Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA
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Author(s)
Cong, Peiwen
Dai, Liang
Chen, Hu
van der Maarel, Johan R.C.
Doyle, Patrick S.
Yan, Jie
Doyle, Patrick S.
Date Issued
December 2015
Journal
Biophysical Journal
Publisher
Elsevier
Citation
Cong, Peiwen, Liang Dai, Hu Chen, Johan R.C. van der Maarel, Patrick S. Doyle, and Jie Yan. “Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.” Biophysical Journal 109, no. 11 (December 2015): 2338–51.
Version
Final published version
Abstract
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1016/j.bpj.2015.10.016
