Figure 3
From: Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
Plectoneme diffusion and sequence-dependent localization:
(a), Diffusion coefficients for plectonemes at positive σ as a function of stretching force. σ is chosen as in Ref. 12 such that approximately 25% of the strand length is in the plectonemic state on average. The diffusion constant Dunp for unpinned plectonemes (green) is compared to the observed effective diffusion constant Deff (red). (b), Fraction of time plectonemes are found without a tip bubble (blue) compared to the relative slowdown of diffusion Deff/Dunp (magenta). The close agreement suggests that the slowing down of the observed Deff compared to Dunp is mainly due to pinning. (c), Position distribution of plectonemes at σ = −0.06 and F = 1.27 pN. Results are shown in red for a random sequence and in blue for a block-random sequence, as explained in the text. Plectoneme formation is suppressed near strand ends because these are clamped. For each sequence, the upper part of the figure shows coloured positions for AT basepairs and white for CG basepairs. Plectonemes in the tip-bubble regime strongly localize to AT-rich regions.
