Oxidation reactions of cytosine DNA components by hydroxyl radical and one-electron oxidants in aerated aqueous solutions

Electrochemical sensor for the analysis of 5-hydroxymethylcytosine in the presence of cytosine using pencil graphite electrode

In recent years, important efforts have been made to elucidate the mechanisms of epigenetic regulation, and one of the most studied epigenetic modifications was DNA methylation/demethylation. In this study, the voltammetric behaviour of 5-hydroxymethylcytosine was studied in the pH range of 2.00-11.00 using pencil graphite electrodes by differential pulse and square wave voltammetry. The effect of buffer solutions, scan rate, square wave voltammetry parameters, and stripping conditions on the voltammetric responses of 5-hydroxymethylcytosine were performed. The electrochemical oxidation process of 5-hydroxymethylcytosine on the pencil graphite electrode was realized under adsorption control. In human urine, by square wave stripping voltammetry, 5-hydroxymethylcytosine was quantified in a concentration range of 1.00 × 10-5 M-2.00 × 10-4 M. The proposed method was tested in the presence of cytosine in human urine. The recovery value of 5-hydroxymethylcytosine was found to be 99.57 %.

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.

Enantioselectively generating imidazolone dIz by the chiral DNA intercalating and "light-switching" Ru(II) polypyridyl complex via a novel flash-quench method

The 2-aminoimidazolone is a major and ubiquitous in vitro product of guanine oxidation. The flash-quench method, combining spectroscopy and product analysis, offers a novel and tunable approach to study guanine oxidation on double helical DNA. Herein we found that imidazolone dIz (2-amino-5-[(2-deoxy-β-D-erythro-pentofuranosyl)amino]-4H-imidazole-4-one) and dZ (2,2-diamino-5-[2-deoxy-β-D-erythro-pentofuranosyl)amino]-5(2H)-oxazolone) were the major oxidation products of double-strand DNA from the visible-light irradiation of the well-known DNA intercalating and light-switching Ru(OP)2dppz2+ (OP = 1,10-phenanthroline, dppz = dipyrido [3,2-a:2',3'-c]phenazine) in the presence of a typical quencher methyl viologen (MV2+). Using ESR spin-trapping method, the radical intermediate MV•+ with typical hyperfine pattern was detected which indicated the successful formation of the corresponding Ru3+ intercalated oxidant. The formation of dIz and dZ decreased markedly with the addition of nitrotetrazolium blue chloride (NBT), a typical O2•- reactant. With a more specific and highly sensitive O2•- probe CT02-H, its ESR signal decayed rapidly in the presence of Ru(OP)2dppz2+ and MV2+, suggesting that O2•- was indeed produced. More interestingly, enantio-selective generation of oxidation products from dsDNA was observed with the two chiral forms of Ru(OP)2dppz2+. This represents the first report that the flash-quench technique with MV2+ as the quencher can oxidize dsDNA effectively to form dIz and dZ via the Ru3+/O2•- mediated mechanism. Our new findings provide a novel method to generate two radicals simultaneously, G (-H)• and O2•-, in close proximity to one another in dsDNA.

Molecular mechanism of the metal-independent production of hydroxyl radicals by thiourea dioxide and H2O2

It is well-known that highly reactive hydroxyl radicals (HO•) can be produced by the classic Fenton system and our recently discovered haloquinone/H2O2 system, but rarely from thiol-derivatives. Here, we found, unexpectedly, that HO• can be generated from H2O2 and thiourea dioxide (TUO2), a widely used and environmentally friendly bleaching agent. A carbon-centered radical and sulfite were detected and identified as the transient intermediates, and urea and sulfate as the final products, with the complementary application of electron spin-trapping, oxygen-18 isotope labeling coupled with HPLC/MS analysis. Density functional theory calculations were conducted to further elucidate the detailed pathways for HO• production. Taken together, we proposed that the molecular mechanism for HO• generation by TUO2/H2O2: TUO2 tautomerizes from sulfinic acid into ketone isomer (TUO2-K) through proton transfer, then a nucleophilic addition of H2O2 on the S atom of TUO2-K, forming a S-hydroperoxide intermediate TUO2-OOH, which dissociates homolytically to produce HO•. Our findings represent the first experimental and computational study on an unprecedented new molecular mechanism of HO• production from simple thiol-derived sulfinic acids, which may have broad chemical, environmental, and biomedical significance for future research on the application of the well-known bleaching agent and its analogs.

Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation

Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.

Copper trafficking systems in cells: insights into coordination chemistry and toxicity

Transition metal ions, such as copper, are indispensable components in the biological system. Copper ions which primarily exist in two major oxidation states Cu(I) and Cu(II) play crucial roles in various cellular processes including antioxidant defense, biosynthesis of neurotransmitters, and energy metabolism, owing to their inherent redox activity. The disturbance in copper homeostasis can contribute to the development of copper metabolism disorders, cancer, and neurodegenerative diseases, highlighting the significance of understanding the copper trafficking system in cellular environments. This review aims to offer a comprehensive overview of copper homeostatic machinery, with an emphasis on the coordination chemistry of copper transporters and trafficking proteins. While copper chaperones and the corresponding metalloenzymes are thoroughly discussed, we also explore the potential existence of low-molecular-mass metal complexes within cellular systems. Furthermore, we summarize the toxicity mechanisms originating from copper deficiency or accumulation, which include the dysregulation of oxidative stress, signaling pathways, signal transduction, and amyloidosis. This perspective review delves into the current knowledge regarding the intricate aspects of the copper trafficking system, providing valuable insights into potential treatment strategies from the standpoint of bioinorganic chemistry.

