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.
CITATION STYLE
Lepage, T., & Junier, I. (2017). Modeling bacterial DNA: Simulation of self-avoiding supercoiled worm-like chains including structural transitions of the helix. In Methods in Molecular Biology (Vol. 1624, pp. 323–337). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7098-8_23
Mendeley helps you to discover research relevant for your work.