Multiscale simulations reveal the role of PcrA helicase in protecting against proton transfer in DNA

06 June 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G*C*) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.


proton transfer

Supplementary materials

Supplementary Information
This document contains the supplementary information for the article entitled: "Multiscale simulations reveal the role of PcrA helicase in protecting against proton transfer in DNA". In addition to the computational methodology (Section 1), additional simulation details (Section 2), and additional simulation results (Section 3), input, parameter, and analysis files sufficient to reproduce the results published in this work are available on Github at

Supplementary weblinks


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