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

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 (SDEs). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FTs) of the inter-base 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.

► DNA dynamics using both AMBER and a stochastic ODE system is modelled. ► 12-base DNA sequence with defective base at centre is modelled. ► A range of twist angles: 30°–40° per base is considered. ► The self-organised critical behaviour in dynamics in both models is shown. ► The log–log plot of Fourier transform of inter-base distance shows the power-law behaviour.