DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Abstract

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.