Methods used for analyses of "environmentally" damaged nucleic acids

Hydrophilic interaction chromatography of nucleotides and their pathway intermediates on titania

Nucleotides and their pathway intermediates play important roles in all living species. They are essential cellular components in energy transfer, metabolic regulatory processes and biosynthesis. Titania (TiO(2)) has strong Lewis acid sites which have an affinity for the strongly electronegative phosphonate group of nucleotides. Herein a bare titania column (150 mm x 4.6 mm I.D., 3 microm) with UV detection at 254 nm was used for the separation of a set of nucleotides (AMP, ADP, ATP, UMP, UDP, UTP, GMP, GDP, GTP, CMP and CTP) and their intermediates (NAD, NADH, UDP-Glu and UDP-GluNAc). Addition of phosphate to the eluent suppresses the ligand-exchange interactions with the titania surface such that hydrophilic interaction chromatography (HILIC) separations may be performed. Increasing the %ACN resulted in increasing retention and efficiency (up to 13,000, 9500 and 4500 plates/m for AMP, ADP and ATP, respectively). The effects of pH, buffer concentration and other eluent anions (fluoride and acetate) were also studied. Fifteen nucleotides and their intermediates were separated in 26 min (R(minimum)>1.3) using an one-step gradient.

First results of a quantitative study of DNA adducts of melphalan in the rat by isotope dilution mass spectrometry using capillary liquid chromatography coupled to electrospray tandem mass spectrometry

Rats were intravenously injected with a single high dose (10 mg/kg) of the alkylating agent melphalan in order to study DNA-adduct formation. Quantitation of a dGuo-melphalan adduct was done by isotope dilution mass spectrometry using capillary liquid chromatography/mass spectrometry (LC/MS) and [15N5]-labeled dGuo-melphalan as internal standard. DNA-adduct levels were studied in bone marrow, liver and kidney. The instrumental detection limit of the method was determined to be 900 fg (S/N 3, pure standard). These first results clearly show a 10 times higher adduct level in bone marrow compared to kidney and a 6 times higher level compared to liver. More experiments will be necessary to gather more information on the pharmacokinetics of melphalan-DNA adducts under in vivo conditions.

DNA damage detection technique applying time-resolved fluorescence measurements

A novel DNA damage detection technique based on the characteristic fluorescence lifetimes exhibited by Pico-Green-single-stranded DNA and -double-stranded DNA complexes is employed to establish the damage produced on DNA isolated from sheep white blood cells following gamma radiation. This technique, which incorporates key concepts such as alkaline unwinding buffers and higher unwinding rates of damaged DNA compared to undamaged DNA, allows for the differentiation of DNA damage resulting from doses of gamma radiation in the 0-100-Gy range, with the potential of analyzing samples consisting of as little as 10(4) cells. Experiments were carried out using commercial DNA sources as well as DNA isolated from sheep white blood cells, suggesting its potential for use with isolated DNA from virtually any eukaryotic cell.

Importance of complete DNA digestion in minimizing variability of 8-oxo-dG analyses

Estimates of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA vary at least one order of magnitude using different quantitative methods or even the same method. Our hypothesis is that an incomplete DNA hydrolysis to nucleosides by the conventional nuclease P1 (NP1) and alkaline phosphatase (AP) digestion system plays an important role in contributing to the variability of measurements using HPLC coupled with UV and electrochemical (EC) detection. We show here that factors, such as the amount of DNA, choice of enzymes, their activities, and incubation time, can affect DNA digestion and, thus, cause variability in 8-oxo-dG levels. The addition of DNase I and phosphodiesterases I and II to the NP1 + AP system improves the DNA digestion by completely releasing normal nucleosides and 8-oxo-dG, thereby reducing the interday variations of 8-oxo-dG levels. Diethylenetriamine pentaacetic acid (DTPA), an iron chelator, prevented background increases of 8-oxo-dG during DNA digestion, as well as during the waiting period in the autosampler when a batch of DNA samples is analyzed by HPLC. After optimization of the DNA digestion conditions, the interday variability of 8-oxo-dG measurements using commercially available salmon testes DNA (ST DNA) were 26% over a period of 2 years. Under these optimal conditions, our laboratory variability may contribute as little as 13% to the overall variability as shown by assessment of oxidative DNA damage in a population of smokers. Based on our results, we believe that the modified DNA digestion conditions will provide much more accurate 8-oxo-dG determinations and, thus, more reliable estimates of cancer risk.

