Literature DB >> 30999490

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.

Stefanos K Nomidis1,2, Enrico Skoruppa1, Enrico Carlon1, John F Marko3.   

Abstract

The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness C_{eff} for small twist-bend coupling. We find that the "bare" G is "screened" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G=0 but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo "triad" and molecular dynamics "oxDNA" models, characterized by different degrees of coarse graining, validating the perturbative and nonperturbative analyses. While our theory is in generally good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely used coarse-grained models.

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Year:  2019        PMID: 30999490      PMCID: PMC6561648          DOI: 10.1103/PhysRevE.99.032414

Source DB:  PubMed          Journal:  Phys Rev E        ISSN: 2470-0045            Impact factor:   2.529


  43 in total

1.  Sequence-dependent elastic properties of DNA.

Authors:  F Lankas; J Sponer; P Hobza; J Langowski
Journal:  J Mol Biol       Date:  2000-06-09       Impact factor: 5.469

2.  Structural transitions and elasticity from torque measurements on DNA.

Authors:  Zev Bryant; Michael D Stone; Jeff Gore; Steven B Smith; Nicholas R Cozzarelli; Carlos Bustamante
Journal:  Nature       Date:  2003-07-17       Impact factor: 49.962

3.  Elastic correlations in nucleosomal DNA structure.

Authors:  Farshid Mohammad-Rafiee; Ramin Golestanian
Journal:  Phys Rev Lett       Date:  2005-06-15       Impact factor: 9.161

4.  Decomposition of the linking number of a closed ribbon: A problem from molecular biology.

Authors:  F B Fuller
Journal:  Proc Natl Acad Sci U S A       Date:  1978-08       Impact factor: 11.205

5.  Conformational fluctuations of DNA helix.

Authors:  D E Depew; J C Wang
Journal:  Proc Natl Acad Sci U S A       Date:  1975-11       Impact factor: 11.205

6.  Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers.

Authors:  Francesco Mosconi; Jean François Allemand; David Bensimon; Vincent Croquette
Journal:  Phys Rev Lett       Date:  2009-02-17       Impact factor: 9.161

7.  How topological constraints facilitate growth and stability of bubbles in DNA.

Authors:  Jae-Hyung Jeon; Wokyung Sung
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

8.  Asymmetric elastic rod model for DNA.

Authors:  B Eslami-Mossallam; M R Ejtehadi
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-07-24

9.  DNA basepair step deformability inferred from molecular dynamics simulations.

Authors:  Filip Lankas; Jirí Sponer; Jörg Langowski; Thomas E Cheatham
Journal:  Biophys J       Date:  2003-11       Impact factor: 4.033

10.  Towards a molecular dynamics consensus view of B-DNA flexibility.

Authors:  Alberto Pérez; Filip Lankas; F Javier Luque; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2008-02-24       Impact factor: 16.971

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  4 in total

1.  Combined Force-Torque Spectroscopy of Proteins by Means of Multiscale Molecular Simulation.

Authors:  Thijs W G van der Heijden; Daniel J Read; Oliver G Harlen; Paul van der Schoot; Sarah A Harris; Cornelis Storm
Journal:  Biophys J       Date:  2020-10-27       Impact factor: 4.033

2.  Design Approaches and Computational Tools for DNA Nanostructures.

Authors:  Heeyuen Koh; Jae Gyung Lee; Jae Young Lee; Ryan Kim; Osamu Tabata; Kim Jin-Woo; DO-Nyun Kim
Journal:  IEEE Open J Nanotechnol       Date:  2021-10-14

Review 3.  Energetics of twisted DNA topologies.

Authors:  Wenxuan Xu; David Dunlap; Laura Finzi
Journal:  Biophys J       Date:  2021-05-08       Impact factor: 3.699

4.  Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.

Authors:  Salvatore Assenza; Rubén Pérez
Journal:  J Chem Theory Comput       Date:  2022-04-08       Impact factor: 6.578

  4 in total

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