论文标题

核酸的机械性能和非本地可扭曲的虫样链模型

Mechanical properties of Nucleic Acids and the non-local Twistable Wormlike Chain model

论文作者

Segers, Midas, Voorspoels, Aderik, Sakaue, Takahiro, Carlon, Enrico

论文摘要

核酸的机械性能在许多生物学过程中起着重要的作用,这些过程通常涉及这些分子的物理变形。在足够长的长度尺度(例如$ \ sim 20-30 $碱基对)下,DNA和RNA双螺旋的力学由均匀的可扭曲虫状链(TWLC)描述,这是一种以扭曲和弯曲刚度为特征的半融合聚合物模型。在较短的尺度下,该模型分解的原因有两个:弹性特性变为序列依赖性,并且远端位点的机械变形被耦合。我们在本文中讨论了后一种效应的起源,它使用非本地扭曲虫状链(NLTWLC)的框架进行了讨论。我们通过比较DNA和RNA双螺旋的全原子模拟数据表明,非本地耦合在这两个分子中具有非常相似的性质:远端位点之间的耦合对于倾斜度和扭曲的自由度和较弱的倾斜度很强。我们介绍并分析了一个简单的双链聚合物模型,该模型阐明了这种通用远端耦合行为的起源。在称为梯子模型的模型中,NLTWLC的描述从将局部(原子)自由度的粗化构成到角度变量中,这些变量描述了分子的扭曲和弯曲。 NLTWLC与本地对应物的不同,其特征是长度依赖性弹性。我们的分析预测,核酸在几个碱基对的尺度上是机械柔软的,并且在较长的长度尺度上渐近地僵硬,这种行为与实验数据相匹配。

Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites gets coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model which clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables which describe the twist and bending of the molecule. Differently from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior which matches experimental data.

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