Oxidatively generated tandem DNA modifications by pyrimidinyl and 2-deoxyribosyl peroxyl radicals

Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Due to the lower oxidation potential than natural nucleic acid bases, one-electron oxidation of DNA is usually funneled into the direction of intermediates for oxidized DNA damage like 8-oxo-7,8-dihydroadenine (8-oxoA) leading to a radical cation, which may undergo facile deprotonation. However, compared to the sophisticated studies devoted to natural bases, much less is known about the radical cation degradation behavior of an oxidized DNA base. Inspired by this, a comprehensive theoretical investigation is performed to illuminate the deprotonation of 8-oxoA radical cation (8-oxoA•+) in both free and encumbered context by calculating the pK a value and mapping the energy profiles. The calculative pK a values of active protons in free 8-oxoA•+ follow the order: N7-H < N9-H < N6-H1< N6-H2, suggesting the preference of proton departure in free 8-oxoA•+. To further illustrate the preferred site and mechanism for 8-oxoA•+ deprotonation, energy profiles are constructed to distinguish the possibility from that of all active protons in both contexts. The results show distinctly that 8-oxoA•+ mainly suffers from the loss of proton from N9 due to the lowest energy barrier but deprotonates N7-H in real DNA as the connection of N9 and ribose. The energy barriers for the deprotonation of N7-H from 8-oxoA•+ in free and encumbered contexts are 1.5 and 1.3 kcal/mol, respectively, indicating a fast deprotonation reaction. It is more interestingly that the N9-H proton transfer (PT, toward N3) to adjacent water follows a stepwise fashion rather than a one-step approach as previously reported. Furthermore, the PT behavior of free N9-H toward O8 is dramatically influenced by base pairing T, where it is localized at neighboring water without further PT to adjacent water in free 8-oxoA•+ but migrated directly to adjacent water in the 8-oxoA•+:T base pair. And the deprotonation of N6-H2 in 8-oxoA•+:T is disturbed as the PT to O4 of the pairing T base is inhibited. It is warmly anticipated that these results could provide an in-depth perspective to understand the important role of 8-oxoA in mutation.

Oxidative Deformylation of the Predominant DNA Lesion 5-Formyl-2'-deoxyuridine

Radical oxidation of DNA gives rise to potentially deleterious lesions such as strand breaks and various nucleobase modifications including 5-formyl-2'-deoxyuridine (5-fo-dU), a prevalent product derived from the oxidation of the C5-methyl group of thymidine. The present study investigates the unusual transformation of 5-fo-dU into 5-hydroxy-2'-deoxyuridine (5-oh-dU) and 5,6-dihydroxy-5,6-dihydro-2'-deoxuridine (gly-dU), two products typically associated with the oxidation of 2'-deoxycytidine. Detailed mechanistic analyses reveal that hydrogen peroxide, either generated as a byproduct of ascorbate autoxidation or added exogenously, mediates the formation of these oxidatively induced C5-dealkylated products. We show that the major product 5-oh-dU results from a Baeyer-Villiger rearrangement of the formyl functionality of 5-fo-dU while the minor product gly-dU derives from α,β-oxidation of the enal portion followed by deformylation. These reactions were observed in both 2'-deoxynucleoside monomers as well as isolated DNA. Our findings further clarify the oxidation chemistry of thymidine and highlight a novel oxidative decomposition pathway that can help understand the fate of certain types of DNA damage. Furthermore, our results underscore the pro-oxidant properties of ascorbate in vitro that can lead to the adventitious oxidation of substrates via the reduction of trace metals ions and generation of hydrogen peroxide.

