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

TL;DR

This paper presents a Monte-Carlo simulation framework for modeling bacterial DNA as a self-avoiding supercoiled worm-like chain, incorporating structural transitions of the helix to better understand DNA folding and denaturation.

Contribution

It introduces an extended ssWLC model that includes structural transitions, providing a detailed methodology for simulating supercoiled DNA with local structural changes.

Findings

The ssWLC model accurately captures DNA folding under supercoiling.

The extended model incorporates helix structural transitions.

Simulation methods are detailed for future research use.

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.