Proton-transfer in hydrogenated guanine–cytosine trimer neutral species, cations, and anions embedded in B-form DNA

Abstract

The neutral DNA trimers with the hydrogen atom added to the C8 site of the middle guanine–cytosine (GC) base pair, the DNA trimers protonated at the N7 site of the middle GC base pair, and the anionic species resulting from hydride addition to the C6 site of the middle GC base pair are investigated using theoretical methods. The canonical Watson–Crick structures (WC), transition state structures (TS) and proton-transferred structures (PT) of each relevant system are optimized in the gas phase and in aqueous solution, in order to understand the processes of proton transfer. The proton transfer reactions of the DNA trimers are compared with the corresponding isolated hydrogenated GC base pairs to explore the influence of the surrounding molecules and the base sequence. The proton transfer reactions of the neutral species, cations, and anions are compared, aiming to clarify the effects of the system's total charge. The results reveal that the surrounding molecules decrease the reaction energies of proton-transfer in aqueous solution. The structures with the dATGCAT and dGCGCGC sequences facilitate proton H4a transfer, but hinder proton H1 transfer. The structures with the dCGGCCG and dTAGCTA sequences facilitate proton H1 transfer. The net charge on the system plays an important role in determining the single and double proton-transfer patterns. Anions are more likely to experience proton-transfer reactions than neutral species and cations, and all the proton-transfer reactions of the anions are exothermic.