How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches?

Abstract

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A·G and C·T DNA base mispairs: a quantum-chemical picture

“…During this tautomeric conversion, the Watson-Crick-like base pairs undergo large-scale structural changes to adopt a wobble (w) geometry. The characteristic difference of this novel mechanism from Löwdin's mechanism consists of the fact that the mutagenic tautomerisation of the pairs is accompanied by signicant changes in their geometry, namely by the transition into the wobble conguration, and is carried out through the highly stable transition states (TS) 21,22 A + $G À , A À $G + , C + $T À and C À $T + (signs "+" and "À" denote protonated and deprotonated DNA bases, respectively). The obtained data shed light on the nature of the spontaneous point A$G/G$A and C$T/T$C replication errors in DNA, when for one reason or another 13,14,19,20 complementary DNA bases randomly change their canonical tautomeric status into a mutagenic status during DNA replication.…”

Theoretical thermodynamic study of the adenine-thymine tautomeric equilibrium: Electronic structure calculations and steered molecular dynamic simulations

“…Although the equilibrium formation constant of these rare tautomers is very low, there may be a significant amount of rare pairs during replication due to the high number of canonical base pairs in a DNA. Rare tautomers may, therefore, cause a mutation only when their stability are high enough to be present when DNA replication occurs …”

A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: a QM/QTAIM highlight

“…The rare tautomer hypothesis of spontaneous point mutagenesis formulated by Watson and Crick [1] has been recently challenged by computational [14,15] and experimental [11,12,[16][17][18] studies demonstrating that displacement of one single proton alters H-bonding scheme of the mispair, making it indistinguishable from the canonical Watson-Crick base pairs, that give impetus to further studies. It is logical to assume within the framework of this hypothesis that exceptionally the C·C*(WC) [19][20][21] and T·T*(WC) [20][21][22] base mispairs possessing Watson-Crick-like (WC) geometry and containing rare tautomers [23,24] of the C and T DNA bases (here and below they are marked with an asterisk) can be enzymatically incorporated into the structure of the DNA double helix and so are implicated in the origin of spontaneous transversions.…”