Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism

Abstract

The misincorporation of a noncomplementary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling firstprinciples quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our calculated rates of genetic error formation are in excellent agreement with experimental observations in DNA. Furthermore, our quantum mechanics/molecular mechanics model predicts the existence of a short-lived "tunnellingready" configuration along the wobble reaction pathway in the polymerase active site, dramatically increasing the rate of proton transfer by a hundredfold, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase.

How proton transfer impacts hachimoji DNA

“…Several QM/MM studies on proton transfer in DNA highlight that complex interactions with the solvent, the rest of the DNA structure, and the DNA replisome could significantly alter the DNA shape. 17,76–78 Furthermore, interactions with the phosphate backbone and stacking interactions with the bases above and below can lead to a sequence dependence on the proton transfer barrier and reaction energy. 16,18,77 In principle, this could extend to the hachimoji bases and consequently lead to modifications of the proton transfer schemes presented in this work, leading to alterations in the proton transfer barrier and hence tunnelling rates.…”

Investigating the Spectroscopy of the Gas Phase Guanine–Cytosine Pair: Keto versus Enol Configurations

“…For instance, going beyond optical spectroscopy, this is being done relative to nuclear magnetic resonance (NMR) experiments. Recent calculations by Slocombe, Sacchi, and coworkers 9 on tunneling rates in the guanine−thymine pair are compatible with NMR rates, opening the possibility that quantum tunneling plays an effective role in DNA transcription errors.…”

“…Finally, we also consider the E9I-1 tautomer because it is formed upon double proton hopping starting from K9K-1, and the presence of E9I-1, even in traces, would suggest the presence of a fastproceeding double proton hopping mechanism, resulting in a stable tautomeric form. [7][8][9][10]12,32 We optimize all of the anticipated tautomers at the DFT-D/ B3LYP level of theory with the def2-TZVP basis set, 62 where DFT-D stands for the density functional theory (DFT) with Grimme's empirical dispersions. 63 The equilibrium geometries with relative energies are listed in Figure 1.…”

“…If this is the case, the hopping tautomer could enter the polymerase λ pocket and be incorporated erroneously . The discussion about tunneling in DNA bases is still open, , and at the moment, this hypothesis has not been confirmed. More specifically, at the moment of our writing, no clear evidence of double proton hopping has been found, but the continuous development of fast and ultrafast techniques might provide the experimentalists with the needed tools to catch this phenomenon if really present.…”

“…Furthermore, we focus on the K9E-1 tautomer because it is indistinguishable from K7E-1 when looking at the high harmonic frequencies, and it is more similar to K9K-1. Finally, we also consider the E9I-1 tautomer because it is formed upon double proton hopping starting from K9K-1, and the presence of E9I-1, even in traces, would suggest the presence of a fast-proceeding double proton hopping mechanism, resulting in a stable tautomeric form. − ,, …”