Differentiated oxidation modes of guanine between CpG and 5mCpG by a photoactivatable Pt(IV) anticancer prodrug

CpG and its cytosine-methylated counterpart (^5mCpG) are a unique reversible pair of sequences in regulating the expression of genes epigenetically. As DNA is the potential target of Pt-based anticancer metallodrugs, herein, we comparatively investigate the interactions of 5'-CpG and 5'-^5mCpG with a photoactivatable anticancer Pt(IV) prodrug, trans,trans,trans-[Pt^IV(N₃)₂(OH)₂(py)₂] (1; py = pyridine), to explore the effects of methylation on the platination and ROS-induced oxidation of the CpG motif. Mono-platinated dinucleotides were demonstrated by ESI-MS to be the main products for both 5'-CpG and 5'-^5mCpG with the bound Pt moiety as [Pt^II(N₃)(py)₂] generated by the photodecomposition of complex 1 under irradiation with blue light, accompanied by the formation of less abundant di-platinated adducts. G-N7 and C-N3/^5mC-N3 were shown to be the major and minor platination sites, respectively, with G-N1 as the third and weakest platination site, in particular, in di-platinated products. Moreover, platinated dinucleotides associated with guanine and/or cytosine oxidation were also observed. Apart from 8-oxo-guanine (^oxG) and N-formylamidoiminohydantoin (RedSp) reported previously, novel oxidation adducts 5-guanidinohydantoin (Gh) derived from guanine and 1-carbamoyl-4,5-dihydroxy-2-oxoimidazolidine (ImidCyt) derived from cytosine in CpG, and diimino imidazole (DIz) and 2,5-diaminoimidazol-4-one (imidazolone, Iz) derived from guanine and Imid^5mCyt derived from ^5mC in ^5mCpG were proposed according to MS information. These results showed that methylation exerted little effects on the platination modes of CpG, but triggered distinct oxidation pathways of CpG, perhaps causing discriminated DNA damage to CpG-rich genes. This work provides novel insights into the role of the anticancer photoactivatable Pt(IV) prodrug through damaging the epigenetically modified DNA sequences.

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

Molecular oxygen sensitizes DNA to damage induced by ionizing radiation, Fenton-like reactions, and other free radical-mediated reactions. It rapidly converts carbon-centered radicals within DNA into peroxyl radicals, giving rise to a plethora of oxidized products consisting of nucleobase and 2-deoxyribose modifications, strand breaks and abasic sites. The mechanism of formation of single oxidation products has been extensively studied and reviewed. However, much evidence shows that reactive peroxyl radicals can propagate damage to vicinal components in DNA strands. These intramolecular reactions lead to the dual alteration of two adjacent nucleotides, designated as tandem or double lesions. Herein, current knowledge about the formation and biological implications of oxidatively generated DNA tandem lesions is reviewed. Thus far, most reported tandem lesions have been shown to arise from peroxyl radicals initially generated at pyrimidine bases, notably thymine, followed by reaction with 5'-flanking bases, especially guanine, although contiguous thymine lesions have also been characterized. Proper biomolecular processing is impaired by several tandem lesions making them refractory to base excision repair and potentially more mutagenic.

Practical Aspects in the Study of Biological Photosensitization Including Reaction Mechanisms and Product Analyses: A Do's and Don'ts Guide†

The interaction of light with natural matter leads to a plethora of photosensitized reactions. These reactions cause the degradation of biomolecules, such as DNA, lipids, proteins, being therefore detrimental to the living organisms, or they can also be beneficial by allowing the treatment of several diseases by photomedicine. Based on the molecular mechanistic understanding of the photosensitization reactions, we propose to classify them in four processes: oxygen-dependent (type I and type II processes) and oxygen-independent [triplet-triplet energy transfer (TTET) and photoadduct formation]. In here, these processes are discussed by considering a wide variety of approaches including time-resolved and steady-state techniques, together with solvent, quencher, and scavenger effects. The main aim of this survey is to provide a description of general techniques and approaches that can be used to investigate photosensitization reactions of biomolecules together with basic recommendations on good practices. Illustration of the suitability of these approaches is provided by the measurement of key biomarkers of singlet oxygen and one-electron oxidation reactions in both isolated and cellular DNA. Our work is an educational review that is mostly addressed to students and beginners.

May Cu(II) binding, DNA cleavage and radicals production by YadA fragments be involved in the promotion of F. nucleatum related cancers?

In many cases, human microbiota is associated with cancer progression. It was concluded that Fusobacterium nucleatum increases neoplastic changes. This bacterium is naturally present in the human dental plaque. However,...

Unexpected Disparity in Photoinduced Reactions of C60 and C70 in Water with the Generation of O2 •- or 1O2

Well-defined fullerene-PEG conjugates, C₆₀-PEG (1) and two C₇₀-PEG (2 and 3 with the addition sites on ab-[6,6] and cc-[6,6]-junctions), were prepared from their corresponding Prato monoadduct precursors. The resulting highly water-soluble fullerene-PEG conjugates 1-3 were evaluated for their DNA-cleaving activities and reactive oxygen species (ROS) generation under visible light irradiation. Unexpectedly, photoinduced cleavage of DNA by C₆₀-PEG 1 was much higher than that by C₇₀-PEG 2 and 3 with higher absorption intensity, especially in the presence of an electron donor (NADH). The preference of photoinduced ROS generation from fullerene-PEG conjugates 1-3 via the type II (energy transfer) or the type I (electron transfer) photoreaction was found to be dependent on the fullerene core (between C₆₀ and C₇₀) and functionalization pattern of C₇₀ (between 2 and 3). This was clearly supported by the electron transfer rate obtained from cyclic voltammetry data and computationally estimated relative rate of each step of the type II and the type I reactions, with the finding that type II energy transfer reactions occurred in the inverted Marcus regime while type I electron transfer reactions proceeded in the normal Marcus regime. This finding on the disparity in the pathways of photoinduced reactions (type I versus type II) provides insights into the behavior of photosensitizers in water and the design of photodynamic therapy drugs.

