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Methods in Molecular Biology (Clifton,... 2014Accelerator mass spectrometry (AMS) is a highly sensitive technique used for the quantification of adducts following exposure to carbon-14- or tritium-labeled chemicals,...
Accelerator mass spectrometry (AMS) is a highly sensitive technique used for the quantification of adducts following exposure to carbon-14- or tritium-labeled chemicals, with detection limits in the range of one adduct per 10(11)-10(12) nucleotides. The protocol described in this chapter provides an optimal method for isolating and preparing DNA samples to measure isotope-labeled DNA adducts by AMS. When preparing samples, special precautions must be taken to avoid cross-contamination of isotope among samples and produce a sample that is compatible with AMS. The DNA isolation method described is based upon digestion of tissue with proteinase K, followed by extraction of DNA using Qiagen isolation columns. The extracted DNA is precipitated with isopropanol, washed repeatedly with 70 % ethanol to remove salt, and then dissolved in water. DNA samples are then converted to graphite or titanium hydride and the isotope content measured by AMS to quantify adduct levels. This method has been used to reliably generate good yields of uncontaminated, pure DNA from animal and human tissues for analysis of adduct levels.
Topics: Animals; DNA Adducts; Humans; Isotope Labeling; Mass Spectrometry
PubMed: 24623226
DOI: 10.1007/978-1-62703-739-6_12 -
Cancer Letters Jun 2013The technique of (32)P-postlabeling, which was introduced in 1982 for the analysis of DNA adducts, has long been the method of choice for in vivo studies because of its... (Review)
Review
The technique of (32)P-postlabeling, which was introduced in 1982 for the analysis of DNA adducts, has long been the method of choice for in vivo studies because of its high sensitivity as it requires only <10μg DNA to achieve the detection of 1 adduct in 10(10) normal bases. (32)P-postlabeling has therefore been utilized in numerous human and animal studies of DNA adduct formation. Like all techniques (32)P-postlabeling does have several disadvantages including the use of radioactive phosphorus, lack of internal standards, and perhaps most significantly does not provide any structural information for positive identification of unknown adducts, a shortcoming that could significantly hamper progress in the field. Structural methods have since been developed to allow for positive identification of DNA adducts, but to this day, the same level of sensitivity and low sample requirements provided by (32)P-postlabeling have not been matched. In this mini review we will discuss the (32)P-postlabeling method and chronicle the transition to mass spectrometry via the hyphenation of gas chromatography, capillary electrophoresis, and ultimately liquid chromatography which, some 30years later, is only just starting to approach the sensitivity and low sample requirements of (32)P-postlabeling. This paper focuses on the detection of bulky carcinogen-DNA adducts, with no mention of oxidative damage or small alkylating agents. This is because the (32)P-postlabeling assay is most compatible with bulky DNA adducts. This will also allow a more comprehensive focus on a subject that has been our particular interest since 1990.
Topics: Animals; Chromatography, High Pressure Liquid; DNA Adducts; Electrophoresis, Capillary; Gas Chromatography-Mass Spectrometry; Humans; Isotope Labeling; Mass Spectrometry; Phosphorus Radioisotopes; Sensitivity and Specificity
PubMed: 22960573
DOI: 10.1016/j.canlet.2012.08.007 -
Mutation Research Mar 1999Recently, we examined normal human pancreas tissue for DNA adducts derived from either exogenous chemical exposure and/or endogenous agents. In an effort to explain the... (Comparative Study)
Comparative Study Review
Recently, we examined normal human pancreas tissue for DNA adducts derived from either exogenous chemical exposure and/or endogenous agents. In an effort to explain the different types and levels of DNA adducts formed in the context of individual susceptibility to cancer, we have focused on gene-environment interactions. Here, we report on the levels of hydrophobic aromatic amines (AAs), specifically those derived from 4-aminobiphenyl (ABP), and DNA adducts associated with oxidative stress in human pancreas. Although these adducts have been reported in several human tissues by different laboratories, a comparison of the levels of these adducts in the same tissue samples has not been performed. Using the same DNA, the genotypes were determined for N-acetyltransferase 1 (NAT1), the glutathione S-transferase (GST) M1, GSTP1, GSTT1, and NAD(P)H quinone reductase-1 (NQO1) as possible modulators of adduct levels because their gene products are involved in the detoxification of AAs, lipid peroxidation products and in redox cycling. These results indicate that ABP-DNA adducts, malondialdehyde-DNA adducts, and 8-oxo-2'-deoxyguanosine (8-oxo-dG) adducts are present at similar levels. Of the metabolic genotypes examined, the presence of ABP-DNA adducts was strongly associated with the putative slow NAT1*4/*4 genotype, suggesting a role for this pathway in ABP detoxification.
