Literature DB >> 16554978

Loops in DNA: an overview of experimental and theoretical approaches.

J-F Allemand1, S Cocco, N Douarche, G Lia.   

Abstract

DNA loop formation plays a central role in many cellular processes. The aim of this paper is to present the state of the art and open problems regarding the experimental and theoretical approaches to DNA looping. A particular attention is devoted to the effects of the protein bridge size and of protein induced sharp DNA bending on DNA loop formation enhancement.

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Year:  2006        PMID： 16554978     DOI： 10.1140/epje/i2005-10073-y

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN： 1292-8941            Impact factor:   1.890


  65 in total

Review 1.  Cre recombinase: the universal reagent for genome tailoring.

Authors:  A Nagy
Journal:  Genesis       Date:  2000-02       Impact factor: 2.487

2.  Single molecule detection of DNA looping by NgoMIV restriction endonuclease.

Authors:  Zivile Katiliene; Evaldas Katilius; Neal W Woodbury
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

3.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

4.  Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping.

Authors:  Giuseppe Lia; David Bensimon; Vincent Croquette; Jean-Francois Allemand; David Dunlap; Dale E A Lewis; Sankar Adhya; Laura Finzi
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-18       Impact factor: 11.205

5.  Protein-mediated DNA loops: effects of protein bridge size and kinks.

Authors:  Nicolas Douarche; Simona Cocco
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-12-02

6.  A general model for site-specific recombination by the integrase family recombinases.

Authors:  Y Voziyanov; S Pathania; M Jayaram
Journal:  Nucleic Acids Res       Date:  1999-02-15       Impact factor: 16.971

Review 7.  Multipartite genetic control elements: communication by DNA loop.

Authors:  S Adhya
Journal:  Annu Rev Genet       Date:  1989       Impact factor: 16.830

8.  An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression.

Authors:  T M Dunn; S Hahn; S Ogden; R F Schleif
Journal:  Proc Natl Acad Sci U S A       Date:  1984-08       Impact factor: 11.205

9.  DNA flexibility studied by covalent closure of short fragments into circles.

Authors:  D Shore; J Langowski; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-08       Impact factor: 11.205

10.  Torsional and bending rigidity of the double helix from data on small DNA rings.

Authors:  M D Frank-Kamenetskii; A V Lukashin; V V Anshelevich; A V Vologodskii
Journal:  J Biomol Struct Dyn       Date:  1985-02
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  21 in total

1.  Stretching short sequences of DNA with constant force axial optical tweezers.

Authors:  Krishnan Raghunathan; Joshua N Milstein; Jens-Christian Meiners
Journal:  J Vis Exp       Date:  2011-10-13       Impact factor: 1.355

2.  Non-Markovian polymer reaction kinetics.

Authors:  T Guérin; O Bénichou; R Voituriez
Journal:  Nat Chem       Date:  2012-06-10       Impact factor: 24.427

3.  Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.

Authors:  Peter J Mulligan; Yi-Ju Chen; Rob Phillips; Andrew J Spakowitz
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

4.  Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy.

Authors:  Anatoly B Kolomeisky
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

Review 5.  Chromatin physics: Replacing multiple, representation-centered descriptions at discrete scales by a continuous, function-dependent self-scaled model.

Authors:  C Lavelle; A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-02-22       Impact factor: 1.890

Review 6.  Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity.

Authors:  Hernan G Garcia; Paul Grayson; Lin Han; Mandar Inamdar; Jané Kondev; Philip C Nelson; Rob Phillips; Jonathan Widom; Paul A Wiggins
Journal:  Biopolymers       Date:  2007-02-05       Impact factor: 2.505

7.  Protein-induced local DNA bends regulate global topology of recombination products.

Authors:  Quan Du; Alexei Livshits; Agnieszka Kwiatek; Makkuni Jayaram; Alexander Vologodskii
Journal:  J Mol Biol       Date:  2007-02-11       Impact factor: 5.469

8.  Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Authors:  Yury S Polikanov; Vladimir A Bondarenko; Vladimir Tchernaenko; Yong I Jiang; Leonard C Lutter; Alexander Vologodskii; Vasily M Studitsky
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

9.  Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs.

Authors:  A Benecke
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-07       Impact factor: 1.890

Review 10.  DNA curvature and flexibility in vitro and in vivo.

Authors:  Justin P Peters; L James Maher
Journal:  Q Rev Biophys       Date:  2010-05-18       Impact factor: 5.318
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