Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation

Abstract

This paper represents careful quantum-mechanical investigation with further generalization of the novel transformation mechanisms for the wobble G·T(wWC) and reverse wobble G·T(rwWC) base pairs into the classical Watson–Crick-like G*·T(WC) base pair, obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in vacuum under normal conditions (T = 298.15 K). These G·T(wWC)↔G·T*(WC)↔G*·T(WC), G·T(wWC)↔G·T*O2(rWC)↔G+·T−(rWC)↔G*·T(rWC)↔G*·T(WC), G·T(rwWC)↔G*·T(rWC)↔G*·T(WC) and G·T(rwWC)↔G·T*(WC)↔G*·T(WC) conformationally-tautomeric reactions are determined by the sequential proton transfer inside the base pair, shifting of the G and T DNA bases relatively each other and cis↔trans changing of their mutual orientation. The main intrigue of the presented results is that two different G·T(wWC)↔G·T*(WC)↔G*·T(WC) and G·T(rwWC)↔G*·T(rWC)↔G*·T(WC) routes guarantee almost the same probability of the acquisition by the wobble G·T(wWC) and reverse wobble G·T(rwWC) base pairs of the G*·T(WC) Watson–Crick-like configuration. Notably, that reverse wobble G·T(rwWC) and reverse Watson–Crick G·T*O2(rWC) base pairs tautomerise via the double proton transfer along the intermolecular H-bonds – G·T(rwWC)↔G*·T*(rwWC) and G·T*O2(rWC)↔G+·T−(rWC)↔G*·T(rWC), respectively. It was also considered conformational mobility of the G·T*(WC), G·T*O2(rWC), G·T(wWC), G·T(rwWC), G*·T*(rwWC) and G*·T(rWC) base pairs through the mutual rotation of the bases around the intermolecular H-bond. Methods of the structural bioinformatics have been used for indication of the G·T base pairs in real biological systems. Revealed conformationally-tautomeric transformations can explain transitions of the DNA molecule from parallel to anti-parallel conformations and vice versa.