DNA base pair hybridization and water-mediated metastable structures studied by molecular dynamics simulations.
DNA base pair hybridization and water-mediated metastable structures studied by molecular dynamics simulations.
复制标题
DOI：
10.1021/bi2002778
复制
发表时间：
2011-10
期刊：
影响因子：
2.9
通讯作者：
Wenpeng Qi;B. Song;Xiaoling Lei;Chunlei Wang;Haiping Fang
中科院分区：
文献类型：
--
作者：
Wenpeng Qi;B. Song;Xiaoling Lei;Chunlei Wang;Haiping Fang
用分子动力学模拟方法研究了DNA片段的碱基对杂交。结果表明，连续的两对碱基对，包括与成对碱基对相邻的未配对碱基对和这对相邻的成对碱基对，杂交成功的概率与水的可及表面积之间存在明显的相关性。重要的是，通过对自由能图谱的分析，发现了A-T碱基对中的两个亚稳态结构。这两种结构都涉及在一个碱基对中的两个碱基之间的连接上添加一个水分子。亚稳态结构的存在为Watson-Crick碱基对提供了势垒，数值模拟表明，在更高的温度下，热涨落可以克服这些势垒。这些研究有助于了解DNA杂交的机制，特别是温度对DNA杂交和聚合酶链式反应的影响。这些观察结果有望有助于促进涉及快速杂交的实验性生物/纳米技术设计。
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 bio/nanotechnology designs involving fast hybridization.