Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity

Tomohiro Yanao; Sosuke Sano; Kenichi Yoshikawa; Tomohiro Yanao; Sosuke Sano; Kenichi Yoshikawa

doi:10.3934/biophy.2015.4.666

AIMS Biophysics

2015, Volume 2, Issue 4: 666-694. doi: 10.3934/biophy.2015.4.666

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Research article Special Issues

Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity

1.
Department of Applied Mechanics and Aerospace Engineering, Waseda University, Tokyo 169-8555, Japan;
2.
Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan

Received: 28 August 2015 Accepted: 29 October 2015 Published: 06 November 2015

Wrapping, crossover, and braiding of DNA are the motifs of fundamental interest in genome packaging, gene regulation, and enzyme recognition. This study explores elastic mechanisms for the selection of chirality in wrapping, crossover, and braiding of DNA based on a coarse-grained model. The DNA model consists of two elastic chains that mutually intertwine in a right-handed manner forming a double-stranded helix with the distinction between major and minor grooves. Although individual potential energy functions of the DNA model have no asymmetry in terms of left and right twist, the model as a whole exhibits an asymmetric propensity to writhe in the left direction upon bending due to the right-handed helical geometry. Monte Carlo simulations of this model suggest that DNA has a propensity to prefer left-handed wrapping around a spherical core particle and also around a uniform rod due to the asymmetric elastic coupling between bending and writhing. This result indicates an elastic origin of the uniform left-handed wrapping of DNA in nucleosomes and also has implications on the wrapping of double-stranded DNA around rod-like molecules. Monte Carlo simulations of the DNA model also suggest that two juxtaposed DNA molecules can braid each other spontaneously under moderate attractive interactions with the preference for left-handed braiding due to the asymmetric coupling between bending and writhing. This result suggests the importance of asymmetric elasticity in the selection of chirality in braiding of a pair of DNA molecules.
- DNA,
- chirality,
- elasticity,
- wrapping,
- braiding,
- crossover,
- nucleosome,
- helical polymer,
- double-strand,
- Monte Carlo simulation
Citation: Tomohiro Yanao, Sosuke Sano, Kenichi Yoshikawa. Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity[J]. AIMS Biophysics, 2015, 2(4): 666-694. doi: 10.3934/biophy.2015.4.666

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Abstract

Wrapping, crossover, and braiding of DNA are the motifs of fundamental interest in genome packaging, gene regulation, and enzyme recognition. This study explores elastic mechanisms for the selection of chirality in wrapping, crossover, and braiding of DNA based on a coarse-grained model. The DNA model consists of two elastic chains that mutually intertwine in a right-handed manner forming a double-stranded helix with the distinction between major and minor grooves. Although individual potential energy functions of the DNA model have no asymmetry in terms of left and right twist, the model as a whole exhibits an asymmetric propensity to writhe in the left direction upon bending due to the right-handed helical geometry. Monte Carlo simulations of this model suggest that DNA has a propensity to prefer left-handed wrapping around a spherical core particle and also around a uniform rod due to the asymmetric elastic coupling between bending and writhing. This result indicates an elastic origin of the uniform left-handed wrapping of DNA in nucleosomes and also has implications on the wrapping of double-stranded DNA around rod-like molecules. Monte Carlo simulations of the DNA model also suggest that two juxtaposed DNA molecules can braid each other spontaneously under moderate attractive interactions with the preference for left-handed braiding due to the asymmetric coupling between bending and writhing. This result suggests the importance of asymmetric elasticity in the selection of chirality in braiding of a pair of DNA molecules.

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