Reactivity and DNA Damage by Independently Generated 2'-Deoxycytidin-N4-yl Radical

Oxidative stress produces a variety of radicals in DNA, including pyrimidine nucleobase radicals. The nitrogen-centered DNA radical 2'-deoxycytidin-N4-yl radical (dC·) plays a role in DNA damage mediated by one electron oxidants, such as HOCl and ionizing radiation. However, the reactivity of dC· is not well understood. To reduce this knowledge gap, we photochemically generated dC· from a nitrophenyl oxime nucleoside and within chemically synthesized oligonucleotides from the same precursor. dC· formation is confirmed by transient UV-absorption spectroscopy in laser flash photolysis (LFP) experiments. LFP and duplex DNA cleavage experiments indicate that dC· oxidizes dG. Transient formation of the dG radical cation (dG^+•) is observed in LFP experiments. Oxidation of the opposing dG in DNA results in hole transfer when the opposing dG is part of a dGGG sequence. The sequence dependence is attributed to a competition between rapid proton transfer from dG^+• to the opposing dC anion formed and hole transfer. Enhanced hole transfer when less acidic O6-methyl-2'-deoxyguanosine is opposite dC· supports this proposal. dC· produces tandem lesions in sequences containing thymidine at the 5'-position by abstracting a hydrogen atom from the thymine methyl group. The corresponding thymidine peroxyl radical completes tandem lesion formation by reacting with the 5'-adjacent nucleotide. As dC· is reduced to dC, its role in the process is traceless and is only detectable because of the ability to independently generate it from a stable precursor. These experiments reveal that dC· oxidizes neighboring nucleotides, resulting in deleterious tandem lesions and hole transfer in appropriate sequences.

Mechanistic Study on Oxidative DNA Damage and Modifications by Haloquinoid Carcinogenic Intermediates and Disinfection Byproducts

Haloquinones (XQs) are a group of carcinogenic intermediates of the haloaromatic environmental pollutants and newly identified chlorination disinfection byproducts (DBPs) in drinking water. The highly reactive hydroxyl radicals/alkoxyl radicals and quinone enoxy/ketoxy radicals were found to arise in XQs and H₂O₂ or organic hydroperoxides system, independent of transition-metal ions. However, it was not clear whether these haloquinoid carcinogens and hydroperoxides can cause oxidative DNA damage and modifications, and if so, what are the underlying molecular mechanisms. We found that 8-oxodeoxyguanosine (8-oxodG), DNA strand breaks, and three methyl oxidation products could arise when DNA was treated with tetrachloro-1,4-benzoquinone and H₂O₂ via a metal-independent and intercalation-enhanced oxidation mechanism. Similar effects were observed with other XQs, which are generally more efficient than the typical Fenton system. We further extended our studies from isolated DNA to genomic DNA in living cells. We also found that potent oxidation of DNA to the more mutagenic imidazolone dIz could be induced by XQs and organic hydroperoxides such as t-butylhydroperoxide or the physiologically relevant hydroperoxide 13S-hydroperoxy-9Z,11E-octadecadienoic acid via an unprecedented quinone-enoxy radical-mediated mechanism. These findings should provide new perspectives to explain the potential genotoxicity, mutagenesis, and carcinogenicity for the ubiquitous haloquinoid carcinogenic intermediates and DBPs.

Photosensitization Reactions of Biomolecules: Definition, Targets and Mechanisms

Photosensitization reactions have been demonstrated to be largely responsible for the deleterious biological effects of UV and visible radiation, as well as for the curative actions of photomedicine. A large number of endogenous and exogenous photosensitizers, biological targets and mechanisms have been reported in the past few decades. Evolving from the original definitions of the type I and type II photosensitized oxidations, we now provide physicochemical frameworks, classifications and key examples of these mechanisms in order to organize, interpret and understand the vast information available in the literature and the new reports, which are in vigorous growth. This review surveys in an extended manner all identified photosensitization mechanisms of the major biomolecule groups such as nucleic acids, proteins, lipids bridging the gap with the subsequent biological processes. Also described are the effects of photosensitization in cells in which UVA and UVB irradiation triggers enzyme activation with the subsequent delayed generation of superoxide anion radical and nitric oxide. Definitions of photosensitized reactions are identified in biomolecules with key insights into cells and tissues.

