  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.
