Insights into the structure of intrastrand cross-link DNA lesion-containing oligonucleotides: G[8-5m]T and G[8-5]C from molecular dynamics simulations

Oxidatively generated complex DNA lesions occur more rarely than single-nucleotide defects, yet they play an important role in carcinogenesis and aging diseases because they have proved to be more mutagenic than simple lesions. Whereas their formation pathways are rather well understood, the field suffers from the absence of structural data that are crucial for interpreting the lack of repair. No experimental structures are available for oligonucleotides featuring such a lesion. Hence, the detailed structural basis of such damaged duplexes has remained elusive. We propose the use of explicit solvent molecular dynamics simulations to build up damaged oligonucleotides containing two intrastrand cross-link defects, namely, the guanine-thymine and guanine-cytosine defects. Each of these lesions, G[8-5m]T and G[8-5]C, is placed in the middle of a dodecameric sequence, which undergoes an important structural rearrangement that we monitor and analyze. In both duplexes, the structural evolution is dictated by the more favorable stacking of guanine G6, which aims to restore π-stacking with the 3' purine nucleobase. Subsequently, transient formation of hydrogen bonds with a strand shifting is observed. Our simulations are combined with density functional theory to rationalize the structural evolution. We report converging computational evidence that the G[8-5m]T- and G[8-5]C-containing structures evolve toward "abasic-like" duplexes, with a stabilization of the interstrand pairing noncovalent interactions. Meanwhile, both lesions restore B-helicity within tens of nanoseconds. The identification of plausible structures characterizes the last hydrogen abstraction step toward the formation of such defects as a non-innocent chemical reaction.