journal:  Mol Biol Int       Date:  2011-08-10

9.  Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions.

Authors:  Yanhui Zhao; Danqi Chen; Hongjun Yue; Michelle M Spiering; Chenglong Zhao; Stephen J Benkovic; Tony Jun Huang
Journal:  Nano Lett       Date:  2014-03-24       Impact factor: 11.189

  9 in total

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