Radical-mediated DNA damage in presence of oxygen

Chemo-Enzymatic Generation of Highly Fluorescent Nucleoside Analogs Using Purine-Nucleoside Phosphorylase

Chemo-enzymatic syntheses of strongly fluorescent nucleoside analogs, potentially applicable in analytical biochemistry and cell biology are reviewed. The syntheses and properties of fluorescent ribofuranosides of several purine, 8-azapurine, and etheno-purine derivatives, obtained using various types of purine nucleoside phosphorylase (PNP) as catalysts, as well as α-ribose-1-phosphate (r1P) as a second substrate, are described. In several instances, the ribosylation sites are different to the canonical purine N9. Some of the obtained ribosides show fluorescence yields close to 100%. Possible applications of the new analogs include assays of PNP, nucleoside hydrolases, and other enzyme activities both in vitro and within living cells using fluorescence microscopy.

Manganese Superoxide Dismutase Polymorphism and Risk of Gastric Lesions, and Its Effects on Chemoprevention in a Chinese Population

Background: Manganese superoxide dismutase is the primary antioxidant enzyme in the mitochondria and is involved in carcinogenesis. To investigate the association between MnSOD Val16Ala polymorphism and risk of advanced gastric lesions, and its effects on chemoprevention, a population-based study was conducted in Linqu, a high-risk area of gastric cancer in China.

Methods: Genotypes were determined by PCR-RFLP analysis in 3,355 subjects with the baseline histopathologic diagnosis in 1994, and 2,758 of these subjects received subsequent three interventions including vitamin supplementation for 7.3 years. Odds ratios (OR) and 95% confidence intervals (CI) were estimated by unconditional logistic regression model.

Results: We found an increased risk of dysplasia in subjects with the Val/Ala+Ala/Ala genotype (OR, 1.31; 95% CI, 1.02-1.68) compared with the Val/Val genotype. Stratified analysis indicated that a significantly elevated risk of intestinal metaplasia (OR, 3.40; 95% CI, 2.64-4.38) or dysplasia (OR, 4.01; 95% CI, 2.79-5.74) was found in subjects carrying the Val/Ala+Ala/Ala genotype and Helicobacter pylori infection, and an interaction between this genotype and a high serum H. pylori IgG titer (>2.94) on the risk of dysplasia was observed (Pinteraction = 0.01). Furthermore, an elevated chance for regression of gastric lesions was observed in subjects with the Val/Ala+Ala/Ala genotype and high IgG titer in an intervention trial with vitamin supplementation (OR, 2.45; 95% CI, 1.37-4.38).

Conclusions: These findings suggest that Val16Ala polymorphism may play an important role in development of advanced gastric lesions and modify the effect of vitamin supplementation on the evolution of gastric lesions.

Impact: Val16Ala polymorphism is related to gastric cancer development. Cancer Epidemiol Biomarkers Prev; 19(4); 1089–97. ©2010 AACR.

Oxidation of 2'-deoxycytidine to four interconverting diastereomers of N1-carbamoyl-4,5-dihydroxy-2-oxoimidazolidine nucleosides

Modification of 2'-deoxycytidine (dCyd) by hydroxyl radicals and direct ionization leads to the formation of various oxidation products, including dCyd 5,6-glycols, 5-hydroxy-2'-deoxycytidine, and ring fragmentation products. The mechanism of oxidation is complex and poorly understood. In the present work, we have prepared four cis- and trans-diastereomers of N1-(2-deoxy-beta-D-erythro-pentofuranosyl)-1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine by bromination of dCyd followed by peroxidation of the resulting dCyd bromohydrins. The structure and stereochemistry of each product were determined by 1H NMR, 13C NMR, and 2D NOE analyses. The formation of imidazolidine products involves rearrangement of initial 5(6)-hydroxy-6(5)-hydroperoxides to C6-C2 endoperoxides, which subsequently decompose by a concerted pathway to imidazolidine products. A remarkable feature of the four diastereomers was their ability to interconvert via single and successive cycles of ring-chain tautomerism at N1-C5 and N3-C4, leading to epimerization of C5 and C4, respectively. The rate of isomerization was greater for cis-diastereomers compared to trans-diastereomers, and the rate sharply increased with pH (pH 9.0>7.0>5.5).

