Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str., 03680, Kyiv, Ukraine.
Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave., 03022, Kyiv, Ukraine.
Sci Rep. 2018 Jul 10;8(1):10371. doi: 10.1038/s41598-018-28636-y.
In this study it was theoretically shown that discovered by us recently (Brovarets' et al., Frontiers in Chemistry, 2018, 6:8; doi: 10.3389/fchem.2018.00008) high-energetical, significantly non-planar (symmetry C), short-lived wobbled conformers of the classical Watson-Crick А·Т(WC), reverse Watson-Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН) DNA base pairs are the intermediates of their pairwise А∙Т(WC)/А∙Т(rWC) ↔ А∙Т(H)/А∙Т(rH) conformational transformations. These transitions do not require for their realization the energy-consumable anisotropic rotation of the amino group of A around the exocyclic C6-N6 bond. They are controlled by the non-planar transition states with quasi-orthogonal geometry (symmetry C) joined by the single intermolecular (Т)N3H···N6(А) H-bond (~4 kcal∙mol). The Gibbs free energies of activation for these non-dissociative, dipole-active conformational transitions consist 7.33 and 7.81 kcal∙mol, accordingly. Quantum-mechanical (QM) calculations in combination with Bader's quantum theory of "Atoms in Molecules" (QTAIM) have been performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory in the continuum with ε = 4 under normal conditions.
在这项研究中，我们从理论上证明了最近发现的（Brovarets 等人，化学前沿，2018 年，6:8；doi:10.3389/fchem.2018.00008）高能、显著非平面（对称 C）、短寿命摆动构象的经典 Watson-Crick А·Т（WC）、反向 Watson-Crick А·Т（rWC）、Hoogsteen А·Т（Н）和反向 Hoogsteen А·Т（rН）DNA 碱基对是它们成对 А·Т（WC）/А·Т（rWC）↔А·Т（H）/А·Т（rH）构象转变的中间体。这些转变不需要实现 A 环外 C6-N6 键的氨基酸基团的耗能各向异性旋转。它们由具有准正交几何形状（对称 C）的非平面过渡态控制，由单个分子间（Т）N3H···N6（А）氢键（~4 kcal·mol）连接。这些非解离、偶极活性构象转变的活化吉布斯自由能分别为 7.33 和 7.81 kcal·mol。在正常条件下，连续体中的 QM 理论 MP2/aug-cc-pVDZ//B3LYP/6-311++G（d，p）水平下，采用量子力学（QM）计算与 Bader 的分子内原子量子理论（QTAIM）相结合。
