Impact of DNA Environment on the Intrastrand Cross-Link Lesions: Hydrogen Atom Release as the Last Step of Formation of G[8-5m]T

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.

Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

We investigate the attack of the nitrogen dioxide radical (NO^•₂) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO^•₂ radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO₂-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO^•₂ radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

One-electron oxidation of gemcitabine and analogs: mechanism of formation of C3' and C2' sugar radicals

Gemcitabine is a modified cytidine analog having two fluorine atoms at the 2'-position of the ribose ring. It has been proposed that gemcitabine inhibits RNR activity by producing a C3'• intermediate via direct H3'-atom abstraction followed by loss of HF to yield a C2'• with 3'-keto moiety. Direct detection of C3'• and C2'• during RNR inactivation by gemcitabine still remains elusive. To test the influence of 2'- substitution on radical site formation, electron spin resonance (ESR) studies are carried out on one-electron oxidized gemcitabine and other 2'-modified analogs, i.e., 2'-deoxy-2'-fluoro-2'-C-methylcytidine (MeFdC) and 2'-fluoro-2'-deoxycytidine (2'-FdC). ESR line components from two anisotropic β-2'-F-atom hyperfine couplings identify the C3'• formation in one-electron oxidized gemcitabine, but no further reaction to C2'• is found. One-electron oxidized 2'-FdC is unreactive toward C3'• or C2'• formation. In one-electron oxidized MeFdC, ESR studies show C2'• production presumably from a very unstable C3'• precursor. The experimentally observed hyperfine couplings for C2'• and C3'• match well with the theoretically predicted ones. C3'• to C2'• conversion in one-electron oxidized gemcitabine and MeFdC has theoretically been modeled by first considering the C3'• and H3O(+) formation via H3'-proton deprotonation and the subsequent C2'• formation via HF loss induced by this proximate H3O(+). Theoretical calculations show that in gemcitabine, C3'• to C2'• conversion in the presence of a proximate H3O(+) has a barrier in agreement with the experimentally observed lack of C3'• to C2'• conversion. In contrast, in MeFdC, the loss of HF from C3'• in the presence of a proximate H3O(+) is barrierless resulting in C2'• formation which agrees with the experimentally observed rapid C2'• formation.