反离子在DNA双螺旋结构周围的结构：分子动力学研究
Structuring of counterions around dna double helix: a molecular dynamics study
摘要：
用分子动力学方法研究了DNA双螺旋周围反离子的结构。模拟了DNA十二聚体d（CGCGAATTCGCG）在含有碱金属反离子Na $^{+}$、K $^{+}$和Cs $^{+}$的水溶液中的反应。在没有过量盐和添加不同盐（0.5 M NaCl、KCl或CsCl）的情况下考虑了系统。结果表明，Na $^{+}$反离子直接从双螺旋的外部和通过DNA小沟顶部边缘的水分子与磷酸基团相互作用。钾离子主要位于双螺旋的凹槽中，铯离子深入小沟内部，直接与核酸碱基的原子键合。由于静电排斥的氯离子往往是本地化在大距离的DNA聚阴离子，但一些Cl $^{-}$阴离子已被检测到附近的双螺旋形成电中性对与抗衡离子已经凝聚在DNA上的原子团。反离子掺入的DNA位点的特征在于双螺旋结构的局部变化。与DNA原子团复合的Na $^{+}$和K $^{+}$的寿命小于0.5 ns，而在铯离子的情况下，其可达到几纳秒。在这个时间尺度上，Cs $^{+}$反离子在DNA小沟中形成了一个结构化的电荷系统，可以被认为是离子晶格。
英文摘要：
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been simulated. The systems have been considered in the regimes without excess salt and with different salts (0.5 M of NaCl, KCl or CsCl) added. The results have showed that the Na$^{+}$ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove being bonded directly to the atoms of nucleic bases. Due to the electrostatic repulsion the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl$^{-}$ anions have been detected near atomic groups of the double helix forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes of double helix structure. The lifetime of Na$^{+}$ and K$^{+}$ in complex with DNA atomic groups is less than 0.5 ns, while in the case of the cesium ions it may reach several nanoseconds. In this time scale, the Cs$^{+}$ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.
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