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(CH(2))), 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(CH(2)))-3′, 5′-(˙U(CH(2)))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/C(8) 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/C(8) addition. Furthermore, markedly positive reaction free energy requirements are estimated for these conformational transformations making the 3′ G/C(8) additions of the three radicals thermodynamically much more unfavorable than the corresponding 5′ G/C(8) additions. Such essential conformational adjustments along the 3′ G/C(8) 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.