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

TL;DR

This study investigates the self-organised criticality in DNA base-pair breathing with a defect, using molecular dynamics and stochastic models, revealing scale-invariant behaviour indicative of phase transition during DNA opening.

Contribution

It demonstrates the presence of self-organised criticality in DNA base-pair breathing through combined MD and SDE analyses, highlighting scale-invariance and phase transition evidence.

Findings

Fourier analysis shows power-law behaviour with gradient near -1.

Both MD and SDE models exhibit pink noise in displacements.

Base-pair breathing linked to DNA melting as a second-order phase transition.

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.