5-Methylation of cytosine in CG:CG base-pair steps: A physicochemical mechanism for the epigenetic control of DNA nanomechanics

Tahir I. Yusufaly, Yun Li, Wilma K. Olson

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)16436-16442
Number of pages7
JournalJournal of Physical Chemistry B
Volume117
Issue number51
DOIs
StatePublished - Dec 27 2013

All Science Journal Classification (ASJC) codes

  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry

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