Literature DB >> 15783354

Exact theory of kinkable elastic polymers.

Paul A Wiggins1, Rob Phillips, Philip C Nelson.   

Abstract

The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection angles, many rod systems exhibit a high-curvature softening. The signature behavior of these rod systems is a kinking transition in which the bending is localized. Recent DNA cyclization experiments by Cloutier and Widom have offered evidence that the linear-elastic bending theory fails to describe the high-curvature mechanics of DNA. Motivated by this recent experimental work, we develop a simple and exact theory of the statistical mechanics of linear-elastic polymer chains that can undergo a kinking transition. We characterize the kinking behavior with a single parameter and show that the resulting theory reproduces both the low-curvature linear-elastic behavior which is already well described by the worm-like chain model, as well as the high-curvature softening observed in recent cyclization experiments.

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Year:  2005        PMID: 15783354      PMCID: PMC3496790          DOI: 10.1103/PhysRevE.71.021909

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


  19 in total

1.  Force-induced melting of the DNA double helix 1. Thermodynamic analysis.

Authors:  I Rouzina; V A Bloomfield
Journal:  Biophys J       Date:  2001-02       Impact factor: 4.033

2.  Single-molecule studies of DNA mechanics.

Authors:  C Bustamante; S B Smith; J Liphardt; D Smith
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

3.  Kinky helix.

Authors:  F H Crick; A Klug
Journal:  Nature       Date:  1975-06-12       Impact factor: 49.962

Review 4.  Making contacts on a nucleic acid polymer.

Authors:  K Rippe
Journal:  Trends Biochem Sci       Date:  2001-12       Impact factor: 13.807

5.  Contribution of the intrinsic curvature to measured DNA persistence length.

Authors:  Maria Vologodskaia; Alexander Vologodskii
Journal:  J Mol Biol       Date:  2002-03-22       Impact factor: 5.469

6.  Theory of high-force DNA stretching and overstretching.

Authors:  C Storm; P C Nelson
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-05-09

7.  Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization.

Authors:  Yongli Zhang; Donald M Crothers
Journal:  Biophys J       Date:  2003-01       Impact factor: 4.033

8.  Spontaneous sharp bending of double-stranded DNA.

Authors:  Timothy E Cloutier; Jonathan Widom
Journal:  Mol Cell       Date:  2004-05-07       Impact factor: 17.970

9.  Monte Carlo simulations of locally melted supercoiled DNAs in 20 mM ionic strength.

Authors:  Christopher A Sucato; David P Rangel; Dan Aspleaf; Bryant S Fujimoto; J Michael Schurr
Journal:  Biophys J       Date:  2004-05       Impact factor: 4.033

10.  Localized single-stranded bubble mechanism for cyclization of short double helix DNA.

Authors:  Jie Yan; John F Marko
Journal:  Phys Rev Lett       Date:  2004-09-03       Impact factor: 9.161

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  62 in total

1.  Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA.

Authors:  John F Marko; Sébastien Neukirch
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2012-01-11

2.  Dynamical modeling of three-dimensional genome organization in interphase budding yeast.

Authors:  Naoko Tokuda; Tomoki P Terada; Masaki Sasai
Journal:  Biophys J       Date:  2012-01-18       Impact factor: 4.033

3.  Looping probabilities in model interphase chromosomes.

Authors:  Angelo Rosa; Nils B Becker; Ralf Everaers
Journal:  Biophys J       Date:  2010-06-02       Impact factor: 4.033

4.  Cyclization of short DNA fragments and bending fluctuations of the double helix.

Authors:  Quan Du; Chaim Smith; Nahum Shiffeldrim; Maria Vologodskaia; Alexander Vologodskii
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-04       Impact factor: 11.205

5.  Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF.

Authors:  Serguei V Kuznetsov; Sawako Sugimura; Paula Vivas; Donald M Crothers; Anjum Ansari
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-21       Impact factor: 11.205

6.  Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.

Authors:  Gregory J Gemmen; Rachel Millin; Douglas E Smith
Journal:  Biophys J       Date:  2006-09-08       Impact factor: 4.033

Review 7.  Determination of thermodynamics and kinetics of RNA reactions by force.

Authors:  Ignacio Tinoco; Pan T X Li; Carlos Bustamante
Journal:  Q Rev Biophys       Date:  2006-10-16       Impact factor: 5.318

Review 8.  Loops in DNA: an overview of experimental and theoretical approaches.

Authors:  J-F Allemand; S Cocco; N Douarche; G Lia
Journal:  Eur Phys J E Soft Matter       Date:  2006-03-23       Impact factor: 1.890

9.  Geometry of mediating protein affects the probability of loop formation in DNA.

Authors:  Neeraj J Agrawal; Ravi Radhakrishnan; Prashant K Purohit
Journal:  Biophys J       Date:  2008-01-11       Impact factor: 4.033

10.  Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

Authors:  Alberto Marin-Gonzalez; Cesar L Pastrana; Rebeca Bocanegra; Alejandro Martín-González; J G Vilhena; Rubén Pérez; Borja Ibarra; Clara Aicart-Ramos; Fernando Moreno-Herrero
Journal:  Nucleic Acids Res       Date:  2020-05-21       Impact factor: 16.971

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