Cross-linked thymine-purine base tandem lesions: synthesis, characterization, and measurement in gamma-irradiated isolated DNA

5-(Phenylthiomethyl)-2'-deoxyuridine has been recently shown to be a specific photolabile precursor of 5-(2'-deoxyuridilyl)methyl radical that is involved in the formation of tandem base lesion with vicinal guanine in oxygen-free aqueous solution. The thionucleoside was incorporated by either liquid or solid-phase phosphoramidite synthesis into dinucleoside monophosphates with a 2'-deoxyadenosine residue as the vicinal nucleoside located either at the 3' or 5'-extremity. UV-C irradiation of the modified dinucleoside monophosphate under anaerobic conditions gives rise to cross-linked thymine(CH2-C8)adenine tandem base lesions which were isolated and characterized by (1)H NMR and mass spectrometry analyses. The formation of the latter tandem lesions involved an intramolecular addition of the 5-(2'-deoxyuridilyl)methyl radical to the C8 of the adenine moiety. A sensitive and specific assay aimed at monitoring the formation of the four thymine(CH2-C8)purine adducts, namely d(T Delta G), d(G Delta T), d(T Delta A), d(A Delta T), within DNA, was designed. This was based on a liquid chromatography analysis coupled to tandem mass spectrometry (HPLC-MS/MS) detection of the dinucleoside monophosphates which were quantitatively released from gamma-irradiated DNA and oligodeoxyribonucleotides by enzymatic hydrolysis. The four lesions were detected in both single-stranded oligodeoxyribonucleotide and isolated DNA upon exposure to gamma-radiation in oxygen-free aqueous solution. It was found that the tandem guanine-thymine lesions were produced more efficiently than the adenine-thymine cross-links. Moreover, a significant sequence effect was observed. Thus, the yield of formation of the tandem lesions is higher when the purine base is located at the 5' position of the 5-(2'-deoxyuridilyl)methyl radical.

Unique response of double-stranded oligonucleotides containing a single 8-oxo-7,8-dihydroguanine to gamma rays in the frozen aqueous state at 77 K

Two kinds of double-stranded oligonucleotides containing a single 8-oxo-7,8-dihydroguanine were labeled with (32)P at their 5' ends and exposed to gamma rays in the frozen aqueous state at 77 K, where both direct and quasi-direct effects of ionizing radiation predominate. Analysis of the oligonucleotides with 20% denaturing polyacrylamide gel electrophoresis revealed no difference in the immediate induction of strand breaks between oligonucleotides containing 8-oxo-7,8-dihydroguanine and their corresponding oligonucleotides with normal guanine, but piperidine-sensitive damage was induced more frequently in the former than in the latter. Sequence analysis of irradiated oligonucleotides showed that not only 8-oxo-7,8-dihydroguanine but also its neighboring bases and the cytosine residue that is paired to it became piperidine-sensitive in both oligonucleotides. These results suggest that 8-oxo-7,8-dihydroguanine, its neighboring bases and the opposite cytosine are candidates for radiation damage hot spots.

Synthesis and UV photolysis of oligodeoxynucleotides that contain 5-(phenylthiomethyl)-2'-deoxyuridine: a specific photolabile precursor of 5-(2'-deoxyuridilyl)methyl radical

[formula: see text] The title exocyclic radical (2) is generated via photochemical cleavage of 5-(phenylthiomethyl)-2'-deoxyuridine (8). The latter thionucleoside (8) was successfully incorporated into DNA oligomers by automated DNA synthesis using phosphoramidite chemistry. UV exposure of 8 containing oligonucleotides under (an)aerobic conditions gives rise to specific base lesions. The photoproducts have been isolated and further characterized on the basis of detailed NMR and mass spectrometric analyses.

Formation of novel C1-oxidised abasic sites in alkylperoxyl radical-damaged plasmid DNA

We have recently shown that peroxyl radicals react with DNA to form alkali-labile sites. To further characterise these lesions, we studied their susceptibility to digestion by repair endonucleases that recognise different types of abasic sites. We found that peroxyl radical-damaged pSP189 plasmids were resistant to cleavage by T4 endonuclease V, an enzyme that incises DNA at "regular" and C4-oxidised abasic residues. In contrast, the DNA was digested by exonuclease III, an enzyme that recognises "regular" and C1-oxidised abasic sites. The presence of Trolox during exposure to peroxyl radicals reduced subsequent DNA cleavage by exonuclease III, while prior incubation of damaged plasmids with methoxyamine potentiated digestion by this enzyme. These findings suggest that peroxyl radical-induced DNA damage involves the generation of novel C1-oxidised deoxyribose residues.

