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DNA Base Pair Hybridization and Water-Mediated Metastable Structures Studied by Molecular Dynamics Simulations

机译：DNA碱基对杂交和水介稳结构的分子动力学模拟研究

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摘要

The base pair hybridization of a DNA segment was studied using molecular dynamics simulation. The results show the obvious correlation between the probability of successful hybridization and the accessible surface area to water of two successive base pairs, including the unpaired base pair adjacent to paired base pair and this adjacent paired base pair. Importantly, two metastable structures in an A-T base pair were discovered by the analysis of the free energy landscape. Both structures involved addition of a water molecule to the linkage between the two nucleobases in one base pair. The existence of the metastable structures provide potential barriers to the Watson-Crick base pair, and numerical simulations show that those potential barriers can be surmounted by thermal fluctuations at higher temperatures. These studies contribute an important step toward the understanding of the mechanism in DNA hybridization, particularly the effect of temperature on DNA hybridization and polymerase chain reaction. These observations are expected to be helpful for facilitating experimental bioanotechnology designs involving fast hybridization.
机译：使用分子动力学模拟研究了DNA片段的碱基对杂交。结果表明，成功杂交的概率与两个连续碱基对（包括与成对碱基对相邻的未配对碱基对和该成对碱基对）的水可及表面积之间的明显相关性。重要的是，通过对自由能态的分析发现了A-T碱基对中的两个亚稳态结构。这两个结构都涉及在一个碱基对中的两个核碱基之间的键上加水分子。亚稳结构的存在为沃森-克里克碱基对提供了势垒，数值模拟表明，这些势垒可以通过较高温度下的热波动来克服。这些研究为理解DNA杂交的机制，特别是温度对DNA杂交和聚合酶链反应的影响，迈出了重要的一步。预期这些观察将有助于促进涉及快速杂交的生物/纳米技术实验设计。

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