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. 2015 Jul 6;43(15):7229–7236. doi: 10.1093/nar/gkv683

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — Juxtapositions between gaps and duplex regions in confined knots are perfectly suited for topoIII unknotting. Snapshots from the steady state situation where continuous rotations at the active swivel site (blue bead) generate supercoils confining and pushing the trefoil knot towards the site of a short gap (indicated as a green region). Notice on a close up views that gapped region bends over a duplex region located within the tightened knot. This specific structure results from the fact that single stranded DNA regions are very flexible and show decreased electrostatic repulsion since the number of charges in ssDNA is twice smaller than in dsDNA.