Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 117, Issue 51, Pages 16436-16442Publisher
AMER CHEMICAL SOC
DOI: 10.1021/jp409887t
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Funding
- Lucent Fellowship
- U.S.P.H.S. [GM 34809]
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van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond. to a tensile opening mode and two shear sliding and tearing modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
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