Rapid excision of oxidized adenine by human thymine DNA glycosylase

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.

Enhanced thermal stability enables human mismatch-specific thymine-DNA glycosylase to catalyse futile DNA repair

Human thymine-DNA glycosylase (TDG) excises T mispaired with G in a CpG context to initiate the base excision repair (BER) pathway. TDG is also involved in epigenetic regulation of gene expression by participating in active DNA demethylation. Here we demonstrate that under extended incubation time the full-length TDG (TDGFL), but neither its isolated catalytic domain (TDGcat) nor methyl-CpG binding domain-containing protein 4 (MBD4) DNA glycosylase, exhibits significant excision activity towards T and C in regular non-damaged DNA duplex in TpG/CpA and CpG/CpG contexts. Time course of the cleavage product accumulation under single-turnover conditions shows that the apparent rate constant for TDGFL-catalysed excision of T from T•A base pairs (0.0014-0.0069 min-1) is 85-330-fold lower than for the excision of T from T•G mispairs (0.47-0.61 min-1). Unexpectedly, TDGFL, but not TDGcat, exhibits prolonged enzyme survival at 37°C when incubated in the presence of equimolar concentrations of a non-specific DNA duplex, suggesting that the disordered N- and C-terminal domains of TDG can interact with DNA and stabilize the overall conformation of the protein. Notably, TDGFL was able to excise 5-hydroxymethylcytosine (5hmC), but not 5-methylcytosine residues from duplex DNA with the efficiency that could be physiologically relevant in post-mitotic cells. Our findings demonstrate that, under the experimental conditions used, TDG catalyses sequence context-dependent removal of T, C and 5hmC residues from regular DNA duplexes. We propose that in vivo the TDG-initiated futile DNA BER may lead to formation of persistent single-strand breaks in non-methylated or hydroxymethylated chromatin regions.

Possible contribution of 8-hydroxydeoxyguanosine to gene mutations in the kidney DNA of gpt delta rats following potassium bromate treatment

8-Hydroxydeoxyguanosine (8-OHdG) is well known not only as an effective biomarker of oxidative stress but also as a mutagenic DNA modification. Incorporation of dAMP at the opposite site of 8-OHdG induces G>T or A>C transversions. However, in vivo analyses of gene mutations caused by potassium bromate (KBrO3), which can induce 8-OHdG at carcinogenic target sites, showed that G>T was prominent in the small intestines of mice, but not in the kidneys of rats. Because KBrO3 was a much clearer carcinogen in the kidneys of rats, detailed analyses of gene mutations in the kidney DNA of rats treated with KBrO3 could improve our understanding of oxidative stress-mediated carcinogenesis. In the current study, site-specific reporter gene mutation assays were performed in the kidneys of gpt delta rats treated with KBrO3. Groups of 5 gpt delta rats were treated with KBrO3 at concentrations of 0, 125, 250, or 500 ppm in the drinking water for 9 weeks. At necropsy, the kidneys were macroscopically divided into the cortex and medulla. 8-OHdG levels in DNA extracted from the cortex were dramatically elevated at concentrations of 250 ppm and higher compared with those from the medulla. Cortex-specific increases in mutant frequencies in gpt and red/gam genes were found at 500 ppm. Mutation spectrum and sequence analyses of their mutants demonstrated significant elevations in A>T transversions in the gpt gene and single base deletions at guanine or adenine in the gpt or red/gam genes. While A>T transversions and single base deletions of adenine may result from the oxidized modification of adenine, the contribution of 8-OHdG to gene mutations was limited despite possible participation of the 8-OHdG repair process in guanine deletion.

8-Oxoadenine: A «New» Player of the Oxidative Stress in Mammals?

Numerous studies have shown that oxidative modifications of guanine (7,8-dihydro-8-oxoguanine, 8-oxoG) can affect cellular functions. 7,8-Dihydro-8-oxoadenine (8-oxoA) is another abundant paradigmatic ambiguous nucleobase but findings reported on the mutagenicity of 8-oxoA in bacterial and eukaryotic cells are incomplete and contradictory. Although several genotoxic studies have demonstrated the mutagenic potential of 8-oxoA in eukaryotic cells, very little biochemical and bioinformatics data about the mechanism of 8-oxoA-induced mutagenesis are available. In this review, we discuss dual coding properties of 8-oxoA, summarize historical and recent genotoxicity and biochemical studies, and address the main protective cellular mechanisms of response to 8-oxoA. We also discuss the available structural data for 8-oxoA bypass by different DNA polymerases as well as the mechanisms of 8-oxoA recognition by DNA repair enzymes.

Discovery and properties of a monoclonal antibody targeting 8-oxoA, an oxidized adenine lesion in DNA and RNA

8-oxoA, a major oxidation product of adenosine, is a mispairing, mutagenic lesion that arises in DNA and RNA when ^•OH radicals or one-electron oxidants attack the C8 adenine atom or polymerases misincorporate 8-oxo(d)ATP. The danger of 8-oxoA is underscored by the existence of dedicated cellular repair machinery that explicitly excise it from DNA, the attenuation of translation induced by 8-oxoA-mRNA or damaged ribosomes, and its potency as a TLR7 agonist. Here we present the discovery, purification, and biochemical characterization of a new mouse IgGk1 monoclonal antibody (6E4) that specifically targets 8-oxoA. Utilizing an AchE-based competitive ELISA assay, we demonstrate the selectivity of 6E4 for 8-oxoA over a plethora of canonical and chemically modified nucleosides including 8-oxoG, A, m6A, 2-oxoA, and 5-hoU. We further show the ability of 6E4 to exclusively recognize 8-oxoA in nucleoside triphosphates (8-oxoATP) and DNA/RNA oligonucleotides containing a single 8-oxoA. 6E4 also binds 8-oxoA in duplex DNA/RNA antigens where the lesion is either paired correctly or base mismatched. Our findings define the 8-oxoAde nucleobase as the critical epitope and indicate mAb 6E4 is ideally suited for a broad range of immunological applications in nucleic acid detection and quality control.