Brovarets' Ol'ha O, Tsiupa Kostiantyn S, Hovorun Dmytro M
Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine.
Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.
Front Chem. 2018 Feb 27;6:8. doi: 10.3389/fchem.2018.00008. eCollection 2018.
For the first time novel high-energy conformers-A·T(w) (5.36), A·T(w) (5.97), A·T(w) (5.78), and A·T(w) (ΔG = 5.82 kcal·mol) (See ) were revealed for each of the four biologically important A·T DNA base pairs - Watson-Crick A·T(WC), reverse Watson-Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of quantum-mechanical theory in the continuum with ε = 4 under normal conditions. Each of these conformers possesses substantially non-planar wobble (w) structure and is stabilized by the participation of the two anti-parallel N6H/N6H'…O4/O2 and N3H…N6 H-bonds, involving the pyramidalized amino group of the A DNA base as an acceptor and a donor of the H-bonding. The transition states - TS, TS, TS, and TS, controlling the dipole-active transformations of the conformers from the main plane-symmetric state into the high-energy, significantly non-planar state and , were localized. They also possess wobble structures similarly to the high-energy conformers and are stabilized by the participation of the N6H/N6H'…O4/O2 and N3H…N6 H-bonds. Discovered conformers of the A·T DNA base pairs are dynamically stable short-lived structures [lifetime τ = (1.4-3.9) ps]. Their possible biological significance and future perspectives have been briefly discussed.
首次在正常条件下，于连续介质中ε = 4时，在MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p)量子力学理论水平上，揭示了四种生物学重要的A·T DNA碱基对（沃森-克里克A·T(WC)、反向沃森-克里克A·T(rWC)、 hoogsteen A·T(H)和反向hoogsteen A·T(rH)）各自的新型高能构象体——A·T(w) (5.36)、A·T(w) (5.97)、A·T(w) (5.78)和A·T(w) (ΔG = 5.82 kcal·mol)（见图）。这些构象体中的每一个都具有显著的非平面摆动（w）结构，并通过两个反平行的N6H/N6H'…O4/O2和N3H…N6氢键的参与而稳定，其中涉及A DNA碱基的锥形化氨基作为氢键的受体和供体。控制构象体从主平面对称状态转变为高能、显著非平面状态的过渡态——TS、TS、TS和TS已被定位。它们也具有与高能构象体类似的摆动结构，并通过N6H/N6H'…O4/O2和N3H…N6氢键的参与而稳定。发现的A·T DNA碱基对构象体是动态稳定的短寿命结构[寿命τ = (1.4 - 3.9) ps]。已简要讨论了它们可能的生物学意义和未来前景。
