Savelyev Alexey, Papoian Garegin A
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
J Am Chem Soc. 2006 Nov 15;128(45):14506-18. doi: 10.1021/ja0629460.
Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, d(CGAGGTTTAAACCTCG), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.
单价抗衡离子在DNA周围的凝聚会影响DNA链的聚合物性质。例如，与K⁺离子相比，Na⁺离子诱导多条DNA链组装成紧密结构的倾向明显更强。为了研究DNA周围钠和钾离子凝聚的异同，我们对由16个碱基对[d(CGAGGTTTAAACCTCG)]₂组成的DNA寡聚物在显式水中进行了大量广泛的全原子分子动力学模拟。我们发现，与K⁺离子相比，Na⁺离子更深入地穿透DNA内部并在DNA外部凝聚到更大程度。我们基于空间、静电和水合作用的综合作用，对Na⁺对DNA的更大亲和力提供了微观解释。出乎意料的是，我们发现Cl⁻共离子对K⁺离子的静电屏蔽比对Na⁺离子更有效，这导致了DNA周围更大的Na⁺凝聚。为了研究水和离子离散性质的重要性，我们还根据平均场静电理论计算了抗衡离子分布，结果表明与全原子模拟存在显著差异。先前关于DNA周围Na⁺和K⁺凝聚相对程度的实验结果有些矛盾。最近的DNA压缩实验可以解释为表明与K⁺相比，DNA周围的Na⁺凝聚更强，这与我们的模拟结果一致。我们还对实验观察到的碱金属系列Li⁺ < Na⁺ < K⁺ < Rb⁺中DNA电泳迁移率的增加提供了一个简单的解释。我们将各种缓冲液中DNA片段的构象偏好与提出的NMR模型进行了比较。
