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

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