Literature DB >> 20723754

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.

Daniel A Koster1, Aurélien Crut, Stewart Shuman, Mary-Ann Bjornsti, Nynke H Dekker.   

Abstract

Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal. Copyright 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID： 20723754      PMCID： PMC2997354          DOI： 10.1016/j.cell.2010.08.001

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  76 in total

1.  Relaxation dynamics of semiflexible polymers.

Authors:  Y Bohbot-Raviv; W Z Zhao; M Feingold; C H Wiggins; R Granek
Journal:  Phys Rev Lett       Date:  2004-03-03       Impact factor: 9.161

2.  Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

Authors:  Daniel A Koster; Vincent Croquette; Cees Dekker; Stewart Shuman; Nynke H Dekker
Journal:  Nature       Date:  2005-03-31       Impact factor: 49.962

3.  Relaxation dynamics of a single DNA molecule.

Authors:  E Goshen; W Z Zhao; G Carmon; S Rosen; R Granek; M Feingold
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-06-28

Review 4.  Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology.

Authors:  Marc Drolet
Journal:  Mol Microbiol       Date:  2006-02       Impact factor: 3.501

Review 5.  Direct measurement of torque in an optical trap and its application to double-strand DNA.

Authors:  László Oroszi; Péter Galajda; Huba Kirei; Sándor Bottka; Pál Ormos
Journal:  Phys Rev Lett       Date:  2006-08-01       Impact factor: 9.161

6.  Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts.

Authors:  C Q Pan; S E Finkel; S E Cramton; J A Feng; D S Sigman; R C Johnson
Journal:  J Mol Biol       Date:  1996-12-13       Impact factor: 5.469

7.  Structure of chromatin and the linking number of DNA.

Authors:  A Worcel; S Strogatz; D Riley
Journal:  Proc Natl Acad Sci U S A       Date:  1981-03       Impact factor: 11.205

8.  Supercoiling of intracellular DNA can occur in eukaryotic cells.

Authors:  G N Giaever; J C Wang
Journal:  Cell       Date:  1988-12-02       Impact factor: 41.582

9.  Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I.

Authors:  Y H Hsiang; R Hertzberg; S Hecht; L F Liu
Journal:  J Biol Chem       Date:  1985-11-25       Impact factor: 5.157

10.  Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.

Authors:  M Lewis; G Chang; N C Horton; M A Kercher; H C Pace; M A Schumacher; R G Brennan; P Lu
Journal:  Science       Date:  1996-03-01       Impact factor: 47.728
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  72 in total

1.  Resolution by unassisted Top3 points to template switch recombination intermediates during DNA replication.

Authors:  M Rebecca Glineburg; Alejandro Chavez; Vishesh Agrawal; Steven J Brill; F Brad Johnson
Journal:  J Biol Chem       Date:  2013-10-07       Impact factor: 5.157

2.  E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA.

Authors:  Mónica Fernández-Sierra; Qing Shao; Chandler Fountain; Laura Finzi; David Dunlap
Journal:  J Mol Biol       Date:  2015-04-19       Impact factor: 5.469

Review 3.  The torsional state of DNA within the chromosome.

Authors:  Joaquim Roca
Journal:  Chromosoma       Date:  2011-05-13       Impact factor: 4.316

4.  How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.

Authors:  Eric J Rawdon; Julien Dorier; Dusan Racko; Kenneth C Millett; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2016-04-22       Impact factor: 16.971

5.  Interplay between DNA supercoiling and transcription elongation.

Authors:  Jie Ma; Michelle Wang
Journal:  Transcription       Date:  2014

Review 6.  DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.

Authors:  Charles J Dorman; Matthew J Dorman
Journal:  Biophys Rev       Date:  2016-06-16

Review 7.  The dynamic interplay between DNA topoisomerases and DNA topology.

Authors:  Yeonee Seol; Keir C Neuman
Journal:  Biophys Rev       Date:  2016-11-14

Review 8.  DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.

Authors:  Charles J Dorman; Matthew J Dorman
Journal:  Biophys Rev       Date:  2016-11-14

Review 9.  Studying genomic processes at the single-molecule level: introducing the tools and applications.

Authors:  David Dulin; Jan Lipfert; M Charl Moolman; Nynke H Dekker
Journal:  Nat Rev Genet       Date:  2012-10-30       Impact factor: 53.242

10.  The Dynamic Interplay Between DNA Topoisomerases and DNA Topology.

Authors:  Yeonee Seol; Keir C Neuman
Journal:  Biophys Rev       Date:  2016-07-02
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