Scavenging of Alkylperoxyl Radicals by Addition to Ascorbate: An Alternative Mechanism to Electron Transfer

Vitamin C (ascorbate; Asc) is a biologically important antioxidant that scavenges reactive oxygen species such as deleterious alkylperoxyl radicals (ROO•), which are generated by radical-mediated oxidation of biomolecules in the presence of oxygen. The radical trapping proprieties of Asc are conventionally attributed to its ability to undergo single-electron transfers with reactive species. According to this mechanism, the reaction between Asc and ROO• results in the formation of dehydroascorbate (DHA) and the corresponding hydroperoxides (ROOH). When studying the reactivity of DNA 5-(2'-deoxyuridinyl)methylperoxyl radicals, we discovered a novel pathway of ROO• scavenging by Asc. The purpose of this study is to elucidate the underlying mechanism of this reaction with emphasis on the characterization of intermediate and final decomposition products. We show that the trapping of ROO• by Asc leads to the formation of an alcohol (ROH) together with an unstable cyclic oxalyl-l-threonate intermediate (cOxa-Thr), which readily undergoes hydrolysis into a series of open-chain oxalyl-l-threonic acid regioisomers. The structure of products was determined by detailed MS and NMR analyses. The above transformation can be explained by initial peroxyl radical addition (PRA) onto the C2=C3 enediol portion of Asc. Following oxidation of the resulting adduct radical, the product subsequently undergoes Baeyer-Villiger rearrangement, which releases ROH and generates the ring expansion product cOxa-Thr. The present investigation provides robust clarifications of the peroxide-mediated oxidation chemistry of Asc and DHA that has largely been obscured in the past by interference with autooxidation reactions and difficulties in analyzing and characterizing oxidation products. Scavenging of ROO• by PRA onto Asc may have beneficial consequences since it directly converts ROO• into ROH, which prevents the formation of potentially deleterious ROOH, although it induces the breakdown of Asc into fragments of oxalyl-l-threonic acid.

8-OxodGuo and Fapy•dG Mutagenicity in Escherichia coli Increases Significantly when They Are Part of a Tandem Lesion with 5-Formyl-2'-deoxyuridine

Tandem lesions, which are defined by two or more contiguously damaged nucleotides, are a hallmark of ionizing radiation. Recently, tandem lesions containing 5-formyl-2'-deoxyuridine (5-fdU) flanked by a 5'-8-OxodGuo or Fapy•dG were discovered, and they are more mutagenic in human cells than the isolated lesions. In the current study, we examined replication of these tandem lesions in Escherichia coli. Bypass efficiency of both tandem lesions was reduced by 30-40% compared to the isolated lesions. Mutation frequencies (MFs) of isolated 8-OxodGuo and Fapy•dG were low, and no mutants were isolated from replication of a 5-fdU construct. The types of mutations from 8-OxodGuo were targeted G → T transversion, whereas Fapy•dG predominantly gave G → T and G deletion. 5'-8-OxodGuo-5-fdU also gave exclusively G → T mutation, which was 3-fold and 11-fold greater, without and with SOS induction, respectively, compared to that of an isolated 8-OxodGuo. In mutY/mutM cells, the MF of 8-OxodGuo and 5'-8-OxodGuo-5-fdU increased 13-fold and 7-fold, respectively. The MF of 5'-8-OxodGuo-5-fdU increased 2-fold and 3-fold in Pol II- and Pol IV-deficient cells, respectively, suggesting that these polymerases carry out largely error-free bypass. The MF of 5'- Fapy•dG-5-fdU was similar without (13 ± 1%) and with (16 ± 2%) SOS induction. Unlike the complex mutation spectrum reported earlier in human cells for 5'- Fapy•dG-5-fdU, with G → T as the major type of errors, in E. coli, the mutations were predominantly from deletion of 5-fdU. We postulate that removal of adenine-incorporated opposite 8-OxodGuo by Fpg and MutY repair proteins is partially impaired in the tandem 5'-8-OxodGuo-5-fdU, resulting in an increase in the G → T mutations, whereas a slippage mechanism may be operating in the 5'- Fapy•dG-5-fdU mutagenesis. This study showed that not only are these tandem lesions more mutagenic than the isolated lesions but they may also exhibit different types of mutations in different organisms.

