FIGURE 4.

(Top) Extension-time-trace for a perfectly periodic DNA of N = 120 basepairs and the same DNA with seven mutations, both under a shear force of f = 12.7 pN (energy parameters as in Fig. 3). Whereas the molecule without mutations starts sliding almost immediately, the molecule with mutations fluctuates about its initial length for some time τ_w before sliding starts. (Bottom) The time-trace of the binding state (open/closed) for the seven mutated basepairs in the sequence. Each mutated basepair (1–7) is unbound wherever the corresponding thick horizontal line is broken, and bound where the line is shown. Note that the mutated basepairs do not open/close independently from each other. Instead, a mutated basepair opens only once all mutated basepairs to the left or right are already open. The black envelope curves emphasize the positions of the outermost bound mutation on each side. Their dynamics resembles a (biased) random walk. Sliding begins when all mutations are open.