DFT investigation of the formation of linear aminols as the first step toward the induction of oxidatively generated interstrand cross-link DNA lesions

Apyrimidinic/apurinic sites feature among the most prevalent DNA lesions. If not repaired, it has been recently evidenced that they are prone to react in situ with vicinal nucleobases, evolving toward more complex and highly mutagenic interstrand cross-links. Information concerning the structure and the multi-step reactivity leading to such clustered defects is scarce due to their low formation yield. This study reports a DFT exploration of the condensation reaction between a ketoaldehyde (derived from an oxidized C4’ abasic site) and three nucleobases featuring an amino group. They are found to present a very similar intrinsic reactivity, indicating in turn that differences of reactivity arise more from the relative positioning of the two reactive fragments within a flexible B-DNA. We also probe the role of a vicinal water molecule for the formation of the aminol and the requirements to reach an adequate estimate of this strongly exothermic reaction, which drives the DNA damage process.