Chromatographic determination of 8-oxo-7,8-dihydro-2'-deoxyguanosine in cellular DNA: a validation study

Although a series of biomarkers are widely used for the estimation of oxidative damage to biomolecules, validations of the analytical methods have seldom been presented. Formal validation, that is the study of the analytical performances of a method, is however recognized as the best safeguard against the generation and publication of data with low reliability. Classical validation parameters were investigated for the determination of an oxidative stress biomarker, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in cellular DNA, by high-performance liquid chromatography coupled to amperometric detection (HPLC-EC); this modified base is increasingly considered as a marker of oxidative damage to DNA, but many questions are still raised on the analytical methods in use. Upon a rigorous statistical evaluation of the quality criteria currently required for assays in biological media, including selectivity, linearity, accuracy, repeatability, sensitivity, limits of detection and quantification, ruggedness and storage at different stop points in the procedure, the HPLC-EC assay method is found mostly reliable. The present validation attempt demonstrates that (i) the HPLC-EC assay of 8-oxo-dG provides consistent data allowing to reliably detect an increase of this biomarker in cellular DNA; (ii) a harsh oxidative stress does not hinder the enzymatic digestion of DNA by nuclease P1; and (iii) the analytical results must be expressed relative to the internal standard dG which significantly improves both repeatability and sensitivity. Whereas the described assay minimizes the artifactual production of the analyte from processing and storage, this cannot be totally ruled out; the true 8-oxo-dG base levels still lack a definitive assay method, which remains a considerable analytical challenge and the object of controversy.

Chloroacetonitrile (CAN) induces glutathione depletion and 8-hydroxylation of guanine bases in rat gastric mucosa

Chloroacetonitrile (CAN) is detected in drinking-water supplies as a by-product of the chlorination process. Gastroesophageal tissues are potential target sites of acute and chronic toxicity by haloacetonitriles (HAN). To examine the mechanism of CAN toxicity, we studied its effect on glutathione (GSH) homeostasis and its impact on oxidative DNA damage in gastric mucosal cells of rats. Following a single oral dose (38 or 76 mg/Kg) of CAN, animals were sacrificed at various times (0-24 h), and mucosa from pyloric stomach were collected. The effects of CAN treatment on gastric GSH contents and the integrity of genomic gastric DNA were assessed. Oxidative damage to gastric DNA was evaluated by measuring the levels of 8-Hydroxydeoxyguanosine (8-OHdG) in hydrolyzed DNA by HPLC-EC. The results indicate that CAN induced a significant, dose- and time-dependent, decrease in GSH levels in pyloric stomach mucosa at 2 and 4 hours after treatment (56 and 39% of control, respectively). DNA damage was observed electrophoretically at 6 and 12 hours following CAN administration. CAN (38 mg/Kg) induced significant elevation in levels of 8-OHdG in gastric DNA. Maximum levels of 8-OHdG in gastric DNA were observed at 6 hours after CAN treatment [9.59+/-0.60 (8-OHdG/10(5)dG) 146% of control]. When a high dose of CAN (76 mg/Kg) was used, a peak level of 8-OHdG [11.59+/-1.30 (8-OHdG/10(5)dG) 177% of control] was observed at earlier times (2 h) following treatment. When CAN was incubated with gastric mucosal cells, a concentration-dependent cyanide liberation and significant decrease in cellular ATP levels were detected. These data indicate that a mechanism for CAN-induced toxicity may be partially mediated by depletion of glutathione, release of cyanide, interruption of the energy metabolism, and induction of oxidative stress that leads to oxidative damage to gastric DNA.