Topics: Aminobiphenyl Compounds; Carcinogens; Chromatography, High Pressure Liquid; DNA Adducts; Genetic Predisposition to Disease; Humans; Lipid Peroxidation; Oxidative Stress; Pancreas; Pancreatic Neoplasms
PubMed: 10064866
DOI: 10.1016/s0027-5107(99)00024-x -
Journal of Biochemistry and Molecular... Jan 2003The causative role of polycyclic aromatic hydrocarbons (PAH) in human carcinogenesis is undisputed. Measurements of PAH-DNA adduct levels in easily accessible white... (Review)
Review
The causative role of polycyclic aromatic hydrocarbons (PAH) in human carcinogenesis is undisputed. Measurements of PAH-DNA adduct levels in easily accessible white blood cells therefore represent useful early endpoints in exposure intervention or chemoprevention studies. The successful applicability of DNA adducts as early endpoints depends on several criteria: i. adduct levels in easily accessible surrogate tissues should reflect adduct levels in target-tissues, ii. toxicokinetics and the temporal relevance should be properly defined. iii. sources of interand intra-individual variability must be known and controllable, and finally iv. adduct analyses must have advantages as compared to other markers of PAHexposure. In general, higher DNA adduct levels or a higher proportion of subjects with detectable DNA adduct levels were found in exposed individuals as compared with nonexposed subjects, but saturation may occur at high exposures. Furthermore, DNA adduct levels varied according to changes in exposure, for example smoking cessation resulted in lower DNA adduct levels and adduct levels paralleled seasonal variations of air-pollution. Intraindividual variation during continuous exposure was low over a short period of time (weeks), but varied significantly when longer time periods (months) were investigated. Inter-individual variation is currently only partly explained by genetic polymorphisms in genes involved in PAH-metabolism and deserves further investigation. DNA adduct measurements may have three advantages over traditional exposure assessment: i. they can smooth the extreme variability in exposure which is typical for environmental toxicants and may integrate exposure over a longer period of time. Therefore, DNA adduct assessment may reduce the monitoring effort. ii. biological monitoring of DNA adducts accounts for all exposure routes. iii. DNA adducts may account for inter-individual differences in uptake, elimination, distribution, metabolism and repair amongst exposed individuals. In conclusion, there is now a sufficiently large scientific basis to justify the application of DNA adduct measurements as biomarkers in exposure assessment and intervention studies. Their use in risk-assessment, however, requires further investigation.
Topics: Animals; Biomarkers; DNA Adducts; Environmental Exposure; Evaluation Studies as Topic; Humans; Neoplasms; Occupational Exposure; Polycyclic Aromatic Hydrocarbons; Rodentia
PubMed: 12542969
DOI: 10.5483/bmbrep.2003.36.1.001 -
Toxicologic Pathology 2000Human exposure to DNA damaging agents can arise from exogenous sources or endogenous processes that occur normally or in pathological states. DNA isolated from human... (Review)
Review
Human exposure to DNA damaging agents can arise from exogenous sources or endogenous processes that occur normally or in pathological states. DNA isolated from human tissues, obtained from the very young to the old, contains detectable amounts of a number of different types of DNA adducts that reflect exposure to both known carcinogens and as yet unidentified genotoxic agents. The levels of DNA damage observed in human studies as a result of exogenous exposures (noniatrogenic) is of the order of 1 adduct per 10(7)-10(9) normal DNA bases, whereas that arising from endogenous exposures may potentially be several orders of magnitude higher. Large interindividual variations in DNA adduct levels have been reported, and these are probably the result of host and environmental factors, although variation in analytical and sampling procedures may also play a role. It is important to recognize that the presence of DNA adducts in a tissue does not necessarily indicate a specific tumorigenic risk for that tissue, as other factors downstream of DNA adduct formation (including DNA repair and cell proliferation) play an important role in determining overall risk.
