<scp>DNA</scp>Biomechanics

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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“…The pink dashed lines represent hydrogen bonds. The schematics were adapted from ref , and the stacked CG step images were computed with X3DNA …”

Section: Introductionmentioning

confidence: 99%

“…In particular, high-resolution DNA crystal structures primarily adopt three right-handed double-helical states, namely, A, BI, and BII. Repetitions of these local conformations throughout the nucleic acid lead to polymers characterized as A-like, B-like, and C-like, respectively. ,, …”

Section: Introductionmentioning

confidence: 99%