Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
Chemistry. 2010 Mar 8;16(10):3057-65. doi: 10.1002/chem.200902068.
Recent experimental studies on the Watson-Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two N-H...O hydrogen bonds separated by one N-H...N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pK(a) data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pK(a) values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.
最近关于三嗪和氨基嘧啶衍生物的 Watson-Crick 型碱基配对的实验研究表明，构成碱基的酸碱性质可能与溶液中测量的双链体稳定性有关。在此，我们使用高级量子化学计算和分子动力学模拟来评估七种常见碱基对的碱基配对和堆积相互作用，这些碱基对通过两个相隔一个 N-H…N 氢键的 N-H…O 氢键稳定。我们表明，碱基配对和碱基堆积相互作用能都与报告的碱基 pK(a)数据和双链体的熔点无关。这表明，双链体的熔点数据与构成碱基的 pK(a)值之间的实验观察到的相关性并非源于内在的碱基配对和堆积性质。因此，观察到的实验相关性的物理化学起源仍未得到解释，需要进一步研究。此外，由于我们的计算是通过原子轨道完全基组外推和包含更高的电子相关效应进行的，因此它们为非天然碱基的堆积和碱基配对能提供了参考数据。
