A Molecular Dynamical Investigation of the 7,8-dihydro-8-oxoguanine Mutation in dsDNA

Abstract

Background: The oxidization of a Guanine (G) base pair to 7,8-dihydro-8-oxoguanine (OG) is one of the most common DNA mutations. OG mutations can undergo a regular Watson-Crick base-pairing, or a reverse Hoogsteen (HG) base-pairing, especially in OG:A mismatches. While the causes of these mutations are well-understood, the kinetic and energetic characteristics of this new pseudo-base have never been fully investigated, especially at temperatures around biological function (17-37°C).

Methods: We created a simulation to derive the Free Energy Surface (FES) of OG:C and OG:A Hoogsteen to Watson-Crick base-pair (bp) transitions under multiple temperatures, relative to 2 collective geometric variables: the dihedral Chi and the pseudo-dihedral CPD angle. To make the simulation, we used the relatively recent Metadynamics algorithms in conjunction with GROMACS 2020.2.

Results: The lowest free energy increased linearly with increasing temperatures (17-37°C). Major Chi and CPD rotations at these minima varied heavily for 27°C and 32°C (the largest was seen in the former), but stayed relatively similar for other temperatures, indicating a highly sensitive relationship to temperature, likely due to DNA flexibility, quantum mechanical (QM) effects, and hydrogen bonding. Free energies had a weak negative linear relationship, and free energy hypersurfaces were given for studied temperatures of 17-37°C. Human body temperature (37°C) results were also included and explained. The simulations showed why OG:A Hoogsteen bps often occur in organisms and are energetically preferable to standard Watson-Crick. OG:C HG base pairings are determined to likely be not as common as OG:A HG.

Limitations: Future investigations must focus on discovering rate constants of these base-pairs, as time constraints did not permit them to be done here, as well as more QM-focused simulations.