Figure 5.

Kymographs showing the typical time evolution along the ring contour of knotted and plectonemically-wound regions, see legend for colour code. The three kymographs are for: (A) supercoiled 5₁-knotted rings, (B) torsionally-relaxed 5₁-knotted rings and (C) supercoiled unknotted rings. The boundaries of the knotted and the main plectonemically-wound regions of case (A) are noticeable stabler than for case (B) and (C) due to the persistent interlocking of multiple strands. This is illustrated in the snapshots above panel (A), where the same region at the knot-superhelix boundary (bp 1000–bp 1200, highlighted in red in the insets) remains entangled with other ring portions throughout the trajectory. The midpoint of this region is marked with a red bead in the insets and with a dotted red line in panel A.