Phosphine-induced oxidative damage in rats: attenuation by melatonin

Phosphine (PH(3)), from hydrolysis of aluminum, magnesium and zinc phosphide, is an insecticide and rodenticide. Earlier observations on PH(3)-poisoned insects, mammals and a mammalian cell line led to the proposed involvement of oxidative damage in the toxic mechanism. This investigation focused on PH(3)-induced oxidative damage in rats and antioxidants as candidate protective agents. Male Wistar rats were treated ip with PH(3) at 2 mg/kg. Thirty min later the brain, liver, and lung were analyzed for glutathione (GSH) levels and lipid peroxidation (as malondialdehyde and 4-hydroxyalkenals) and brain and lung for 8-hydroxydeoxyguanosine (8-OH-dGuo) in DNA. PH(3) caused a significant decrease in GSH concentration and elevation in lipid peroxidation in brain (36-42%), lung (32-38%) and liver (19-25%) and significant increase of 8-OH-dGuo in DNA of brain (70%) and liver (39%). Antioxidants administered ip 30 min before PH(3) were melatonin, vitamin C, and beta-carotene at 10, 30, and 6 mg/kg, respectively. The PH(3)-induced changes were significantly or completely blocked by melatonin while vitamin C and beta-carotene were less effective or inactive. These findings establish that PH(3) induces and melatonin protects against oxidative damage in the brain, lung and liver of rats and suggest the involvement of reactive oxygen species in the genotoxicity of PH(3).

Chromium(III) interactions with nucleosides and nucleotides: a mass spectrometric study

Interactions of [Cr(salprn)(H(2)O)(2)]ClO(4) with nucleosides and dinucleotides were studied using electrospray ionization mass spectrometry. The nucleosides 2'-deoxycytidine, thymidine, 2'-deoxyadenosine, 2'-deoxyguanosine, cytidine, adenosine and guanosine form 1 : 1 and 2 : 1 adducts with [Cr(salprn)](+), whereas the dinucleotides CpG, GpC, ApT, TpA and TpC form only the 1 : 1 adducts. Collisional activation (CA) spectra of these adducts reveal that Cr(+) attaches to the bases in nucleosides and to both the phosphate and base, especially cytosine and guanine moieties, in the nucleotides. The sugar residues appear to offer no binding sites as elimination of sugar residues is fairly abundant in the CA spectra of the adducts of many of the nucleosides.

Safrole-induced oxidative damage in the liver of Sprague-Dawley rats

Safrole is a weak hepatocarcinogen, and its carcinogenic effect has been linked to the formation of stable safrole DNA adducts. In this study, we tested whether safrole also induces oxidative damages in Sprague-Dawley rats. By single i.p. injection, safrole dose-dependently induced the formation of hepatic lipid hydroperoxides (LHP) and 8-hydroxy-2'-deoxyguanosine (8-OH-dG). The safrole-induced LHP reached peak level on day 3 and gradually returned to the basal level on day 15. On the other hand, 8-OH-dG levels from the similarly treated rats peaked on day 5 and returned to basal level on day 15. Safrole also dose-dependently induced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities. We also examined the protective effect of vitamin E, deferoxamine and N-acetylcysteine against the safrole-induced oxidative damage. N-Acetylcysteine, the precursor of glutathione, exerted the greatest protective effect among the three antioxidants tested. In contrast, buthionine sulfoximine, the glutathione synthesis inhibitor, enhanced the safrole-induced oxidative damage, as evidenced by the elevation of LHP and 8-OH-dG levels on day 3 (P<0.05). These findings demonstrate that safrole treatment induces oxidative damage in rat hepatic tissue, and glutathione plays an important protective role. This oxidative damage may be involved in the hepatocarcinogenic effect of safrole.

