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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Chemically accurate coarse graining of double-stranded DNA
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Chemically accurate coarse graining of double-stranded DNA

机译：化学精确的双链DNA粗粒化

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Coarse-grained (CG) modeling approaches are widely used to simulate many important biological processes involving DNA, including chromatin folding and genomic packaging. The bending propensity of a semiflexible DNA molecule critically influences these processes. However, existing CG DNA models do not retain a sufficient fidelity of the important local chain motions, whose propagation at larger length scales would generate correct DNA persistent lengths, in particular when the solution's ionic strength is widely varied. Here we report on a development of an accurate CG model for the double-stranded DNA chain, with explicit treatment of mobile ions, derived systematically from all-atom molecular dynamics simulations. Our model generates complex local motions of the DNA chain, similar to fully atomistic dynamics, leading also to a quantitative agreement of our simulation results with the experimental data on the dependence of the DNA persistence length on the solution ionic strength. We also predict a structural transition in a torsionally stressed DNA nanocircle as the buffer ionic strength is increased beyond a threshold value.
机译：粗粒度（CG）建模方法已广泛用于模拟涉及DNA的许多重要生物过程，包括染色质折叠和基因组包装。半柔性DNA分子的弯曲倾向会严重影响这些过程。但是，现有的CG DNA模型不能对重要的局部链运动保持足够的保真度，特别是当溶液的离子强度变化很大时，其在较大的长度尺度上的传播会生成正确的DNA持久长度。在这里，我们报告了一种对双链DNA链的精确CG模型的开发过程，其中对移动离子进行了显式处理，这是从全原子分子动力学模拟系统地得出的。我们的模型生成了DNA链的复杂局部运动，类似于完全原子动力学，这也导致了我们的模拟结果与实验数据的定量一致性，实验数据依赖于DNA持久长度对溶液离子强度的依赖性。我们还预测当缓冲离子强度增加到阈值以上时，扭转应力的DNA纳米圆会发生结构转变。

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