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Simulation snapshots of negatively supercoiled DNA molecules forming right-handed trefoil knots. The modeled molecules correspond to plasmids with about 3000 bp and ΔLk = −16. The shaded regions indicate the position of the knotted portions of the modeled molecules. (A) A configuration with the knot localized in the apical loop of the supercoiled plasmid. (B) A configuration with the knotted portion moving between the two apical loops.
