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Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

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The Bacterial Nucleoid

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1624))

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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Authors and Affiliations

  1. CNRS, TIMC-IMAG, F-38000, Grenoble, France

    Thibaut Lepage & Ivan Junier

  2. University of Grenoble Alpes, TIMC-IMAG, F-38000, Grenoble, France

    Thibaut Lepage & Ivan Junier

Authors
  1. Thibaut Lepage
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  2. Ivan Junier
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Corresponding author

Correspondence to Ivan Junier .

Editor information

Editors and Affiliations

  1. UMR CNRS 7241, INSERM U1050, CIRB, Collège de France, Paris, France

    Olivier Espéli

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Lepage, T., Junier, I. (2017). Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix. In: Espéli, O. (eds) The Bacterial Nucleoid. Methods in Molecular Biology, vol 1624. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7098-8_23

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  • DOI: https://doi.org/10.1007/978-1-4939-7098-8_23

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7097-1

  • Online ISBN: 978-1-4939-7098-8

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