Figure 5.

(a) The writhe of the over wound 65 bp loop [65A⁽⁺¹⁾] increases from zero to around 0.75 as the circle to plectoneme transformation takes place (blue). As the writhe increases the two base pairs, 40 and 61 are brought into close contact as they form the crossover necessary to create the plectoneme (red). The distance shown is measured between the centre of masses of the two base pairs. (b) A representative molecular structure of the two strands forming a crossover taken from the MD simulation. Isodensity surface of Na⁺ counterions is shown in red. The ion density is shown at 120 ions per ų, as calculated over the final 25 ns (25 000 snapshots) of simulation 65A⁽⁺¹⁾.