Rejnek Jaroslav, Hobza Pavel
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nAm. 2, 166 10 Prague 6, Czech Republic.
J Phys Chem B. 2007 Jan 25;111(3):641-5. doi: 10.1021/jp0661692.
The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.
计算了总共15个含有不寻常碱基互变异构体的氢键核酸碱基对的总相互作用能。所有选定的腺嘌呤 - 胸腺嘧啶和鸟嘌呤 - 胞嘧啶氢键碱基对的几何性质使其能够掺入DNA中。将不寻常的碱基配对模式与腺嘌呤 - 胸腺嘧啶和鸟嘌呤 - 胞嘧啶对的沃森 - 克里克氢键结构进行了比较。评估了MP2相互作用能的完全基组（CBS）极限以及CCSD（T）校正项，该校正项确定为CCSD（T）和MP2相互作用能之间的差值。使用aug-cc-pVDZ和aug-cc-pVTZ结果外推到MP2 CBS极限，并使用6-31G*（0.25）基组确定CCSD（T）校正项。在考虑CBS水平确定的互变异构体惩罚以及溶剂化/去溶剂化自由能的同时，对最终相互作用能进行了校正。腺嘌呤 - 胸腺嘧啶对的情况很简单，互变异构体对比由标准形式组成的沃森 - 克里克对明显不稳定。对于鸟嘌呤 - 胞嘧啶对，由标准形式构成的沃森 - 克里克结构再次是最稳定的。然而，另外两种结构在能量上相当相似（相差5和6千卡/摩尔），这为在DNA双螺旋中检测到这些结构提供了非常小但不可忽略的机会（1:5000）。由于掺入DNA中的DNA碱基和碱基对比在孤立系统中溶剂化不利，这个概率代表了非常高的上限。结果清楚地表明了DNA分子的标准构建块是如何精确选择的以及它们的稳定性是如何得到良好维持的。
