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. 2016 Sep 22;44(19):9121–9130. doi: 10.1093/nar/gkw815

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© The Author(s) 2016. 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. — (A) Sequence-dependent denaturation probability observed in negatively supercoiled DNA minicircles at ΔLk ≈ −1 of the RANDOM, FUSE-embedded, and DESIGNED sequences. This probability was calculated using the SIDD model (green) and oxDNA simulation (blue). A-T base pairs are shaded in grey. Secondary denaturation sites due to the cooperative long-ranged kinking predicted by oxDNA simulations are circled. (B) 2D colour plots of the log of the probability for a given pair of base pairs to be simultaneously denatured in ΔLk ≈ −1 minicircles, calculated with oxDNA for the same three sequences. Unsampled states are coloured black. Denaturation is enhanced at specific sites separated by ∼180° (e.g. situated antipodally) along the minicircle, as demonstrated by the off-diagonal peaks in the mutual denaturation probability profile (indicated with red arrows).