Structural dynamics of DNA depending on methylation pattern
Structural dynamics of DNA depending on methylation pattern
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DOI：
10.1103/physreve.103.012404
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发表时间：
2021-01-11
影响因子：
2.4
通讯作者：
Togashi, Yuichi
中科院分区：
文献类型：
--
作者：
Kameda, Takeru;Suzuki, Miho M.;Togashi, Yuichi
DNA甲基化与许多生物学现象有关，在真核基因表达的表观遗传调控中起着至关重要的作用。研究还表明，DNA甲基化改变了DNA分子的机械性质，这可能会影响表观遗传调节。然而，甲基化如何改变DNA的结构和动态特征还没有得到系统的研究。在本研究中，为了阐明甲基化对DNA力学的影响，对具有几种甲基化模式的双链DNA进行了全原子分子动力学模拟。通过分析核苷酸的相对位置(基步变量)，观察到局部柔性方面的特征变化，这进一步影响了整体DNA的几何形状和硬度。这些发现可以作为讨论生理条件下甲基化依赖的DNA动力学的基础。
DNA methylation is associated with a number of biological phenomena, and plays crucial roles in epigenetic regulation of eukaryotic gene expression. It is also suggested that DNA methylation alters the mechanical properties of DNA molecules, which is likely to affect epigenetic regulation. However, it has not been systematically investigated how methylation changes the structural and dynamic features of DNA. In this research, to elucidate the effects of methylation on DNA mechanics, a fully atomic molecular dynamics simulation of double-stranded DNA with several methylation patterns was performed. Through the analysis of the relative positioning of the nucleotides (base-step variables), characteristic changes in terms of local flexibility were observed, which further affected the overall DNA geometry and stiffness. These findings may serve as a basis for a discussion on methylation-dependent DNA dynamics in physiological conditions.