Molecular Dynamics Simulations of DNA Solvation Dynamics
Molecular Dynamics Simulations of DNA Solvation Dynamics
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DOI：
10.1021/jz100485e
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发表时间：
2010-06-17
影响因子：
5.7
通讯作者：
Corcelli, S. A.
中科院分区：
文献类型：
--
作者：
Furse, K. E.;Corcelli, S. A.
荧光探针分子掺入DNA的时间依赖性斯托克斯位移实验已经揭示了从飞秒到几十纳秒的广泛时间尺度。最近的一系列分子动力学模拟研究了最长的溶剂化动力学时间尺度，有时相互矛盾的解释。这些计算研究的结论进行了审查沿着与理论方法，利用分解计算的溶剂化反应中存在的系统中的水，DNA和离子的成分。广泛验证染料分子的一种此类分解程序。Hoechst 33258与DNA结合表明，实验测得的19 ps的长时间尺度是由于DNA。未来的机遇和挑战，从理论和实验的角度也简要强调。
Time-dependent Stokes shift experiments of flourescent probe molecules incorporated into DNA have uncovered a broad range of time scales from femtoseconds to tens of nanoseconds. A series of recent molecular dynamics simulations have investigated the longest solvation dynamics time scales with some times conflicting interpretations. The conclusions of these computational studies are reviewed along with the theoretical methodologies that are utilized to decomposed calculated solvation responses in terms of the components present in the system water, DNA and ions. Extensive validation of one such decomposition procedure for the dye molecule. Hoechst 33258 bound to DNA reveals that the long time scale measured experimentally, 19 ps, is due to DNA. Future opportunities and challenges from both a theoretical and experimental perspective are also briefly highlighted.