Structure of a duplex DNA containing a thymine glycol residue in solution

Oxidative stress, ionizing radiation, and other events can induce the oxidation of the thymine in DNA to thymine glycol. The presence of thymine glycol can have significant biological consequences, and there are specific repair enzymes for thymine glycol in a wide range of organisms. The structure of a duplex DNA containing a single thymine glycol (5,6-dihydroxy-5,6-dihydrothymidine) has been determined by the combined use of NMR and restrained molecular dynamics. The duplex of d(C1G2C3G4A5Tg6A7C8G9C10C11) paired with d(G22C21G20C19T18A17T16G15C14G13G12), with Tg indicating thymine glycol, has been used for these studies. The structure shows that the thymine glycol induces a significant, localized structural change with the thymine glycol largely extrahelical. This structural information is consistent with the biological consequences of thymine glycol in DNA. This structure is compared with that of a DNA duplex with an abasic site in the same sequence context.

Investigation of ascorbate-Cu (II) induced cleavage of DNA by scanning tunneling microscopy

Scanning Tunneling Microscopy (STM) was used for the investigation of oxidative DNA damage. A PCR amplified fragment of human beta-globin gene was used as a model for time dependent cleavage reaction by ascorbate and copper. Cleavage reactions were carried out in a medium containing 0.5 microgram/20 microliters DNA, 20 nM Tris-HC1 pH, 7.8 and ascorbate-Cu (II) in the final concentrations of 1 mM and 30 microM, respectively. The mixtures were incubated at 37 degrees C for 5, 15 and 30 min. For STM studies, 3 pg/5 microliters DNA samples were deposited on the gold coated mica and dried in a water flow vacuum drier. The STM was operated in air at atmospheric pressure with a tip-to-substrate bias of 100 mV and tunneling currents of < 10 pA. Etched tips of Pt/Ir wires were used in a constant current mode. The degradated DNA structure can be distinguished from the intact DNA and the sizes of the degradation products can be identified in the STM micrographs. The size of fragments decreased from approximately 3000 A to 34 A in ascorbate-Cu (II) medium, after 30 min of incubation.

Role of oxygen free radicals in cancer development

In aerobic life, oxidative stress arises from both endogenous and exogenous sources. Despite antioxidant defence mechanisms, cell damage from oxygen free radicals (OFR) is ubiquitous. OFR-related lesions that do not cause cell death can stimulate the development of cancer. This review discusses the effects of oxidative stress at the different stages of carcinogenesis. Mutagenesis through oxidative DNA damage is widely hypothesised to be a frequent event in the normal human cell. A large body of evidence suggests important roles of OFR in the expansion of tumour clones and the acquisition of malignant properties. In view of these facts, OFR may be considered as an important class of carcinogens. Therefore, the ineffectiveness of preventive antioxidant treatments, as documented in several recent clinical trials, is surprising. However, the difficulties of antioxidant intervention are explained by the complexity of both free radical chemistry and cancer development. Thus, reducing the avoidable endogenous and exogenous causes of oxidative stress is, for the present, the safest option. In the near future, new insights in the action of tumour suppressor genes and the DNA repair mechanisms may lead the way to additional tools against carcinogenesis from OFR.

Enzymatic release of 5-formyluracil by mammalian liver extracts from DNA irradiated with ionizing radiation

To identify a repair enzyme for 5-formyluracil (5-FU) caused by ionizing radiation in DNA, we used a radiolabelled product-release assay for this thymine-damaged substrate. Double-stranded poly(dA-dT)-poly(dA-dT) was radiolabelled by nick translation with [2-14C]-thymidine triphosphate. The DNA was irradiated with X-rays and incubated with cell extract from mouse liver. Radiolabelled products released from the irradiated DNA into an ethanol-soluble fraction were analysed by reversed-phase hplc. Released 5-FU was detected as a free base during reaction with the cell extract. 5-Formyl-2'-deoxyuridine was not detected in the ethanol supernatant. Boiling the extract at 97 degrees C for 15 min completely abolished its ability to release 5-FU. Similar enzymatic activity was observed with rat liver extract. These results demonstrated that mammalian cells have enzymatic activity to release 5-FU from DNA.

Thymidine free radicals generated during metallo-phthalocyanine photosensitization: a comparison with gamma-radiation

In order to obtain information concerning the mechanism(s) of metallo-phthalocyanine (MePcS4) photosensitized damage of DNA constituents, the EPR-spin trapping method in conjunction with liquid chromatography was used to study thymidine (dThd) free radicals formed during photosensitization or exposure to gamma-radiation in solution. Under specified conditions two dThd free radical species, 5-hydroxy-5,6-dihydrothymidine-6-yl and 6-hydroxy-5,6-dihydrothymidine-5-yl, were formed both during exposure to ionizing radiation and photosensitization. These results imply that identical reactive intermediates (*OH radicals) are involved in the radiolytic and photosensitized oxidation of dThd. A light-dependent, Fenton-type mechanism is proposed to explain the generation of hydroxyl radicals during MePcS4 photosensitization.