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首页> 外文期刊>Chemistry: A European journal >Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation:Correlated Ab Initio Calculations and Molecular Dynamics Simulations
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Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation:Correlated Ab Initio Calculations and Molecular Dynamics Simulations

机译：非极性碱基类似物修饰的DNA双链体的出色热力学稳定性是由于增加的堆叠相互作用和良好的溶剂化作用：相关的从头算和分子动力学模拟

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摘要

The geometries of DNA hex-amer(5'-GGAACC-3')and DNA 13-mer(5'-GCGTACACATGCG-3')have been determined by molecular dynamics(MD)simulations using an empirical force field.The central canonical base pair was replaced by a pair of nonpolar base analogues,2,2'-bipyridyl and 3-methylisocarbostyril.The stabilization energy of the model system(model A)consisting of a central base pair(base-analogue pair)and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set.The geometry of the model was averaged from structures determined by MD simulations.The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system(model B)which also contained a sugar-phosphate backbone.The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair(model A)were comparable to the stability of both duplexes experimentally determined.This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair.The selectivity of the base-analogue pair was reproduced(model B)when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.
机译：DNA六聚体（5'-GGAACC-3'）和DNA 13-mer（5'-GCGTACACATGCG-3'）的几何结构已通过分子动力学（MD）模拟使用经验力场进行了确定。该对被一对非极性碱基类似物2,2'-联吡啶和3-甲基异咔唑取代。模型系统（模型A）的稳定能由一个中心碱基对（碱基类似物对）和两个相邻碱基对组成使用扩展的aug-cc-pVDZ基集通过RI-MP2方法确定，模型的几何形状由MD模拟确定的结构求平均值，COSMO连续介质溶剂模型涵盖了溶剂的作用并进行了计算对于较大的模型系统（模型B），它也包含糖磷酸盐骨架。未扰动系统和被碱基类似物对（模型A）扰动的系统的总稳定能与实验确定的两个双链体的稳定性相当这是由于大量堆叠碱基-类似物自对的相互作用能补偿被取代的腺嘌呤...胸腺嘧啶碱基对的缺失氢键能。当包括其去溶剂化能时，复制了碱基-类似物对的选择性（模型B）通过近似SCC-DFTB-D方法确定两条链的相互作用能。

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