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首页> 外文期刊>Chemistry: A European journal >On the nature of DNA-duplex stability
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On the nature of DNA-duplex stability

机译：DNA双链体稳定性的本质

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The unwinding free energy of 128 DNA octamers was correlated with the sum of interaction energies among DNA bases and their solvation energies. ne former energies were determined by using the recently developed density functional theory procedure augmented by London dispersion energy (RI-DFT-D) that provides accurate hydrogen-bonding and stacking energies highly comparable with CCSD(T)/complete basis set limit benchmark data. Efficient tight-binding DFT covering dispersion energy was also used and yielded satisfactory results. The latter method can be used for extended systems. The solvation energy was determined by using a CPCM continuum solvent at HF level calculations. Various models were adopted to correlate theoretical energies with experimental unwinding free energies. Unless all energy components (hydrogen-bonding, intra- and interstrand-stacking, and solvation energies) were included and weighted individually, no satisfactory correlation resulted. The most advanced model yielded very close correlation (RMSE=0.32 kcal mol(-1)) fully comparable with the entirely empirical correlation introduced in the original paper. 131 Analysis of the theoretical results shows the importance of inter- and intramolecular stacking energies, and especially the latter term plays a key role in determining DNA-duplex stabilization.
机译：128个DNA八聚体的释放自由能与DNA碱基之间的相互作用能之和及其溶剂化能相关。通过使用最近开发的密度泛函理论方法（由伦敦色散能量（RI-DFT-D）增强）来确定前一种能量，该方法可提供与CCSD（T）/完全基准集极限基准数据高度可比的精确氢键和堆积能。还使用了覆盖分散能量的高效紧密结合DFT，并获得令人满意的结果。后一种方法可用于扩展系统。通过在HF水平计算中使用CPCM连续溶剂确定溶剂化能。采用各种模型将理论能量与实验展开自由能相关联。除非包括所有能量成分（氢键，链内和链间堆叠以及溶剂化能）并分别加权，否则不会产生令人满意的相关性。最先进的模型产生了非常接近的相关性（RMSE = 0.32 kcal mol（-1）），与原始论文中引入的完全经验相关性完全可比。 131对理论结果的分析表明了分子间和分子内堆积能量的重要性，尤其是后一项在确定DNA双链体的稳定中起着关键作用。

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