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Van der Waals density functional theory is integrated with analysis of anon-redundant set of protein-DNA crystal structures from the Nucleic AcidDatabase to study the stacking energetics of CG:CG base-pair steps,specifically the role of cytosine 5-methylation. Principal component analysisof the steps reveals the dominant collective motions to correspond to a tensile'opening' mode and two shear 'sliding' and 'tearing' modes in the orthogonalplane. The stacking interactions of the methyl groups globally inhibit CG:CGstep overtwisting while simultaneously softening the modes locally viapotential energy modulations that create metastable states. Additionally, theindirect effects of the methyl groups on possible base-pair steps neighboringCG:CG are observed to be of comparable importance to their direct effects onCG:CG. The results have implications for the epigenetic control of DNAmechanics.

5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics