胞嘧啶的 5-甲基化在 CG：CG 碱基对步骤中：DNA 纳米力学的表观遗传控制的物理化学机制。
5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics.
机构信息
Department of Physics and Astronomy, Rutgers, the State University of New Jersey , Piscataway, New Jersey 08854, United States.
出版信息
J Phys Chem B. 2013 Dec 27;117(51):16436-42. doi: 10.1021/jp409887t. Epub 2013 Dec 16.
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.
摘要
范德华密度泛函理论与非冗余的一组来自核酸数据库的蛋白质-DNA 晶体结构分析相结合，研究 CG:CG 碱基对梯段的堆积能，特别是胞嘧啶 5-甲基化的作用。梯段的主成分分析揭示了主要的集体运动对应于拉伸的“张开”模式和两个剪切的“滑动”和“撕裂”模式在正交平面内。甲基的堆积相互作用全局抑制 CG:CG 步过度扭曲，同时通过局部势能调制使模式软化，从而产生亚稳态。此外，观察到甲基对 CG:CG 相邻碱基对梯段的间接影响与它们对 CG:CG 的直接影响相当重要。研究结果对 DNA 力学的表观遗传控制具有重要意义。
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