Formation of pyrimidine–pyrimidine type DNA intrastrand cross-links: a theoretical verification

Abstract

Pyrimidine-type radicals have been demonstrated to be able to attack their 3′ or 5′ neighboring purine nucleotides forming diverse DNA intrastrand cross-links, but whether or not these radicals can attack their surrounding pyrimidine nucleotides forming pyrimidine–pyrimidine type DNA intrastrand cross-links remains unclear. To resolve this question, probable additions of the uracil-5-methyl (˙U_CH2) radical to the C₅C₆ double bond of its 3′/5′ neighboring pyrimidine nucleotides in the four models, 5′-T(˙U_CH2)-3′, 5′-C(˙U_CH2)-3′, 5′-(˙U_CH2)T-3′, and 5′-(˙U_CH2)C-3′, are explored in the present work employing density functional theory (DFT) methods. The C₆ site of its 5′ neighboring thymidine is the preferred target for ˙U_CH2 radical addition, while additions of the ˙U_CH2 radical to the C₆ and C₅ sites of its 5′ neighboring deoxycytidine are found to be competitive reactions. The ˙U_CH2 radical can react with both the C₆ and C₅ sites of its 3′ neighboring pyrimidine nucleotides, but the efficiencies of these reactions are predicted to be much lower than those of the corresponding addition reactions to its 5′ neighboring pyrimidine nucleotides, indicating the existence of an obvious sequence effect. All the addition products could be finally transformed into closed-shell intrastrand cross-links, the molecular masses of which are found to be exactly the same as certain MS values determined in a recent study of an X-irradiated deoxygenated aqueous solution of calf thymus DNA. The present study thus not only definitely corroborates the fact that the reactive ˙U_CH2 radical can attack its 3′/5′ neighboring pyrimidine nucleotides forming several pyrimidine–pyrimidine type DNA intrastrand cross-links, but also provides a plausible explanation for the identities of these structurally unknown intrastrand cross-links.