Why the tautomerization of the G·C Watson–Crick base pair <i>via</i> the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis
Creators: name: Ol’ha O. Brovarets’
name: Hovorun, Dmytro M.
Publisher: name: Taylor & Francis
Year: 2014
Subjects: Molecular Biology

description: The ground-state tautomerization of the G·C Watson–Crick base pair by the double proton transfer (DPT) was comprehensively studied <i>in vacuo</i> and in the continuum with a low dielectric constant (<i>ϵ</i> = 4), corresponding to a hydrophobic interface of protein–nucleic acid interactions, using DFT and MP2 levels of quantum-mechanical (QM) theory and quantum theory “Atoms in molecules” (QTAIM). Based on the sweeps of the electron-topological, geometric, polar, and energetic parameters, which describe the course of the G·C ↔ G<sup>∗</sup>·C<sup>∗</sup> tautomerization (mutagenic tautomers of the G and C bases are marked with an asterisk) through the DPT along the intrinsic reaction coordinate (IRC), it was proved that it is, strictly speaking, a <i>concerted asynchronous</i> process both at the DFT and MP2 levels of theory, in which protons move with a small time gap in vacuum, while this time delay noticeably increases in the continuum with <i>ϵ</i> = 4. It was demonstrated using the conductor-like polarizable continuum model (CPCM) that the continuum with <i>ϵ</i> = 4 does not qualitatively affect the course of the tautomerization reaction. The DPT in the G·C Watson–Crick base pair occurs without any intermediates both in vacuum and in the continuum with <i>ϵ</i> = 4 at the DFT/MP2 levels of theory. The nine key points along the IRC of the G·C base pair tautomerization, which could be considered as electron-topological “fingerprints” of a concerted asynchronous process of the tautomerization <i>via</i> the DPT, have been identified and fully characterized. These key points have been used to define the reactant, transition state, and product regions of the DPT reaction in the G·C base pair. Analysis of the energetic characteristics of the H-bonds allows us to arrive at a definite conclusion that the middle N1H⋯N3/N3H⋯N1 and the lower N2H⋯O2/N2H⋯O2 parallel H-bonds in the G·C/G<sup>∗</sup>·C<sup>∗</sup> base pairs, respectively, are anticooperative, that is, the strengthening of the middle H-bond is accompanied by the weakening of the lower H-bond. At that point, the upper N4H⋯O6 and O6H⋯N4 H-bonds in the G·C and G<sup>∗</sup>·C<sup>∗</sup> base pairs, respectively, remain constant at the changes of the middle and the lower H-bonds at the beginning and at the ending of the G·C ↔ G<sup>∗</sup>·C<sup>∗</sup> tautomerization. Aiming to answer the question posed in the title of the article, we established that the G<sup>∗</sup>·C<sup>∗</sup> Löwdin’s base pair satisfies all the requirements necessary to cause point mutations in DNA except its lifetime, which is much less than the period of time required for the replication machinery to forcibly dissociate a base pair into the monomers (several ns) during DNA replication. So, from the physicochemical point of view, the G<sup>∗</sup>·C<sup>∗</sup> Löwdin’s base pair cannot be considered as a source of point mutations arising during DNA replication.