Reactions of a photoactivatable diazido Pt(iv) anticancer complex with a single-stranded oligodeoxynucleotide

Platinum based anticancer agents are widely applied in clinic and their major target is believed to be DNA. Herein, the interaction of a photoactivatable diazido Pt(iv) anticancer prodrug trans,trans,trans-[Pt(N3)2(OH)2(py)2] (py = pyridine; 1) with a 15-mer single-G-containing oligodeoxynucleotide (ODN I: 5'-CT2CTCTTG8T9CT11TCTC-3') was investigated by mass spectrometric methods. Up to penta-platinated ODN I adducts were identified from primary mass spectra while the mono- and di-platinated adducts had the highest intensity. Fragmentation of mono-, di- and tri-platinated I adducts in tandem MS revealed that T2, G8, T11 and T9 are binding sites. No cytosine sites were identified which may be due to the facile loss of Pt adducts from cytosine during CID. The intensity of {Pt(py)2}-bound adducts was comparable to that of {Pt(N3)(py)2}-bound adducts, indicating that the photo-reduction pathway of complex 1 from Pt(iv) to Pt(ii) through two one-electron donations from two azides was substantial. Moreover, no transformation of N3 to NH3 on the {Pt(N3)(py)2}-bound adducts was observed, whereas it is very popular during the reactions of complexes with short ODNs or mono-nucleotides. The oxidation on I induced by the reactive oxygen species (ROS) formed by the photodecomposition of complex 1 was significant, and the oxidation of G8 to 8-hydroxyguanine (8-OH-G), spiroiminodihydantoin (Sp) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) was discovered. These results unambiguously revealed a sequence-length-dependent photochemical reactivity of complex 1 when it interacted with different ODNs, providing deeper understanding in the reactivity of photoactivatable diazido anticancer Pt(iv) prodrugs to DNA.

Harnessing Genomic Stress for Antitumor Immunity

Significance: Genomic instability, a hallmark of cancer, renders cancer cells susceptible to genomic stress from both endogenous and exogenous origins, resulting in the increased tendency to accrue DNA damage, chromosomal instability, or aberrant DNA localization. Apart from the cell autonomous tumor-promoting effects, genomic stress in cancer cells could have a profound impact on the tumor microenvironment. Recent Advances: Recently, it is increasingly appreciated that harnessing genomic stress could provide a promising strategy to revive antitumor immunity, and thereby offer new therapeutic opportunities in cancer treatment. Critical Issues: Genomic stress is closely intertwined with antitumor immunity via mechanisms involving the direct crosstalk with DNA damage response components, upregulation of immune-stimulatory/inhibitory ligands, release of damage-associated molecular patterns, increase of neoantigen repertoire, and activation of DNA sensing pathways. A better understanding of these mechanisms will provide molecular basis for exploiting the genomic stress to boost antitumor immunity. Future Directions: Future research should pay attention to the heterogeneity between individual cancers in the genomic instability and the associated immune response, and how to balance the toxicity and benefit by specifying the types, potency, and treatment sequence of genomic stress inducer in therapeutic practice. Antioxid. Redox Signal. 34, 1128-1150.

Photoactivatable diazido Pt(IV) anticancer complex can bind to and oxidize all four nucleosides

Photoactivatable diazidodihydroxido Pt(iv) complex trans,trans,trans-[Pt(N3)2(OH)2(py)2] (1; py = pyridine) is a promising anticancer agent which can be activated by visible light to induce cancer cell death. DNA has been thought to be involved in the mechanism of action of this kind of Pt(iv) prodrug. However, the detailed photodecomposition pathways of complex 1 and its interaction modes with DNA are complex. Herein we report that upon light irradiation complex 1 can bind to all four nucleosides covalently with the reduced Pt(ii) species. Moreover, apart from the covalent coordination, various oxidation adducts of these four nucleosides induced by the reactive oxidative species (ROS) generated during the photoactivation of the complex 1 have also been identified, especially the induced oxidation of adenosine and cytidine which was firstly reported for this kind of photoactivatable Pt(iv) prodrug. Such dual-action may contribute to the highly potent photo-antiproliferativity of complex 1 towards cancer cells, which may account for the unique mechanism of action of the photoactivatable diazido Pt(iv) anticancer complexes.

Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment

In this work, electron-induced site-specific formation of neutral π-type aminyl radicals (RNH·) and their reactions with pyrimidine nucleoside analogs azidolabeled at various positions in the sugar moiety, e.g., at 2'-, 3'-, 4'-, and 5'- sites along with a model compound 3-azido-1-propanol (3AZPrOH), were investigated. Electron paramagnetic resonance (EPR) studies confirmed the site and mechanism of RNH· formation via dissociative electron attachment-mediated loss of N₂ and subsequent facile protonation from the solvent employing the ¹⁵N-labeled azido group, deuterations at specific sites in the sugar and base, and changing the solvent from H₂O to D₂O. Reactions of RNH· were investigated employing EPR by warming these samples from 77 K to ca. 170 K. RNH· at a primary carbon site (5'-azido-2',5'-dideoxyuridine, 3AZPrOH) facilely converted to a σ-type iminyl radical (R═N·) via a bimolecular H-atom abstraction forming an α-azidoalkyl radical. RNH· when at a secondary carbon site (e.g., 2'-azido-2'-deoxyuridine) underwent bimolecular electrophilic addition to the C5═C6 double bond of a proximate pyrimidine base. Finally, RNH· at tertiary alkyl carbon (4'-azidocytidine) underwent little reaction. These results show the influence of the stereochemical and electronic environment on RNH· reactivity and allow the selection of those azidonucleosides that would be most effective in augmenting cellular radiation damage.

