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arXiv 2008.05686cond-mat.soft
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环状DNA的扭转动力学与屈曲不稳定性:沟槽不对称性与各向异性弯曲的影响

Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending

Yair Augusto Gutierrez Fosado, Fabio Landuzzi, Takahiro Sakaue

AI总结:

结合解析理论与分子动力学模拟,研究了环状DNA质粒在局部扭转扰动下的弛豫动力学,揭示了三个特征时间尺度,发现沟槽不对称性引起的扭转-弯曲耦合显著影响各阶段,并指出各向同性可扭转蠕虫链模型无法定量预测屈曲转变的不稳定性模式。

摘要:

通过结合解析理论与分子动力学模拟,我们研究了最初经历局部扭转扰动的DNA环状质粒的弛豫动力学。我们识别出三个独特的时间尺度:(I)局部弯曲的快速弛豫,(II)缓慢的扭转扩散,以及(III)在更长的时间尺度上发生的屈曲转变。在所有这些阶段中,由DNA双螺旋的沟槽不对称性引起的扭转-弯曲耦合均有明显表现。特别是,时间尺度的分离使得能够在阶段(II)中推导出一个有效扩散方程,其扩散系数受扭转-弯曲耦合影响。我们还讨论了使用重整化的弯曲和扭转模量将现实的DNA模型映射到最简单的各向同性可扭转蠕虫链;尽管这在许多情况下是有用的,但它无法对屈曲转变的不稳定性模式做出定量预测。

英文摘要:

By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation of local bending, (II) the slow twist spreading, and (III) the buckling transition taking place in a much longer time scale. In all of these stages, the twist-bend coupling arising from the groove asymmetry in DNA double helix clearly manifests. In particular, the separation of time scales allows to deduce an effective diffusion equation in stage (II), with a diffusion coefficient influenced by the twist-bend coupling. We also discuss the mapping of the realistic DNA model to the simplest isotropic twistable worm-like chain using the renormalized bending and twist moduli; although useful in many cases, it fails to make a quantitative prediction on the instability mode of buckling transition.

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