Chapter title |
Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix
|
---|---|
Chapter number | 23 |
Book title |
The Bacterial Nucleoid
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-7098-8_23 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7097-1, 978-1-4939-7098-8
|
Authors |
Thibaut Lepage, Ivan Junier, Lepage, Thibaut, Junier, Ivan |
Abstract |
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. |
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