Figure 3.
Kinetic analysis of cruciform extrusion and rewinding for Charomid 9-5 kb DNA. (A) As negative DNA supercoiling increases, progressively less time is spent in the B-DNA state and more time is spent in the extruded-cruciform state. Experiments were performed at F = 0.45 pN. (B) Free energy barrier to cruciform extrusion (blue) and rewinding (red) as a function of negative supercoiling. The barrier to cruciform extrusion decreases linearly with negative supercoiling at a rate of 0.31 ± 0.015 kBT/turn (B-DNA is destabilized by unwinding), while the barrier to rewinding increases linearly by 0.71 ± 0.014 kBT/turn (cruciform DNA is stabilized by unwinding). At least ∼300 events were measured at each rotation point to determine each mean transition rate.