Literature DB >> 17358190

Equation of state of looped DNA.

Igor M Kulić1, Hervé Mohrbach, Rochish Thaokar, Helmut Schiessel.   

Abstract

We derive the equation of state of DNA under tension that features a loop. Such loops occur transiently during DNA condensation in the presence of multivalent ions or permanently through sliding protein linkers such as condensin. The force-extension relation of such looped-DNA modeled as a wormlike chain is calculated via path integration in the semiclassical limit. This allows us to rigorously determine the high stretching asymptotics. Notably the functional form of the force-extension curve resembles that of straight DNA, yet with a strongly renormalized apparent persistence length. We also present analogous results for DNA under tension with several protein-induced kinks and/or loops. That means that the experimentally extracted single-molecule elasticity does not necessarily only reflect the bare DNA stiffness, but can also contain additional contributions that depend on the overall chain conformation and length.

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Year:  2007        PMID: 17358190     DOI: 10.1103/PhysRevE.75.011913

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  10 in total

1.  Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling.

Authors:  Andrey G Cherstvy
Journal:  J Biol Phys       Date:  2011-01-18       Impact factor: 1.365

2.  Looping charged elastic rods: applications to protein-induced DNA loop formation.

Authors:  A G Cherstvy
Journal:  Eur Biophys J       Date:  2010-10-21       Impact factor: 1.733

3.  Squeezed helical elastica.

Authors:  Lila Bouzar; Martin Michael Müller; Pierre Gosselin; Igor M Kulić; Hervé Mohrbach
Journal:  Eur Phys J E Soft Matter       Date:  2016-11-29       Impact factor: 1.890

4.  Competition between supercoils and toroids in single molecule DNA condensation.

Authors:  David Argudo; Prashant K Purohit
Journal:  Biophys J       Date:  2012-07-03       Impact factor: 4.033

5.  Mechanical and structural properties of archaeal hypernucleosomes.

Authors:  Bram Henneman; Thomas B Brouwer; Amanda M Erkelens; Gert-Jan Kuijntjes; Clara van Emmerik; Ramon A van der Valk; Monika Timmer; Nancy C S Kirolos; Hugo van Ingen; John van Noort; Remus T Dame
Journal:  Nucleic Acids Res       Date:  2021-05-07       Impact factor: 16.971

6.  Kinetics and thermodynamics of phenotype: unwinding and rewinding the nucleosome.

Authors:  Andrew H Mack; Daniel J Schlingman; Robielyn P Ilagan; Lynne Regan; Simon G J Mochrie
Journal:  J Mol Biol       Date:  2012-08-31       Impact factor: 5.469

7.  Discontinuous growth of DNA plectonemes due to atomic scale friction.

Authors:  Yifei Min; Prashant K Purohit
Journal:  Soft Matter       Date:  2018-09-26       Impact factor: 3.679

8.  Mechanosensing of DNA bending in a single specific protein-DNA complex.

Authors:  Shimin Le; Hu Chen; Peiwen Cong; Jie Lin; Peter Dröge; Jie Yan
Journal:  Sci Rep       Date:  2013-12-16       Impact factor: 4.379

9.  Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends.

Authors:  Rosalie P C Driessen; He Meng; Gorle Suresh; Rajesh Shahapure; Giovanni Lanzani; U Deva Priyakumar; Malcolm F White; Helmut Schiessel; John van Noort; Remus Th Dame
Journal:  Nucleic Acids Res       Date:  2012-11-15       Impact factor: 16.971

10.  Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.

Authors:  Babette E de Jong; Thomas B Brouwer; Artur Kaczmarczyk; Bert Visscher; John van Noort
Journal:  Biophys J       Date:  2018-10-11       Impact factor: 4.033

  10 in total

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