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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 3. — Pushing of DNA knots towards nicks and gaps does not require antipodal locations of active and passive swivel sites and it applies to all tested knot types. (A, B) snapshots of the simulation where active and passive swivel sites (indicated as blue and reddish beads, respectively) are placed 90° apart on the circular map of 3 kb large plasmid forming a trefoil knot. (C, D) snapshots from the simulation where a complex knot with 8 crossings (8₁₈) is pushed towards the nick site. Notice that also in this case the knot is progressively tightened and localizes in the vicinity of a nick site (reddish bead). Inset shows 8₁₈ knot in a form with its minimal number of perceived crossings.