Quantification of 5-(hydroxymethyl)uracil in DNA by gas chromatography/mass spectrometry: problems and solutions

Oxidation of the thymine methyl group results in the formation of 5-(hydroxymethyl)uracil (HmU). HmU is a recognized endogenous DNA damage product, and HmU levels in DNA are increased by oxidant stress. Previous studies have reported substantially conflicting values for HmU levels in DNA. In studies utilizing postlabeling methods, HmU levels have been reported to be as high as or higher than the levels of some of the more commonly described DNA oxidation damage products such as 8-oxoguanine. In some studies utilizing GC/MS methods, however, HmU has been undetectable. In acid solution, the hydroxymethyl group of HmU can undergo condensation reactions with carboxylic acids, alcohols, and amines. While HmU can be accurately measured by GC/MS, the first step in the preparation of samples for GC/MS analysis is acid hydrolysis of the DNA. Such hydrolysis would be expected to result in substantial derivatization of HmU. We have utilized chemically synthesized oligonucleotides containing a known amount of HmU as well as an isotopically enriched standard to investigate the chemical modification of HmU during the acid hydrolysis of DNA. We conclude that HmU levels reported by GC/MS following acid hydrolysis may be up to an order of magnitude lower than the actual levels. Further, we propose modifications to the standard hydrolysis protocols which maximize recovery of HmU prior to silylation and analysis by GC/MS.

Detection of 8-oxoguanine in cellular DNA using 2,6-diamino-8-oxopurine as an internal standard for high-performance liquid chromatography with electrochemical detection

The quantitative aspect of the electrochemical detection method to detect 8-oxo-7,8-dihydroguanine (8-oxoGua) has been improved by using an internal standard. In addition, emphasis was placed on the reduction of artifactual oxidation of DNA during isolation and hydrolysis. Nuclear DNA was isolated from rat organs and purified on an anion-exchange column following treatment with proteinase K and RNase. DNA hydrolysis to nucleobases or nucleosides was performed using either formic acid treatment or enzymatic digestion, respectively. The levels of either 8-oxoGua or 8-hydroxy-7,8-dihydro-2'-deoxyguanosine were comparable. For accurate quantification, 2,6-diamino-8-oxopurine [(NH2)2-OH-Pur], added prior to hydrolysis, was used as an internal standard for the high-performance liquid chromatography with electrochemical detection assay. The baseline level of 8-oxoGua in DNA of Sprague-Dawley rats was estimated to be 2 to 5 8-oxoGua residues per 10(6) DNA bases, with slight differences depending on the tissue origin. In agreement with the results of previous observations, the level of the oxidized base in the kidney of animal treated with iron complexed to nitrilotriacetic acid (Fe-NTA) (15 mg/kg) was three- to fourfold higher than that of untreated rats or animals treated with a saline solution, while there was no change in 8-oxoGua levels in the liver and colon of these treated animals.

Oxidative damage to DNA induced by areca nut extract

In Taiwan, people chew betel quid which contains tender areca nut with husk. In other countries, people prefer ripe and dried areca nut without husk. In this study, we compared the reactive oxygen species-induced oxidative DNA damage in isolated DNA and CHO-K1 cells between treatments with tender areca nut extract (ANE) and ripe ANE. Incubation of these two ANE preparations with isolated DNA generated 8-hydroxy-2'-deoxyguanosine (8-OH-dG) in an alkaline environment in a dose-dependent manner. Ripe ANE generated higher levels of 8-OH-dG compared to tender ANE. The addition of iron(II) (100 microM) resulted in 1.4- and 3.1-fold increases of 8-OH-dG when incubated with 1 mg/ml each of tender and ripe ANE. In testing the effect of ANE to cellular DNA, CHO-K1 cells were used for its documented sensitivity to reactive oxygen species. In CHO-K1 cells, ripe ANE was more cytotoxic than tender ANE following an 18-h incubation. The cytotoxicity to CHO-K1 cells was positively correlated with the formation of 8-OH-dG following tender (r=0.97) and ripe (r=0.91) ANE treatment. Addition of the iron chelating agent o-phenanthroline (10 and 20 microM) to cells prior to ri ANE exposure significantly increased (p<0.05) the survival of CHO-K1 cells. In addition, ripe ANE induced dichlorofluorescein-mediated fluorescence which indicated the formation of hydrogen peroxide in CHO-K1 cells. In conclusion, this study demonstrated that ANE-induced oxidative damage to isolated and cellular DNA which may result from the generation of hydrogen peroxide, and iron may serve as a catalyst in this process. Furthermore, ripe ANE generated higher oxidative DNA damage levels compared to tender ANE.