What singles out the G[8-5]C intrastrand DNA cross-link? Mechanistic and structural insights from quantum mechanics/molecular mechanics simulations.

Naturally occurring intrastrand oxidative cross-link lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the C5 atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be ∼12.4 kcal/mol, which is ∼3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, J., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc.134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (∼10.5 kcal/mol). The order of reactivity in DNA (T(•) > mC(•) > C(•)) is reversed compared to that in the reacting subsystems in the gas phase (C(•) > mC(•) > T(•)), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.