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

Tomohiro Yanao*, Sosuke Sano, Kenichi Yoshikawa

*この研究の対応する著者

研究成果: Article査読

1 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)666-694
ページ数29
ジャーナルAIMS Biophysics
2
4
DOI
出版ステータスPublished - 2015

ASJC Scopus subject areas

  • 生物理学
  • 構造生物学
  • 生化学
  • 分子生物学

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