Self-organised criticality in base-pair breathing in DNA with a defect

Abstract

We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to −1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or ’melting’) and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

DOI: 10.1016/j.physd.2011.04.018

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Cite this paper

@inproceedings{Duduial2011SelforganisedCI, title={Self-organised criticality in base-pair breathing in DNA with a defect}, author={Ciprian-Ionuţ Duduială and Jonathan A D Wattis and Charles A. Laughton}, year={2011} }