Literature DB >> 11414929

Structural transitions in DNA driven by external force and torque.

A Sarkar1, J F Léger, D Chatenay, J F Marko.   

Abstract

Experiments on single DNA molecules have shown that abrupt transitions between states of different extensions can be driven by stretching and twisting. Here we show how a simple statistical-mechanical model can be used to globally fit experimental force-extension data of Léger et al. [Phys. Rev. Lett. 83, 1066 (1999)], over a wide range of DNA molecule twisting. We obtain the mean twists, extensions, and free energies of the five DNA states found experimentally. We also predict global force-torque and force-linking number phase diagrams for DNA. At zero force, the unwinding torque for zero-force structural transition from the double helix to an unwound structure is found to be approximately -2kBT, while the right-handed torque needed to drive DNA to a highly overwound state approximately 7kBT.

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Year:  2001        PMID: 11414929     DOI: 10.1103/PhysRevE.63.051903

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


  31 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.  Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA.

Authors:  Florian C Oberstrass; Louis E Fernandes; Zev Bryant
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-02       Impact factor: 11.205

3.  Ionic effects on overstretching transition of B-DNA.

Authors:  Hongxia Fu; Chan Ghee Koh; Hu Chen
Journal:  Eur Phys J E Soft Matter       Date:  2005-05-27       Impact factor: 1.890

4.  On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension.

Authors:  Jeff Wereszczynski; Ioan Andricioaei
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-23       Impact factor: 11.205

5.  Force-induced structural transitions in cross-linked DNA films.

Authors:  A André; F Fontaine-Vive; H M Möller; T Fischer; G Maret; V T Forsyth; T Gisler
Journal:  Eur Biophys J       Date:  2008-01-31       Impact factor: 1.733

6.  Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner.

Authors:  Artem K Efremov; Yuanyuan Qu; Hugo Maruyama; Ci J Lim; Kunio Takeyasu; Jie Yan
Journal:  J Biol Chem       Date:  2015-04-30       Impact factor: 5.157

7.  Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: effects of structural defects on structure and force-extension relation.

Authors:  H Li; T Gisler
Journal:  Eur Phys J E Soft Matter       Date:  2009-10-22       Impact factor: 1.890

8.  PicoNewton-millisecond force steps reveal the transition kinetics and mechanism of the double-stranded DNA elongation.

Authors:  Pasquale Bianco; Lorenzo Bongini; Luca Melli; Mario Dolfi; Vincenzo Lombardi
Journal:  Biophys J       Date:  2011-08-17       Impact factor: 4.033

9.  Statistical mechanics of a double-stranded rod model for DNA melting and elasticity.

Authors:  Jaspreet Singh; Prashant K Purohit
Journal:  Soft Matter       Date:  2020-08-26       Impact factor: 3.679

10.  Physiological levels of salt and polyamines favor writhe and limit twist in DNA.

Authors:  Qing Shao; Sachin Goyal; Laura Finzi; David Dunlap
Journal:  Macromolecules       Date:  2012-03-30       Impact factor: 5.985

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