采用分子动力学和量子力学计算研究拉伸 DNA。
Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.
机构信息
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
出版信息
Biophys J. 2010 Jan 6;98(1):101-10. doi: 10.1016/j.bpj.2009.08.062.
Abstract
We combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our combined quantum-mechanical/molecular-mechanical approach demonstrates that molecular-mechanical force fields are able to describe both the backbone and base-base interactions within the highly distorted nucleic acid structures produced by stretching the DNA from the 5' ends, which include conformations containing disassociated basepairs, just as well as these force fields describe relaxed DNA conformations. The molecular-dynamics simulations indicate that the force-induced melting pathway is sequence-dependent and is influenced by the availability of noncanonical hydrogen-bond interactions that can assist the disassociation of the DNA basepairs. The biological implications of these results are discussed.
摘要
我们结合原子分子动力学模拟和量子力学计算来研究双链 DNA 拉伸行为的序列依赖性。我们的量子力学/分子力学方法表明，分子力学力场能够描述由拉伸 DNA 从 5' 端产生的高度扭曲的核酸结构中的骨架和碱基对之间的相互作用，这些力场同样能够描述松弛的 DNA 构象。分子动力学模拟表明，力致熔融途径是序列依赖性的，并受到非经典氢键相互作用的可用性的影响，这些相互作用可以辅助 DNA 碱基对的解离。讨论了这些结果的生物学意义。
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