A theoretical study on the role of stability of cytosine and its tautomers in DNA (deoxyribonucleic acid), and investigation of interactions of Na+, K+, Mg2+, Ca2+, Zn2+ metal ions and OH radical with cytosine tautomers

In the present study, 21 cytosine tautomers were investigated so that some tautomers were reported for the first time in the gas phase and aqueous solution. C₃ tautomer was the most stable tautomer in gas phase but C₁ was the most stable structure in aqueous solution. The potential energy surface of all trajectories was determined for 21 tautomers and 22 transition states. Also, interactions of cytosine tautomers with Na⁺, K⁺, Mg²⁺, Ca²⁺ and Zn²⁺ metal ions were studied in gas phase and aqueous solution. Three types of interactions among metal ions and (N1 and O10), (N3 and O10) and (N3 and N9) of cytosine tautomers were investigated. The study of interaction energies of all complexes showed the stability of complexes in which interactions among Mg²⁺ and Zn²⁺ with tautomers were stronger than interactions among Ca²⁺, Na⁺ and K⁺ with tautomers, respectively. Some interactions of metal ions with cytosine tautomers made the most stable tautomers. So, the stability of rare tutomeric forms had a significant effect on stabilization of anomalous DNA (deoxyribonucleic acid) double helix and spontaneous mutations. Also, one of the most important causes of mutations in DNA (deoxyribonucleic acid) was the reaction of OH radical with nucleotide bases. So, interactions of OH radical with cytosine and its tautomers were investigated in gas phase and aqueous solution.Communicated by Ramaswamy H. Sarma.

First Direct and Unequivocal Electron Spin Resonance Spin-Trapping Evidence for pH-Dependent Production of Hydroxyl Radicals from Sulfate Radicals

Recently, the sulfate radical (SO₄^•-) has been found to exhibit broad application prospects in various research fields such as chemical, biomedical, and environmental sciences. It has been suggested that SO₄^•- could be transformed into a more reactive hydroxyl radical (^•OH); however, no direct and unequivocal experimental evidence has been reported yet. In this study, using an electron spin resonance (ESR) secondary radical spin-trapping method coupled with the classic spin-trapping agent 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and the typical ^•OH-scavenging agent dimethyl sulfoxide (DMSO), we found that ^•OH can be produced from three SO₄^•--generating systems from weakly acidic (pH = 5.5) to alkaline conditions (optimal at pH = 13.0), while SO₄^•- is the predominant radical species at pH < 5.5. A comparative study with three typical ^•OH-generating systems strongly supports the above conclusion. This is the first direct and unequivocal ESR spin-trapping evidence for ^•OH formation from SO₄^•- over a wide pH range, which is of great significance to understand and study the mechanism of many SO₄^•--related reactions and processes. This study also provides an effective and direct method for unequivocally distinguishing ^•OH from SO₄^•-.

Oxidative Stress and Genotoxicity in Melanoma Induction: Impact on Repair Rather Than Formation of DNA Damage?

Keratinocytes and melanocytes, two cutaneous cell types located within the epidermis, are the origin of most skin cancers, namely carcinomas and melanomas. These two types of tumors differ in many ways. First, carcinomas are almost 10 times more frequent than melanomas. In addition, the affected cellular pathways, the mutated genes and the metastatic properties of the tumors are not the same. This review addresses another specificity of melanomas: the role of photo-oxidative stress. UVA efficiently produces reactive oxygen species in melanocytes, which results in more frequent oxidatively generated DNA lesions than in other cell types. The question of the respective contribution of UVB-induced pyrimidine dimers and UVA-mediated oxidatively generated lesions to mutagenesis in melanoma remains open. Recent results based on next-generation sequencing techniques strongly suggest that the mutational signature associated with pyrimidine dimers is overwhelming in melanomas like in skin carcinomas. UVA-induced oxidative stress may yet be indirectly linked to the genotoxic pathways involved in melanoma through its ability to hamper DNA repair activities.

Tandem Lesions Arising from 5-(Uracilyl)methyl Peroxyl Radical Addition to Guanine: Product Analysis and Mechanistic Studies

The reaction of hydroxyl radical (HO^•) with thymine in DNA generates 5-(uracilyl)-methyl radicals (T^•) and the corresponding methylperoxyl radical (TOO^•) in the presence of O₂, which in turn propagates damage by reacting with a vicinal nucleobase. This leads to so-called double or tandem lesions. Because methyl oxidation products of thymine are major products, we investigated the reactivity of TOO^• using a photolabile precursor: 5-(phenylthiomethyl)uracil (T^SPh). The precursor was prepared and incorporated into a DNA trinucleotide: 5'-d(GpT^SPhpA)-3' (G-T^SPh-A). Upon photolysis, the resulting products were characterized by LC-MS/MS. Thereby, we identified four tandem lesions involving GpT, which include either 2,6-diamino-4-hydroxy-5-formamidopyrimidine (fapyG) or 8-oxo-7,8-dihydroguanine (oxoG) in tandem with either 5-formyluracil (fU) or 5-hydroxymethyluracil (hmU). The formation of these tandem lesions is explained by initial addition of TOO^• to the C8 of guanine moiety, giving an N7-guanine cross-linked radical. The latter radical undergoes either reduction to an 7,8-saturated endoperoxide or oxidation to an 7,8-unsaturated endoperoxide, which transform into fapyG-fU-A and oxoG-fU-A, respectively. This is supported by the effect of a reducing (dithiothreitol) and oxidizing agent (Fe³⁺) on product formation. This study expands the repertoire of tandem lesions that can occur at GpT sequences and underlines the importance of redox environment.

