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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 2. — Arising supercoiling in nicked circular DNA pushes the trefoil knot towards the site of the nick. (A). A thermalized configuration of trefoil-forming nicked DNA molecule with ca 3000 bp with the sites of active swivel (gyrase) and passive swivel (nick) indicated as blue and reddish beads, respectively. (B, C) Working gyrase progressively confines the knotted portion and pushes it towards the site of the nick. (D) A snapshot from the steady state situation where the knot is localized in the vicinity of the nick and where the rate of supercoil generation by the gyrase is equal to the rate of supercoil dissipation at the site of the nick. Notice that knotted portion is highly localized and highly curved.