论文标题
通过分子模拟探测氧化DNA的显微镜结构和柔韧性
Probing the microscopic structure and flexibility of oxidized DNA by molecular simulations
论文作者
论文摘要
DNA的氧化损伤是分子生物物理学中一个引人注目的问题,因为它在基因表达的表观遗传控制中起着至关重要的作用,并且被认为与诱变,致癌作用和衰老有关。为了了解DNA物理特性的显微镜结构变化以及由于其核苷酸碱基的氧化损伤而对其功能产生的影响,我们已经对双链DNA(DSDNA)进行了全原子分子动态模拟,其鸟嘌呤碱基被氧化。鸟嘌呤碱基更容易受到氧化损伤,因为所有核碱基中氧化还原电位的最低值。我们已经分析了天然和氧化dsDNA的局部和全球机械性能,并通过微观结构参数和热力学计算来解释了这些结果。我们的结果表明,DsDNA的氧化损伤不会变形Watson-Crick几何形状。取而代之的是,发现氧化的DNA结构可以通过静电相互作用更好地稳定。此外,氧化损伤改变了DSDNA的机械,螺旋和凹槽参数。 The persistence length, stretch modulus, and torsional stiffness are found to be 48.87 nm, 1239.26 pN, and 477.30 pN.nm^2, respectively, for native dsDNA, and these values are 61.31 nm, 659.91 pN, and 407.79 pN.nm^2, respectively, when all the guanine bases of the dsDNA are oxidized.与全球机械性能相比,发现螺旋和凹槽特性的变化更为突出,在氧化位点局部集中,并导致氧化损伤区域从BI到BII的骨架构象的过渡。
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the microscopic structural changes in physical properties of DNA and the resulting influence on its function due to oxidative damage of its nucleotide bases, we have conducted all-atom molecular dynamic simulations of double-stranded DNA (dsDNA) with its guanine bases being oxidized. The guanine bases are more prone to oxidative damage due to the lowest value of redox potential among all nucleobases. We have analyzed the local as well as global mechanical properties of native and oxidized dsDNA and explained those results by microscopic structural parameters and thermodynamic calculations. Our results show that the oxidative damage of dsDNA does not deform the Watson-Crick geometry; instead, the oxidized DNA structures are found to be better stabilized through electrostatic interactions. Moreover, oxidative damage changes the mechanical, helical, and groove parameters of dsDNA. The persistence length, stretch modulus, and torsional stiffness are found to be 48.87 nm, 1239.26 pN, and 477.30 pN.nm^2, respectively, for native dsDNA, and these values are 61.31 nm, 659.91 pN, and 407.79 pN.nm^2, respectively, when all the guanine bases of the dsDNA are oxidized. Compared to the global mechanical properties, the changes in helical and groove properties are found to be more prominent, concentrated locally at the oxidation sites, and causing the transition of the backbone conformations from BI to BII at the regions of oxidative damage.