Lepage Thibaut, Junier Ivan
CNRS, TIMC-IMAG, F-38000, Grenoble, France.
University of Grenoble Alpes, TIMC-IMAG, F-38000, Grenoble, France.
Methods Mol Biol. 2017;1624:323-337. doi: 10.1007/978-1-4939-7098-8_23.
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Like Chain (ssWLC) model, which is known to capture the folding properties of supercoiled DNA, and provide a detailed explanation of a standard MC simulation method. On the other hand, we explain how to extend this ssWLC model to include structural transitions of the helix.
在超螺旋约束下，裸露的DNA，比如大部分细菌DNA，会折叠成称为麻花状结构的辫状结构。双螺旋也会经历局部结构转变，导致变性泡和其他替代结构的形成。已经开发了各种聚合物模型来捕捉这些特性，蒙特卡罗（MC）方法专门用于推断热力学性质。在本章中，我们将按照两个目标解释如何进行此类蒙特卡罗模拟。一方面，我们介绍自回避超螺旋类蠕虫链（ssWLC）模型，该模型已知能捕捉超螺旋DNA的折叠特性，并详细解释一种标准的MC模拟方法。另一方面，我们解释如何扩展这个ssWLC模型以纳入螺旋的结构转变。
