Formation Mechanism and Structure of a Guanine–Uracil DNA Intrastrand Cross-Link

The formation and structure of the 5′–G[8–5]U–3′ intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine–pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5′–G[8–5]U–3′ within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5′–G[8–5]U–3′, may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.