Figure 2

Plectoneme tip-bubble regime:

(a), The 600-bp plectoneme system for σ = −0.05 and F = 1.27 pN. Enlarged structures show the end loops with and without denatured bases (coloured green). The formation of a 3-bp tip bubble leads to a smaller plectoneme, because the tip can bend more easily and absorb extra undertwist, leading to an increased extension of the full strand by ΔL. (b), A free-energy landscape for σ = −0.08 and F = 1.5 pN. The white line schematically shows the variation of the most likely plectoneme size with bubble size, illustrating the initial size reduction due to end-loop kinking. (c), A free-energy landscape for σ = −0.08 and F = 2.3 pN illustrating how the growth of bubbles leads to shrinking of the plectoneme. Tip-bubble plectonemes with small size () are hard to detect or distinguish from writhed bubbles and so are classed here as bubbles. See SM Section V for further information on the free energy landscape of tip bubbles. (d), Plectoneme kinetics depicted by kymographs of the plectoneme boundaries (green lines). Red denotes the centre of denatured base-pair stretches (bubbles), which pin the plectoneme and slow diffusion. The upper panel shows a simulation at σ = −0.05 and F = 1.27 pN, from which the structures in (a) are taken. The lower panel shows a simulation for a fully pinned state at positive supercoiling, σ = +0.08, F = 7.9 pN, exhibiting much slower effective diffusion. (e), Structure of a tip-bubble plectoneme at σ = −0.08 and F = 2.3 pN, posessing a 12-bp tip bubble and a 134-bp plectoneme. Denatured nucleotides are coloured green.