(5'R)-and (5'S)-purine 5',8-cyclo-2'-deoxyribonucleosides: reality or artifactual measurements? A reply to Chatgilialoglu's comments (this issue)

This rebuttal letter is aimed at refuting the poor and false arguments elaborated by Chatgilialoglu (preceding article) in his response to the position article (Cadet et al. Free Radic Res 2019;53:574-577) that focussed on the putative reliability of the HPLC-MS/MS measurements of five radiation-induced damage to cellular DNA, which included 8-oxo-7,8-dihydro-2'-deoxyadenosine and the (5'R) and (5'S) diastereomers of 5',8-cyclo-2'-deoxyadenosine and 5',8-cyclo-2'-deoxyadenosine (Krokidis et al. Free Radic Res 2017;51:470-482). Unfortunately, none of the main issues we raised on the suitability of the analytical approach and the shortcomings associated with DNA extraction in HPLC based measurement methods of oxidatively generated damage in cells were properly considered in Chatigilialolu's letter. The main questionable issues include the lack of information on the sensitivity of HPLC-MS/MS analysis, the absence of a dose curve that is essential in the formation of damage and the nonconsideration of artifactual oxidation.

Mechanism of unprecedented hydroxyl radical production and site-specific oxidative DNA damage by photoactivation of the classic arylhydroxamic acid carcinogens

The carcinogenicity of N-hydroxy-2-acetamidofluorene (N-OHAAF), the major genotoxic metabolite of the classic model aromatic amine (AA) carcinogen 2-acetylaminofluorene, has been attributed mainly to the formation of DNA adducts via arylnitrenium upon enzymatic activation. Here, we show, unexpectedly, that exposure of N-OHAAF to UV or sunlight irradiation can not only induce the formation of the well-known covalent DNA adducts, but, more interestingly, simultaneous generation of oxidative DNA damage was also observed as measured by the formation of DNA single-/double-strand breaks (SSBs/DSBs) and 8-oxo-2'-deoxyguanosine (8-oxodG), which were partly inhibited by the typical hydroxyl radical (•OH) scavengers. Electron spin resonance spin-trapping and fluorescent studies unequivocally confirmed that the highly reactive •OH was generated from photolysis of N-OHAAF. Further DNA sequencing investigations suggest that photoactivation of N-OHAAF caused preferential cleavage at guanine, thymine and cytosine sites. More importantly, the formation of 8-oxodG and DSBs were also observed when fibroblast Balb/c-3T3 cells were co-exposed to N-OHAAF/UV irradiation as measured by double immunofluorescence staining. Taken together, we propose that both •OH and amidyl radicals can be readily produced via N-OH homolysis in N-OHAAF by photoirradiation, which can induce both oxidative and covalent DNA damage. This represents the first report of •OH production and site-specific DNA damage via photoactivation of the genotoxic hydroxamic acid intermediate, which provides a new free radical perspective to better understand the molecular mechanism for the carcinogenicity of AAs.

Formation and biological consequences of 5-Formylcytosine in genomic DNA

5-Formyl-2'-deoxycytidine (5fdC) is a naturally occurring nucleobase that is broadly distributed in genomic DNA. 5fdC is produced via the oxidation of 5-methylcytosine (5mdC) by ten-eleven translocation enzyme (TET) and can be further converted to 5-carboxylcytosine (5cadC) by TET. Both 5fdC and 5cadC can be restored to dC by TDG-mediated base excision repair and direct deformylation/decarboxylation. Thus, 5fdC is considered an intermediate in the TET-mediated DNA demethylation pathway. 5fdC also alters the structure and stability of genomic DNA and affects genetic expression. This review summarizes the recent research on 5fdC, detailing its formation, detection and distribution, biological functions and transformation in cells. The challenges and future prospects to further explore the function and metabolism of 5fdC are briefly discussed at the end.

DNA Base Modifications Mediated by Femtosecond Laser-Induced Cold Low-Density Plasma in Aqueous Solutions

Applications based on near-infrared femtosecond laser-induced plasma in biological materials involve numerous ionization events that inevitably mediate physicochemical effects. Here, the physical chemistry underlying the action of such plasma is characterized in a system of biological interest. We have implemented wavefront shaping techniques to control the generation of laser-induced low electron density plasma channels in DNA aqueous solutions, which minimize the unwanted thermo-mechanical effects associated with plasma of higher density. The number of DNA base modifications per unit of absolute energy deposited by such cold plasma is compared to those induced by either ultraviolet or standard ionizing radiation (γ-rays). Analyses of various photoinduced, oxidative, and reductive DNA base products show that the effects of laser-induced cold plasma are mainly mediated by reactive radical species produced upon the ionization of water, rather than by the direct interaction of the strong laser field with DNA. In the plasma environment, reactions among densely produced primary radicals result in a dramatic decrease in the yields of DNA damages relative to sparse ionizing radiation. This intense radical production also drives the local depletion of oxygen.

Genotoxic effects of PM10 and PM2.5 bound metals: metal bioaccessibility, free radical generation, and role of iron

The present study was undertaken to examine the possible genotoxicity of ambient particulate matter (PM₁₀ and PM_2.5) in Pune city. In both size fractions of PM, Fe was found to be the dominant metal by concentration, contributing 22% and 30% to the total mass of metals in PM₁₀ and PM_2.5, respectively. The speciation of soluble Fe in PM₁₀ and PM_2.5 was investigated. The average fraction of Fe³⁺ and Fe²⁺ concentrations in PM_2.5 was 80.6% and 19.3%, respectively, while in PM_2.5 this fraction was 71.1% and 29.9%, respectively. The dominance of Fe(III) state in both PM fractions facilitates the generation of hydroxyl radicals (^·OH), which can damage deoxyribose nucleic acid (DNA), as was evident from the gel electrophoresis study. The DNA damage by ^·OH was supported through the in silico density functional theory (DFT) method. DFT results showed that C8 site of guanine (G)/adenine (A) and C6 site of thymine (T)/cytosine (C) would be energetically more favorable for the attack of hydroxyl radicals, when compared with the C4 and C5 sites. The non-standard Watson-Crick base pairing models of oxidative products of G, A, T and C yield lower-energy conformations than canonical dA:dT and dG:dC base pairing. This study may pave the way to understand the structural consequences of base-mediated oxidative lesions in DNA and its role in human diseases.

