Institute of Applied Physics, National Academy of Sciences of Ukraine, Petropavlivska st. 58, Sumy, 40030, Ukraine.
Phys Chem Chem Phys. 2012 Feb 21;14(7):2250-4. doi: 10.1039/c2cp23499h. Epub 2012 Jan 13.
Numerous theoretical and experimental studies disagree on the impact of surrounding mobile ions on DNA conformational flexibility at high salt content. Specifically, it is not clear how the DNA persistence length varies when concentration of monovalent mobile ions is increased beyond the physiological value of ∼0.1 M. In the present Communication we address this biologically important issue computationally by means of molecular dynamics simulations. We utilize our recently developed chemically accurate coarse-grained model for the double-stranded DNA with explicit mobile ions. We find that in a range of moderate-to-high ionic concentrations, ∼0.1-1 M, DNA persistence length drops noticeably by ∼25%. Our results contradict some experimental works and the celebrated theory of Odijk, Skolnick and Fixman (Skolnick et al., Macromolecules, 1977, 10, 944), suggesting a negligible variation of DNA persistence length at these concentrations. On the other hand, our findings are in near quantitative agreement with a number of other theoretical and experimental studies. Combined with our recent work on elucidating the role of elastic and electrostatic effects in maintaining DNA shape, the results reported here may indicate that conceptually new understanding of DNA rigidity needs to be developed.
许多理论和实验研究在周围移动离子对高盐含量下 DNA 构象灵活性的影响上存在分歧。具体来说，当单价移动离子的浓度超过生理值约 0.1 M 时，DNA 持久性长度如何变化尚不清楚。在本通讯中，我们通过分子动力学模拟从计算上解决了这个具有生物学重要意义的问题。我们利用最近开发的具有显式移动离子的双链 DNA 的化学精确粗粒模型。我们发现，在中等至高离子浓度范围内，约 0.1-1 M，DNA 持久性长度明显下降约 25%。我们的结果与一些实验工作和著名的 Odijk、Skolnick 和 Fixman 理论（Skolnick 等人，Macromolecules，1977，10，944）相矛盾，表明在这些浓度下 DNA 持久性长度几乎没有变化。另一方面，我们的发现与许多其他理论和实验研究非常吻合。结合我们最近关于阐明弹性和静电效应对维持 DNA 形状的作用的工作，这里报告的结果可能表明需要开发对 DNA 刚性的新概念理解。