Topics: Animals; Carcinogens; DNA; DNA Adducts; DNA Damage; DNA Repair; Environmental Exposure; Female; Guanine; Humans; Male
PubMed: 10862557
DOI: 10.1177/019262330002800308 -
Mutation Research Jun 1996Sensitive methods for quantifying DNA adducts from (i) benzo[a]pyrene (BP), (ii) alkylation exposure, and (iii) etheno(epsilon)-DNA adduct-forming chemicals were... (Review)
Review
Sensitive methods for quantifying DNA adducts from (i) benzo[a]pyrene (BP), (ii) alkylation exposure, and (iii) etheno(epsilon)-DNA adduct-forming chemicals were developed and applied to humans and animal models. The aims were to identify hitherto unknown sources and mechanisms of exogenous and endogenous DNA damage, to examine the effect of drug polymorphism on BP adduct levels, and to develop QSAR between tumorigenic potency, heritable genetic damage and structural elements of alkylating carcinogens (Vogel and Nivard (1994) Mutation Res., 395, 13-32). (i) BP-DNA adducts: An HPLC/fluorimetry assay suitable for measuring (+)-anti-BP-diol-epoxide (BPDE) adducts in human tissues and white blood cells (WBC) was developed (Alexandrov et al. (1992) Cancer Res., 52, 6248-6253). In smokers, a positive correlation was found between pulmonary CYP1A1-related catalytic activity (AHH) and the level of lung BPDE-DNA adducts. In coke oven workers, an enhancing effect of smoking on BPDE-adduct levels in WBC was demonstrated (Rojas et al. (1995) Carcinogenesis, 16, 1373-1376). (ii) 3-Alkyladenines (3-alkAde): Alkylating carcinogens form 3-alkAde adducts in DNA which depurinate to yield 3-alkAde in urine, for which a detection method was developed (Friesen et al. (1991) Chem. Res. Toxicol., 4, 102-106; Prevost et al. (1990) Carcinogenesis, 11, 1747-1751), using immunoaffinity purification and GC-MS analysis. The usefulness of 3-alkAde analysis for the determination of the whole-body dose of alkylating agents derived from exogenous and endogenous sources was demonstrated. (iii) Etheno-DNA adduct-forming agents: Etheno(epsilon)-DNA base adducts (epsilon A, epsilon dC, epsilon dG) are promutagenic DNA lesions that are formed by occupational (vinyl halides) and environmental (urethane) carcinogens. An ultrasensitive detection method was developed (Nair et al. (1995) Carcinogenesis, 16, 613-617), based on immunoaffinity purification and 32P-postlabelling of epsilon-nucleoside 3'-monophosphates. Liver DNA from unexposed rats, mice and from human samples contained background levels of epsilon dA and epsilon dC (Bartsch et al. (1994) Drug. Metab. Rev., 26, 349-371). As formation of epsilon dA and epsilon dC adducts by lipid peroxidation products was demonstrated (El Ghissassi et al. (1995) Chem. Res. Toxicol., 8, 278-283), they may serve as markers for oxidative stress. Results from testing this hypothesis are presented.
Topics: Animals; Carcinogenicity Tests; DNA Adducts; Humans; Neoplasms; Neoplasms, Experimental; Structure-Activity Relationship
PubMed: 8692183
DOI: 10.1016/s0165-1110(96)90040-8 -
Chemical Research in Toxicology Jan 2007Acetaldehyde is one of the most prevalent carcinogens in cigarette smoke. It is also a major metabolite of ethanol and is found widely in the human diet and environment....
Acetaldehyde is one of the most prevalent carcinogens in cigarette smoke. It is also a major metabolite of ethanol and is found widely in the human diet and environment. Acetaldehyde DNA adducts are critical for its carcinogenic properties. The role of acetaldehyde DNA adducts in human cancer related to tobacco and alcohol exposure could be investigated with a suitable biomarker. Therefore, in this study, we have developed a method for analysis of the major DNA adduct of acetaldehyde, N2-ethylidene-dGuo (1), in human leukocyte DNA. Leukocyte DNA was subjected to enzyme hydrolysis in the presence of NaBH3CN, which converts adduct 1 to N2-ethyl-dGuo (2). [15N5]N2-ethyl-dGuo was used as the internal standard. After solid-phase extraction, N2-ethyl-dGuo was quantified by LC-ESI-MS/MS-SRM. The method was sensitive, accurate, and precise, and applicable to low microgram amounts of DNA. It was applied to investigate the effect of smoking cessation on levels of adduct 1, measured as adduct 2. Twenty-five smokers who were only light drinkers were eligible for the study. Levels of adduct 2 were quantified at two baseline time points separated by one week and again after four weeks of abstinence from smoking and alcohol consumption. The mean (+/-S.D.) levels of adduct 2 measured in the leukocytes of the smokers were 1310 +/- 1720 (range 124-7700) and 1120 +/- 1140 (range 138-5760) fmol/micromol dGuo at the two baseline points and 705 +/- 438 (range 111-1530) fmol/micromol dGuo after 4 weeks of cessation. The median level of adduct 2 decreased significantly by 28% upon quitting smoking (P = 0.02). These results demonstrate that the major acetaldehyde DNA adduct can be reliably quantified by MS/MS methods in human leukocyte DNA and that cigarette smoking has a modest but significant effect on its levels.
