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首页> 外文期刊>The journal of physical chemistry, C. Nanomaterials and interfaces >Can Charge Recombination in DNA Hairpins Be Controlled by Counterions?
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Can Charge Recombination in DNA Hairpins Be Controlled by Counterions?

机译：可以通过抗衡离子控制的DNA发夹中的重组吗？

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摘要

To decide whether counterforts can affect the rate of charge recombination in DNA hairpins, the influence of the salt concentration on the free energy of this process was studied computationally using molecular dynamics simulations. The calculations were performed using the implicit treatment of the surroundings (the MM-PBSA and MM-GBSA techniques) and the explicit description of counterions and water molecules (thermodynamic integration). The data obtained with these distinct approaches were found to be in good agreement. The effect of counterions on the free energy of the charge recombination process was found to be small. For the hairpins with six A/T base pairs between the donor and acceptor chromophores, the difference in the value of the free energy does not exceed 0.5 kcal/mol when the environment changes from pure water to the 0.1 M NaCl solution typical for kinetic measurements of charge recombination in DNA hairpins. Even a smaller salt effect has numerically been obtained for a shorter hairpin containing three A/T pairs. These results suggest that under typical experimental conditions, the counterions cannot control the rate of charge recombination. For a highly concentrated salt solution (1M NaCl), the influence of counterions on the energetics of the process becomes stronger. Since in this case the free energy for charge recombination exhibits a more substantial but still kinetically insignificant increase, the calculated rate of the process only slightly decreases with the salt concentration.
机译：为了确定是否可以影响DNA发夹中的电荷重组速率，使用分子动力学模拟在计算上研究了盐浓度对该方法的自由能的影响。使用隐含的周围处理（MM-PBSA和MM-GBSA技术）和分子和水分子的明确描述进行计算（热力学集成）。发现通过这些不同方法获得的数据很吻合。对抗对电荷重组过程的自由能的影响是小的。对于在供体和受体发色团之间的六个A / T碱基对的发夹，当环境从纯水变为0.1M NaCl溶液以进行动力测量时，自由能值的差异不会超过0.5kcal / mol DNA发夹中的电荷重组。甚至在含有三个A / T对的较短发夹的较短发夹的情况下也是较小的盐效应。这些结果表明，在典型的实验条件下，抗衡离子不能控制电荷重组速率。对于高度浓缩的盐溶液（1M NaCl），抗衡离子对过程的能量的影响变得更强。由于在这种情况下，用于电荷重组的自由能表现出更显着但仍然动态的增加的增加，因此该方法的计算速率仅略微降低盐浓度。

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