title: 5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.
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.
authors: Department of Physics and Astronomy, Rutgers, the State University of New Jersey , Piscataway, New Jersey 08854, United States.
authors: Tahir I
authors: TI
authors: Yusufaly
authors: Yun
authors: Y
authors: Li
authors: Wilma K
authors: WK
authors: Olson
mesh_terms: D020029:Base Pairing; D055598:Chemical Phenomena; D003596:Cytosine / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D008958:Models, Molecular; D011789:Quantum Theory
chemical_list: D003596:Cytosine; D004247:DNA