Formation of UV-induced DNA damage contributing to skin cancer development

UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.

Biphotonic Ionization of DNA: From Model Studies to Cell

Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.

Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer

In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.

Vertical Ultrafiltration-Facilitated DNA Digestion for Rapid and Sensitive UHPLC-MS/MS Detection of DNA Modifications

LC-MS/MS technologies provide important and powerful analytical tools for chemical structure-dependent identification and quantification of epigenetically crucial DNA modifications. To perform LC-MS/MS analysis, it is better to convert DNA to 2'-deoxynucleosides through enzymatic digestion. Here, we observed that inorganic cations Na⁺ and K⁺ and phosphate buffers, which were often found in various DNA solutions, significantly inhibited DNA digestion as catalyzed by typical set of DNase I, snake venom phosphodiesterase, and calf intestine alkaline phosphatase, leading to poor or varying performance on UHPLC-MS/MS analysis. We then developed an efficient and unique vertical-ultrafiltration approach, enabling us to remove these inorganic salts without DNA loss. Consequently, the removal of inorganic salts by ultrafiltration facilitated the followed DNA digestion and thus enhanced the final UHPLC-MS/MS detection. Benefiting from the developed vertical-ultrafiltration approach, it is also feasible to integrate the desalting step with the other two steps of DNA digestion and protein removal. By investigating the time course of DNA digestion, we observed a differential release rate of 2'-deoxycytidine and 5-methyl-2'-deoxycytidine causing a measurement bias on the methylation frequency. We further exploited Mg²⁺ to eliminate this bias by stimulating DNase set-based DNA digestion. These innovative approaches enable us to perform rapid, sensitive, and robust UHPLC-MS/MS analysis of methylated DNA 2'-deoxycytidine, demethylation intermediates, and probably other DNA modifications.

Melatonin: A Versatile Protector against Oxidative DNA Damage

Oxidative damage to DNA has important implications for human health and has been identified as a key factor in the onset and development of numerous diseases. Thus, it is evident that preventing DNA from oxidative damage is crucial for humans and for any living organism. Melatonin is an astonishingly versatile molecule in this context. It can offer both direct and indirect protection against a wide variety of damaging agents and through multiple pathways, which may (or may not) take place simultaneously. They include direct antioxidative protection, which is mediated by melatonin's free radical scavenging activity, and also indirect ways of action. The latter include, at least: (i) inhibition of metal-induced DNA damage; (ii) protection against non-radical triggers of oxidative DNA damage; (iii) continuous protection after being metabolized; (iv) activation of antioxidative enzymes; (v) inhibition of pro-oxidative enzymes; and (vi) boosting of the DNA repair machinery. The rather unique capability of melatonin to exhibit multiple neutralizing actions against diverse threatening factors, together with its low toxicity and its ability to cross biological barriers, are all significant to its efficiency for preventing oxidative damage to DNA.

Controlled potential electro-oxidation of genomic DNA

Exposure of mammalian cells to oxidative stress can result in DNA damage that adversely affects many cell processes. Lack of dependable DNA damage reference materials and standardized measurement methods, despite many case-control studies hampers the wider recognition of the link between oxidatively degraded DNA and disease risk. We used bulk electrolysis in an electrochemical system and gas chromatographic mass spectrometric analysis (GC/MS/MS) to control and measure, respectively, the effect of electrochemically produced reactive oxygen species on calf thymus DNA (ct-DNA). DNA was electro-oxidized for 1 h at four fixed oxidizing potentials (E = 0.5 V, 1.0 V, 1.5 V and 2 V (vs Ag/AgCl)) using a high surface area boron-doped diamond (BDD) working electrode (WE) and the resulting DNA damage in the form of oxidatively-modified DNA lesions was measured using GC/MS/MS. We have shown that there are two distinct base lesion formation modes in the explored electrode potential range, corresponding to 0.5 V < E < 1.5 V and E > 1.5 V. Amounts of all four purine lesions were close to a negative control levels up to E = 1.5 V with evidence suggesting higher levels at the lowest potential of this range (E = 0.5 V). A rapid increase in all base lesion yields was measured when ct-DNA was exposed at E = 2 V, the potential at which hydroxyl radicals were efficiently produced by the BDD electrode. The present results demonstrate that controlled potential preparative electrooxidation of double-stranded DNA can be used to purposely increase the levels of oxidatively modified DNA lesions in discrete samples. It is envisioned that these DNA samples may potentially serve as analytical control or quality assurance reference materials for the determination of oxidatively induced DNA damage.

The Sequence Preference of Gamma-Radiation-Induced Damage in End-Labeled DNA after Heat Treatment

In this work, we examined the DNA sequence preference of gamma-radiation-induced DNA damage in purified DNA sequences after heat treatment. DNA was fluorescently end-labeled and gamma-radiation-induced DNA cleavage was examined using capillary electrophoresis with laser-induced fluorescence detection. Our findings provide evidence that gamma-radiation-induced DNA damage to end-labeled DNA is nonrandom and has a sequence preference. The degree of cleavage was quantified at each nucleotide, and we observed that preferential cleavage occurred at C nucleotides with lesser cleavage at G nucleotides, while being very low at T nucleotides. The differences in percentage cleavage at individual nucleotides ranged up to sixfold. The DNA sequences surrounding the most intense radiation-induced DNA cleavage sites were examined and a consensus sequence 5'-AGGC*C (where C* is the cleavage site) was found. The highest intensity gamma-radiation-induced DNA cleavage sites were found at the dinucleotides, 5'-GG*, 5'-GC*, 5'-C*C and 5'-G*G and at the trinucleotides, 5'-GG*C, 5'-TC*A, 5'-GG*G and 5'-GC*C. These findings have implications for our understanding of ionizing radiation-induced DNA damage.

