We describe here methods for sensitive and accurate quantification of the lesions 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo), 1,N6-etheno-2'-deoxyadenosine (1,N6-dAdo) and 1,N2-etheno-2'-deoxyguanosine (1,N2-dGuo) in DNA. The methods were applied to the assessment of the effects of ambient fine particulate matter (PM2.5) in tissues (lung, liver and kidney) of exposed A/J mice.
DNA adducts and oxidized DNA bases are examples of DNA lesions that are useful biomarkers for the toxicity assessment of substances that are electrophilic, generate reactive electrophiles upon biotransformation, or induce oxidative stress. Among the oxidized nucleobases, the most studied one is 8-oxo-7,8-dihydroguanine (8-oxoGua) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo), a biomarker of oxidatively induced base damage in DNA. Aldehydes and epoxyaldehydes resulting from the lipid peroxidation process are electrophilic molecules able to form mutagenic exocyclic DNA adducts, such as the etheno adducts 1,N2-etheno-2'-deoxyguanosine (1,N2-εdGuo) and 1,N6-etheno-2'-deoxyadenosine (1,N6-εdAdo), which have been suggested as potential biomarkers in the pathophysiology of inflammation. Selective and sensitive methods for their quantification in DNA are necessary for the development of preventive strategies to slow down cell mutation rates and chronic disease development (e.g., cancer, neurodegenerative diseases). Among the sensitive methods available for their detection (high performance liquid chromatography coupled to electrochemical or tandem mass spectrometry detectors, comet assay, immunoassays, 32P-postlabeling), the most selective are those based on high performance liquid chromatography coupled to tandem mass spectrometry (HPLC-ESI-MS/MS). Selectivity is an essential advantage when analyzing complex biological samples and HPLC-ESI-MS/MS evolved as the gold standard for quantification of modified nucleosides in biological matrices, such as DNA, urine, plasma and saliva. The use of isotopically labeled internal standards adds the advantage of corrections for molecule losses during the DNA hydrolysis and analyte enrichment steps, as well as for differences of the analyte ionization between samples. It also aids in the identification of the correct chromatographic peak when more than one peak is present.
We present here validated sensitive, accurate and precise HPLC-ESI-MS/MS methods that were successfully applied for the quantification of 8-oxodGuo, 1,N6-dAdo and 1,N2-dGuo in lung, liver and kidney DNA of A/J mice for the assessment of the effects of ambient PM2.5 exposure.
Some reactive oxygen species (ROS) are able to oxidize carbon double bonds of DNA bases and some carbons in the deoxyribose moiety, generating oxidized bases and DNA strand breaks1. As a negatively charged molecule rich in nitrogen and oxygen atoms, DNA is also a target for electrophilic groups that covalently react with the nucleophilic sites (nitrogen and oxygen), giving products that are called DNA adducts2. So, DNA adducts and oxidized DNA bases are examples of DNA lesions that are useful biomarkers for the toxicity assessment of substances that are electrophilic, generate reactive electrophiles upon biotransformation, or induce oxidative stress1,2. Although the modified DNA bases can be removed from DNA by base or nucleotide excision repair (BER or NER), the induction of an imbalance between the generation and removal of DNA lesions in favor of the former leads to a net increase of their levels in DNA overtime3. Outcomes are the increase of DNA mutation rates, reduced gene expression, and diminished protein activity2,4,5,6,7, effects that are closely related to the development of diseases. DNA mutations may affect diverse cellular functions, such as cell signaling, cell cycle, genome integrity, telomere stability, the epigenome, chromatin structure, RNA splicing, protein homeostasis, metabolism, apoptosis, and cell differentiation8,9. Strategies to slow down cell mutation rates and chronic disease development (e.g., cancer, neurodegenerative diseases) pass through the knowledge of the mutation sources, among them, DNA lesions and their causes.
ROS generated endogenously in excess, due to pollutant exposure, persistent inflammation, disease pathophysiology (e.g., diabetes), etc., are important causes of biomolecule damage, including DNA and lipid damage1. As an example, the highly reactive hydroxyl radical (OH) formed from H2O2 reduction by transition metal ions (Fe2+, Cu+) oxidizes the DNA bases, DNA sugar moiety and polyunsaturated fatty acids at diffusion-controlled rates10. Among the 80 already characterized oxidized nucleobases3, the most studied one is 8-oxo-7,8-dihydroguanine (8-oxoGua) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo, Figure 1), a lesion that is able to induce GT transversions in mammalian cells10,11. It is formed by the mono electronic oxidation of guanine, or by hydroxyl radical or singlet oxygen attack of guanine in DNA1. Polyunsaturated fatty acids are other important targets of highly reactive oxidants, such as •OH, which initiate the process of lipid peroxidation1,12. It gives rise to fatty acid hydroperoxides that may decompose to electrophilic aldehydes and epoxyaldehydes, such as malondialdehyde, 4-hydroxy-2-nonenal, 2,4-decadienal, 4,5-epoxy-(2E)-decenal, hexenal, acrolein, crotonaldehyde, which are able to form mutagenic exocyclic DNA adducts, such as malondialdehyde-, propano-, or etheno adducts1,12,13. The etheno adducts 1,N2-etheno-2'-deoxyguanosine (1,N2-εdGuo, Figure 1) and 1,N6-etheno-2'-deoxyadenosine (1,N6-εdAdo, Figure 1) have been suggested as potential biomarkers in the pathophysiology of inflammation14,15.