Electron-Induced Damage by UV Photolysis of DNA Attached to Gold Nanoparticles

Photolysis of DNA attached to gold nanoparticles (AuNPs) with ultraviolet (UV) photons induces DNA damage. The release of nucleobases (Cyt, Gua, Ade, and Thy) from DNA was the major reaction (99%) with an approximately equal release of pyrimidines and purines. This reaction contributes to the formation of abasic sites in DNA. In addition, liquid chromatography-mass spectrometry/MS (LC-MS/MS) analysis revealed the formation of reduction products of pyrimidines (5,6-dihydrothymidine and 5,6-dihydro-2'-deoxyuridine) and eight 2',3'- and 2',5'-dideoxynucleosides. In contrast, there was no evidence of the formation of 5-hydroxymethyluracil and 8-oxo-7,8-dihydroguanine, which are common oxidation products of thymine and guanine, respectively. Using appropriate filters, the main photochemical reactions were found to involve photoelectrons ejected from AuNPs by UV photons. The contribution of "hot" conduction band electrons with energies below the photoemission threshold was minor. The mechanism for the release of free nucleobases by photoelectrons is proposed to take place by the initial formation of transient molecular anions of the nucleobases, followed by dissociative electron attachment at the C1'-N glycosidic bond connecting the nucleobase to the sugar-phosphate backbone. This mechanism is consistent with the reactivity of secondary electrons ejected by X-ray irradiation of AuNPs attached to DNA, as well as the reactions of various nucleic acid derivatives irradiated with monoenergetic very-low-energy electrons (∼2 eV). These studies should help us to understand the chemistry of nanoparticles that are exposed to UV light and that are used as scaffolds and catalysts in molecular biology, curative agents in photodynamic therapy, and components of sunscreens and cosmetics.

Computational model of radiation oxygen effect with Monte Carlo simulation: effects of antioxidants and peroxyl radicals

PURPOSE

Oxygen plays a crucial role in radiation biology. Antioxidants and peroxyl radicals affect the oxygen effect greatly. This study aims to establish a computational model of the oxygen effect and explore the effect attributed to antioxidants and peroxyl radicals.

MATERIALS AND METHODS

Oxygen-related reactions are added to our track-structure Monte Carlo code NASIC, including oxygen fixation, chemical repair by antioxidants and damage migration from base-derived peroxyl radicals. Then the code is used to simulate the DNA damage under various oxygen, antioxidant and damage migration rate conditions. The oxygen enhancement ratio(OER) is calculated quantifying by the number of double-strand breaks for each condition. The roles of antioxidants and peroxyl radicals are examined by manipulating the relevant parameters.

RESULTS AND CONCLUSIONS

Our results indicate that antioxidants are capable of rapidly restoring DNA radicals through chemical reactions, which compete with natural and oxygen fixation processes. Additionally, antioxidants can react with peroxyl radicals derived from bases, thereby preventing the damage from migrating to DNA strands. By quantitatively accounting for the impact of peroxyl radicals and antioxidants on the OER curves, our study establishes a more precise and comprehensive model of the radiation oxygen effect.

Radiation-Chemical Perspective of the Radiobiology of Pulsed (High Dose-Rate) Radiation (FLASH): A Postscript

An earlier commentary (Wardman P, Radiat Res. 2020; 194:607-617) discussed possible chemical reaction pathways that might be involved in the differential responses of tissues to high- vs. low-dose-rate irradiation, focusing on reactions between radicals, and radiolytic depletion of a chemical influencing radiosensitivity. This brief postscript updates discussion to consider recent modeling and experimental studies, and presents more detail to support the earlier suggestion that rapid depletion of nitric oxide will certainly occur after a radiation pulse of a few grays, underlining the need to include the consequences of such a change when considering FLASH effects.

Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance?

PURPOSE

Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation.

CONCLUSIONS

The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.