Reaction mechanism of the cation radicals of thymine and thymine derivatives in aqueous solution: A theoretical study

Mechanisms of decomposition reaction of thymine cation radicals (T[Formula: see text]), 1-methyl substituted T[Formula: see text] (1-MeT[Formula: see text]), and 1,3-dimethyl substituted T[Formula: see text] (1,3-Me2T[Formula: see text]) generated by ionizing radiation or one-electron oxidation to thymine, 1-methylthymine and 1,3-dimethylthymine in aqueous solution have been investigated by theoretical calculations. Seven reaction paths including H2O or OH[Formula: see text] addition, and deprotonation were considered. The most likely reaction for T[Formula: see text] decomposition is N1 deprotonation forming T(-N1H)[Formula: see text]. When N1 hydrogen is replaced by methyl, T[Formula: see text] would deprotonate from C5 methyl group generating 1-methyl substituted UCH[Formula: see text] in neutral solution, and reaction with OH[Formula: see text] producing 1-methyl substituted T6OH[Formula: see text] in basic solution. When N1 and N3 hydrogens are both replaced by methyl, T[Formula: see text] decomposition reaction is similar to 1-MeT[Formula: see text], indicating that N3 hydrogen barely influences the subsequent reaction of 1-MeT[Formula: see text]. These results can provide theoretical support for experimental observations.

Intrinsic chemiluminescence production from the degradation of haloaromatic pollutants during environmentally-friendly advanced oxidation processes: Mechanism, structure-activity relationship and potential applications

The ubiquitous distribution of halogenated aromatic compounds (XAr) coupled with their carcinogenicity has raised public concerns on their potential risks to both human health and the ecosystem. Recently, advanced oxidation processes (AOPs) have been considered as an "environmentally-friendly" technology for the remediation and destruction of such recalcitrant and highly toxic XAr. During our study on the mechanism of metal-independent production of hydroxyl radicals (OH) by halogenated quinones and H₂O₂, we found, unexpectedly, that an unprecedented OH-dependent two-step intrinsic chemiluminescene (CL) can be produced by H₂O₂ and tetrachloro-p-benzoquinone, the major carcinogenic metabolite of the widely used wood preservative pentachlorophenol. Further investigations showed that, in all OH-generating systems, CL can also be produced not only by pentachlorophenol and all other halogenated phenols, but also by all XAr tested. A systematic structure-activity relationship study for all 19 chlorophenolic congeners showed that the CL increased with an increasing number of Cl-substitution in general. More importantly, a relatively good correlation was observed between the formation of quinoid/semiquinone radical intermediates and CL generation. Based on these results, we propose that OH-dependent formation of quinoid intermediates and electronically excited carbonyl species is responsible for this unusual CL production; and a rapid, sensitive, simple, and effective CL method was developed not only to detect and quantify trace amount of XAr, but also to provide useful information for predicting the toxicity or monitoring real-time degradation kinetics of XAr. These findings may have broad chemical, environmental and biological implications for future studies on halogenated aromatic persistent organic pollutants.

Hide and seek: How do DNA glycosylases locate oxidatively damaged DNA bases amidst a sea of undamaged bases?

The first step of the base excision repair (BER) pathway responsible for removing oxidative DNA damage utilizes DNA glycosylases to find and remove the damaged DNA base. How glycosylases find the damaged base amidst a sea of undamaged bases has long been a question in the BER field. Single molecule total internal reflection fluorescence microscopy (SM TIRFM) experiments have allowed for an exciting look into this search mechanism and have found that DNA glycosylases scan along the DNA backbone in a bidirectional and random fashion. By comparing the search behavior of bacterial glycosylases from different structural families and with varying substrate specificities, it was found that glycosylases search for damage by periodically inserting a wedge residue into the DNA stack as they redundantly search tracks of DNA that are 450-600bp in length. These studies open up a wealth of possibilities for further study in real time of the interactions of DNA glycosylases and other BER enzymes with various DNA substrates.

Formation and repair of oxidatively generated damage in cellular DNA

In this review article, emphasis is placed on the critical survey of available data concerning modified nucleobase and 2-deoxyribose products that have been identified in cellular DNA following exposure to a wide variety of oxidizing species and agents including, hydroxyl radical, one-electron oxidants, singlet oxygen, hypochlorous acid and ten-eleven translocation enzymes. In addition, information is provided about the generation of secondary oxidation products of 8-oxo-7,8-dihydroguanine and nucleobase addition products with reactive aldehydes arising from the decomposition of lipid peroxides. It is worth noting that the different classes of oxidatively generated DNA damage that consist of single lesions, intra- and interstrand cross-links were unambiguously assigned and quantitatively detected on the basis of accurate measurements involving in most cases high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The reported data clearly show that the frequency of DNA lesions generated upon severe oxidizing conditions, including exposure to ionizing radiation is low, at best a few modifications per 106 normal bases. Application of accurate analytical measurement methods has also allowed the determination of repair kinetics of several well-defined lesions in cellular DNA that however concerns so far only a restricted number of cases.