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. 2014 Aug 13;42(16):10786–10794. doi: 10.1093/nar/gku735

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© The Author(s) 2014. 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 5. — J factor comparison. The J factor was computed using a fixed end-to-end distance of 5 nm without end-to-end angular or torsional constraints. We used the WHAM to calculate J factors predicted by the WLC model (black circles), the KWLC model with and (red triangles), and with and (blue squares). The dash-dotted line is the WLC prediction according to the Douarche–Cocco approximation (47). For comparison, the J factors from Vafabakhsh and Ha (24) are also shown. Symbols marked with ‘x’ indicate J factors measured from surface-immobilized DNA in 1 M [Na⁺] and symbols marked with ‘+’ from vesicle-encapsulated DNA at 10 mM [Mg²⁺]. For consistency with our calculation, we shifted the original data (24) by 10 bp to the left to account for the linker length. The arrows indicate where the KWLC model deviates from the WLC model. We performed four simulations to generate the SEM error bars for each J factor.

Inline graphic — J factor comparison. The J factor was computed using a fixed end-to-end distance of 5 nm without end-to-end angular or torsional constraints. We used the WHAM to calculate J factors predicted by the WLC model (black circles), the KWLC model with and (red triangles), and with and (blue squares). The dash-dotted line is the WLC prediction according to the Douarche–Cocco approximation (47). For comparison, the J factors from Vafabakhsh and Ha (24) are also shown. Symbols marked with ‘x’ indicate J factors measured from surface-immobilized DNA in 1 M [Na⁺] and symbols marked with ‘+’ from vesicle-encapsulated DNA at 10 mM [Mg²⁺]. For consistency with our calculation, we shifted the original data (24) by 10 bp to the left to account for the linker length. The arrows indicate where the KWLC model deviates from the WLC model. We performed four simulations to generate the SEM error bars for each J factor.