Topics: Acetaldehyde; Chromatography, High Pressure Liquid; DNA Adducts; Humans; Leukocytes; Smoking Cessation; Spectrometry, Mass, Electrospray Ionization
PubMed: 17226933
DOI: 10.1021/tx060232x -
Chemical Research in Toxicology May 2016Mutagenic semicarbazide (SEM) is a hydrazine-containing food contaminant found in a wide variety of foods. Despite decades of research, the toxicity of SEM remains...
Mutagenic semicarbazide (SEM) is a hydrazine-containing food contaminant found in a wide variety of foods. Despite decades of research, the toxicity of SEM remains incompletely understood. In this study, we demonstrate for the first time that SEM reacts rapidly with apurinic/apyrimidinic sites in an endogenous DNA lesion to form covalently bonded DNA adducts in vitro and in bacteria. Specifically, we performed high-performance liquid chromatography with high accuracy and tandem mass spectrometry to characterize the DNA adduct formed by reacting SEM with 2'-deoxyribose and single- and double-stranded oligonucleotides containing abasic sites under physiologically relevant conditions. By analyzing the reaction mixture at different time points, the reaction kinetics of SEM with DNA was also elucidated. Moreover, by using a highly sensitive and selective liquid chromatography-tandem mass spectrometry method, we show that SEM induces the dose-dependent formation of DNA adducts in Escherichia coli. The results from our studies provide the first direct evidence suggesting that SEM may exert genotoxicity by forming covalently bonded DNA adducts.
Topics: Chromatography, High Pressure Liquid; DNA; DNA Adducts; DNA Damage; Kinetics; Semicarbazides
PubMed: 27058397
DOI: 10.1021/acs.chemrestox.6b00011 -
Drug Metabolism Reviews Nov 2014DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA... (Review)
Review
DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target.
Topics: Animals; Biocatalysis; DNA Adducts; DNA Topoisomerases, Type I; Humans; Models, Molecular; Molecular Targeted Therapy; Phosphodiesterase Inhibitors; Phosphoric Diester Hydrolases
PubMed: 25327705
DOI: 10.3109/03602532.2014.971957 -
Chemical Research in Toxicology 1995The food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) forms adducts to DNA guanine bases at the C-8 position. No other DNA adduction site has been...
The food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) forms adducts to DNA guanine bases at the C-8 position. No other DNA adduction site has been verified for PhIP, nor has any experimental data been collected on the conformation of the PhIP-DNA covalent complex. To determine if multiple PhIP-DNA adduct species exist, or if PhIP-DNA adducts assume multiple conformations, 2-(acetoxyamino)-1-methyl-6-phenylimidazo[4,5-b]-pyridine (N-acetoxy-PhIP) was reacted with calf thymus DNA, followed by an evaluation of the resulting adduct complexes by fluorescence spectroscopy. Approximately 20% of the N-acetoxy-PhIP formed covalent complexes with DNA. Two major and several minor spots were observed by 32P-postlabeling, suggesting a minimum of two major adduct species. UV/vis spectra of the PhIP-modified DNA also showed heterogeneous formation of PhIP-DNA adducts. Fluorescence excitation and emission spectroscopy with or without fluorescence quenching (silver ion and acrylamide) was used to evaluate the number of adducts formed, and the low-resolution conformation of each adduct. Four adduct fluorophores were observed and assigned the nomenclature PAi, where "PA" denotes PhIP Adduct and i = 1-4 in order of fluorescence emission band energies, with 1 the highest and 4 the lowest energy, respectively. Excitation maxima for the adduct fluorophores ranged from 340 to 370 nm, and emission maxima ranged from 390 to 420 nm. The fluorescence from adduct PA1 was quenched by silver but not acrylamide, suggesting a helix-internal configuration. Adduct PA2 fluorescence was strongly enhanced upon silver binding but was not affected by acrylamide, also indicating that this adduct was internal. The fluorescence from adducts PA3 and PA4 was quenched by acrylamide but not silver; thus PA2 and PA3 were tentatively assigned as solvent-accessible. These data are the first suggesting heterogeneous formation of PhIP adducts to intact DNA, but we cannot as yet determine how many chemical species of adduct are formed or if a given species exists in multiple conformations.
Topics: Acrylamide; Acrylamides; Animals; DNA Adducts; Imidazoles; In Vitro Techniques; Kinetics; Mutagens; Pyridines; Silver; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet
PubMed: 7548748
DOI: 10.1021/tx00047a005