Are dinucleoside monophosphates relevant models for the study of DNA intrastrand cross-link lesions? The example of g[8-5m]T

Theoretical studies on the purine radical induced purine-purine type intrastrand cross-links

At the density functional theory (DFT) level, addition reactions between the guanine-8-yl radical and its 3'/5' neighboring purine deoxynucleosides forming the purine-purine type intrastrand cross-links were studied. It is found that addition of the guanine-8-yl radical to the C8 site of its 5' neighboring deoxyguanosine or deoxyadenosine is a two-step reaction consisting of a structurally relatively unfavourable conformational transformation step, while the corresponding 3' C8 addition is straightforward and kinetically more efficient. The 3' C8 preference of the guanine-8-yl radical additions indicates the existence of an obvious sequence effect, which is completely opposite to that observed in the formation of pyrimidine radicals induced DNA intrastrand cross-links. The detrimental effects from steric hindrance and stabilizing weak interactions make these addition reactions markedly suppressed in double stranded DNA. This work broadens our knowledge about the possible types of DNA intrastrand cross-links.

DNA intrastrand cross-links induced by the purine-type deoxyguanosine-8-yl radical: a DFT study

Currently, all known DNA intrastrand cross-links are found to be induced by pyrimidine-type radicals; however, whether or not purine-type radicals are able to cause DNA intrastrand cross-links remains unclear. In the present study, probable additions of the highly reactive deoxyguanosine-8-yl radical to its 3'/5' neighboring pyrimidine nucleotides in four model compounds, 5'-G˙T-3', 5'-TG˙-3', 5'-G˙C-3', and 5'-CG˙-3', were studied using density functional theory (DFT) methods. In single-stranded DNA, the deoxyguanosine-8-yl radical is preferred to efficiently attack the C5 site of its 3' neighboring deoxythymidine or deoxycytidine, forming the G[8-5]T or G[8-5]C intrastrand cross-link rather than the C6 site forming the G[8-6]T or G[8-6]C intrastrand cross-link. The four corresponding sequence isomers, namely T[5-8]G, T[6-8]G, C[5-8]G, and C[6-8]G, formed by additions of deoxyguanosine-8-yl radical to its 5' neighboring pyrimidine nucleotides are predicted to be formed inefficiently. In double-stranded DNA, considering the detrimental effects of stabilizing weak interactions on related structural adjustments required in each addition reaction path, relatively lower reaction yields are suggested for the G[8-5]T and G[8-5]C intrastrand cross-links, while the formation of the other six intrastrand cross-links becomes quite difficult. All calculations definitely demonstrate that, in addition to pyrimidine-type radicals, the purine-type deoxyguanosine-8-yl radical is able to attack its 3'/5' neighboring pyrimidine nucleotides forming several DNA intrastrand cross-links.

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

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 C₅[double bond, length as m-dash]C₆ 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.

Mechanism studies of addition reactions between the pyrimidine type radicals and their 3′/5′ neighboring deoxyguanosines

To clarify the biologically significant sequence effect existing in the formation of the pyrimidine-type radicals induced DNA intrastrand cross-links, addition mechanisms between the uridine-5-methyl (˙U_CH2), 6-hydroxy-5,6-dihydrothymidine-5-yl (˙T_6OH), and 6-hydroxy-5,6-dihydrocytidine-5-yl (˙C_6OH) radicals and their 3′/5′ neighboring deoxyguanosines (dG) are explored in the present study employing the model 5′-G(˙U_CH2)-3′, 5′-(˙U_CH2)G-3′, 5′-G(˙T_6OH)-3′, 5′-(˙T_6OH)G-3′, 5′-G(˙C_6OH)-3′, and 5′-(˙C_6OH)G-3′ sequences. It is found that the 5′ G/C₈ additions of the three radicals are all simple direct one-step reactions inducing only relatively small structural changes, while a conformational adjustment involving orientation transitions of both nucleobase moieties and twisting of the DNA backbone is indispensable for each 3′ G/C₈ addition. Furthermore, markedly positive reaction free energy requirements are estimated for these conformational transformations making the 3′ G/C₈ additions of the three radicals thermodynamically much more unfavorable than the corresponding 5′ G/C₈ additions. Such essential conformational adjustments along the 3′ G/C₈ addition paths that structurally greatly influence the local DNA structures and thermodynamically substantially reduce the addition efficiencies may be the reasons responsible for the differences in the formation yields and biological consequences of the pyrimidine-type radicals induced DNA intrastrand cross-link lesions.

For each radical, the 5′ G/C₈ addition is a simple direct one-step reaction, while a structurally significant and thermodynamically markedly unfavorable conformational adjustment is indispensable for the 3′ G/C₈ addition.