Literature DB >> 16547610

Polymer chain models of DNA and chromatin.

J Langowski1.   

Abstract

Many properties of the genome in the cell nucleus can be understood by modeling DNA and chromatin as a flexible polymer chain. This article introduces into current models for such a coarse-grained description and reviews some recent results from our own group. Examples given are the unrolling of DNA from the histone core and the response of the 30 nm chromatin fiber to mechanical stretching.

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Year:  2006        PMID： 16547610     DOI： 10.1140/epje/i2005-10067-9

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


  62 in total

1.  Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

Authors:  D A Beard; T Schlick
Journal:  Biopolymers       Date:  2001-01       Impact factor: 2.505

2.  Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

Authors:  Brent D Brower-Toland; Corey L Smith; Richard C Yeh; John T Lis; Craig L Peterson; Michelle D Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-19       Impact factor: 11.205

3.  Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.

Authors:  M L Bennink; S H Leuba; G H Leno; J Zlatanova; B G de Grooth; J Greve
Journal:  Nat Struct Biol       Date:  2001-07

4.  Salt-induced conformation and interaction changes of nucleosome core particles.

Authors:  Stéphanie Mangenot; Amélie Leforestier; Patrice Vachette; Dominique Durand; Françoise Livolant
Journal:  Biophys J       Date:  2002-01       Impact factor: 4.033

5.  Brownian dynamics simulations of supercoiled DNA with bent sequences.

Authors:  G Chirico; J Langowski
Journal:  Biophys J       Date:  1996-08       Impact factor: 4.033

6.  Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.

Authors:  S B Smith; Y Cui; C Bustamante
Journal:  Science       Date:  1996-02-09       Impact factor: 47.728

7.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

8.  A chromatin folding model that incorporates linker variability generates fibers resembling the native structures.

Authors:  C L Woodcock; S A Grigoryev; R A Horowitz; N Whitaker
Journal:  Proc Natl Acad Sci U S A       Date:  1993-10-01       Impact factor: 11.205

9.  Structure of the 300A chromatin filament: X-ray diffraction from oriented samples.

Authors:  J Widom; A Klug
Journal:  Cell       Date:  1985-11       Impact factor: 41.582

10.  Kinetics of site-site interactions in supercoiled DNA with bent sequences.

Authors:  Malte Bussiek; Konstantin Klenin; Jörg Langowski
Journal:  J Mol Biol       Date:  2002-09-27       Impact factor: 5.469
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  45 in total

1.  Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.

Authors:  Olga I Kulaeva; Guohui Zheng; Yury S Polikanov; Andrew V Colasanti; Nicolas Clauvelin; Swagatam Mukhopadhyay; Anirvan M Sengupta; Vasily M Studitsky; Wilma K Olson
Journal:  J Biol Chem       Date:  2012-04-19       Impact factor: 5.157

2.  Chemically accurate coarse graining of double-stranded DNA.

Authors:  Alexey Savelyev; Garegin A Papoian
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-08       Impact factor: 11.205

3.  Local geometry and elasticity in compact chromatin structure.

Authors:  Elena F Koslover; Colin J Fuller; Aaron F Straight; Andrew J Spakowitz
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

Review 4.  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

5.  Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy.

Authors:  Tatyana Romantsov; Itzhak Fishov; Oleg Krichevsky
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

6.  Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

Authors:  Alexey Savelyev; Garegin A Papoian
Journal:  Biophys J       Date:  2009-05-20       Impact factor: 4.033

7.  Tension-dependent structural deformation alters single-molecule transition kinetics.

Authors:  B Sudhanshu; S Mihardja; E F Koslover; S Mehraeen; C Bustamante; A J Spakowitz
Journal:  Proc Natl Acad Sci U S A       Date:  2011-01-18       Impact factor: 11.205

8.  Quantitative theory of telomere length regulation and cellular senescence.

Authors:  Ignacio A Rodriguez-Brenes; Charles S Peskin
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-05       Impact factor: 11.205

9.  ICM Web: the interactive chromatin modeling web server.

Authors:  Richard C Stolz; Thomas C Bishop
Journal:  Nucleic Acids Res       Date:  2010-06-11       Impact factor: 16.971

10.  Spatial and topological organization of DNA chains induced by gene co-localization.

Authors:  Ivan Junier; Olivier Martin; François Képès
Journal:  PLoS Comput Biol       Date:  2010-02-12       Impact factor: 4.475
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