The Influence of the Terminal Phosphorothioate Diester Bond on the DNA Oxidation Process. An Experimental and Theoretical Approach

The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study

Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents, such as ionization radiation. In this paper, the electronic properties of single, tandem, and clustered DNA damage in comparison with native ds-DNA are discussed as a comparative analysis for the first time. A single lesion—8-oxo-7,8-dihydro-2′-deoxyguanosine (G^oxo), a tandem lesion—(5′S) and (5′R) 5′,8-cyclo-2′-deoxyadenosine (cdA), and the presence of both of them in one helix turn as clustered DNA damage were chosen and taken into consideration. The lowest vertical and adiabatic potential (VIP ~ 5.9 and AIP ~ 5.5 eV, respectively) were found for G^oxo, independently of the discussed DNA lesion type and their distribution within the double helix. Moreover, the VIP and AIP were assigned for ds-trimers, ds- dimers and single base pairs isolated from parental ds-hexamers in their neutral and cationic forms. The above results were confirmed by the charge and spin density population, which revealed that G^oxo can be considered as a cation radical point of destination independently of the DNA damage type (single, tandem, or clustered). Additionally, the different influences of cdA on the charge transfer rate were found and discussed in the context of tandem and clustered lesions. Because oligonucleotide lesions are effectively produced as a result of ionization factors, the presented data in this article might be valuable in developing a new scheme of anticancer radiotherapy efficiency.

The influence of the phosphorothioate diester bond on the DNA oxidation process

This study describes the influence of the phosphorothioate internucleotide bond on the deoxyribonucleic acid (DNA) oxidation process. The interaction of an ultraviolet radiation (UVA) with a targeted double-stranded (ds) oligonucleotide, in which one strand contains an antraquinone (AQ) moiety on the 5’-end, may lead to a hole migration process through the double helix. In the end, the migration of theformed radical cation terminates in a suitable place. Usually, this is a guanine-rich sequence. In another experiment, phosphorothioate internucleotide bonds were detected in the bacterial genome as a natural modification. In this study, a polyacrylamide gel electrophoresis (PAGE) autoradiogram analysis of irradiated ds-DNA showed that the oxidation reaction was not inhibited by an isolated guanine. Instead, irrespective of the absence or presence of a phosphorothioate bond, the termination of the ds-DNA oxidation process was predominantly observed on the thymine moieties. Based on the obtained results, it can be concluded that in the discussed case, a hole migration by a hopping mechanism is in competition with an oxidation reaction with a superoxide radical anion. Alternatively, the radical cation migration process is sequence-dependent due to its different ionization potentials. Therefore, the presence of a phosphorothioate internucleotide bond did not change the stability of ds-DNA under UVA irradiation conditions.