Figure 1. Chemical structures of the DNA lesions quantified in the present study. dR = 2´-deoxyribose. This figure has been modified from Oliveira et al.34. Please click here to view a larger version of this figure.
Studies carried out in the early 1980s allowed the sensitive detection of 8-oxodGuo by high performance liquid chromatography coupled to electrochemical detection (HPLC-ECD). Quantification of 8-oxodGuo by HPLC-ECD in several biological systems subjected to oxidizing conditions led to the recognition of 8-oxodGuo as a biomarker of oxidatively induced base damage in DNA1,16. Although robust and allowing the quantification of 8-oxodGuo in the low fmol range17, HPLC-ECD measurements rely on the accuracy of the analyte retention time for analyte identification and on the chromatography resolution to avoid interferences of other sample constituents. As the electrochemical detection requires the use of salt (e.g., potassium phosphate, sodium acetate) in the mobile phase, the maintenance of adequate analytical conditions needs routine column and equipment cleaning time.
Alternatively, the use of the bacterial DNA repair enzyme formamidopyrimidine DNA glycosylase (FPG) and, afterwards, human 8-oxoguanine glycosylase 1 (hOGG1), for detection and removal of 8-oxoGua from DNA, emerged as a way for the induction of DNA alkali labile sites. The alkali labile sites are converted to DNA strand breaks and allow the very high sensitive indirect quantification of 8-oxoGua by alkaline single cell gel electrophoresis ("comet assay"). The high sensitivity and the accomplishment of the analyses without the need of cellular DNA extraction are the main advantages of this type of assay. It gives the lowest steady-state levels of 8-oxoGua in DNA, typically 7-10 times lower than the levels obtained by bioanalytical methods based on HPLC. However, it is an indirect measurement of 8-oxoGua and some drawbacks are the lack of specificity or the unknown efficiency of the repair enzymes used1,16,18.
Immunoassays are other set of methods used for the detection of 8-oxoGua1 and exocyclic DNA adducts, such as 1,N6-dAdo and 1,N2-dGuo12. Despite the sensitivity, a shortcoming of the use of antibodies for detection of DNA lesions is the lack of specificity due to cross-reactivity to other components of biological samples, including the normal DNA bases1,12. The exocyclic DNA adducts, including 1,N6-dAdo and 1,N2-dGuo, may also be detected and quantified by highly sensitive 32P-postlabeling assays12. The high sensitivity of 32P-postlabeling allows the use of very small amounts of DNA (e.g., 10 µg) for detection of about 1 adduct per 1010 normal bases19. However, the use of radio-chemicals, lack of chemical specificity and low accuracy are some disadvantages19,20.
A shared limitation of the methods cited above is the low selectivity or specificity for the detection of the desired molecules. In this scenario, HPLC coupled to electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS and HPLC-MS3) evolved as the gold standard for quantification of modified nucleosides in biological matrices, such as DNA, urine, plasma and saliva1,19,20. Advantages of HPLC-ESI-MS/MS methods are the sensitivity (typically in the low fmol range) and the high specificity provided by i) the chromatographic separation, ii) the characteristic and known pattern of molecule fragmentation inside the mass spectrometer collision chamber, and iii) the accurate measurement of the selected mass to charge ratio (m/z) in multiple reaction monitoring mode1,19. The use of isotopically labeled internal standards adds the advantage of corrections for molecule losses during the DNA hydrolysis and analyte enrichment steps, as well as for differences of the analyte ionization between samples. It also aids in the identification of the correct chromatographic peak when more than one peak is present1,12,19,20.
Several methods based on HPLC-ESI-MS/MS have been used for quantification of 8-oxodGuo, 1,N6-dAdo and 1,N2-dGuo in DNA extracted from different biological samples12,15,20,21,22,23,24,25,26,27,28,29. Fine particles (PM2.5) carry organic and inorganic chemicals, such as polycyclic aromatic hydrocarbons (PAHs), nitro-PAHs, aldehydes, ketones, carboxylic acids, quinolines, metals, and water-soluble ions, which may induce inflammation and oxidative stress, conditions that favor the occurrence of biomolecule damage and disease30,31,32,33. We present here validated HPLC-ESI-MS/MS methods that were successfully applied for the quantification of 8-oxodGuo, 1,N6-dAdo and 1,N2-dGuo in lung, liver and kidney DNA of A/J mice for the assessment of the effects of ambient PM2.5 exposure34.
Four week old male A/J mice, specific pathogen free, were obtained from the Breeding Center of Laboratory Animals of Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil, and were treated accordingly to the Ethics Committee of the Faculty of Medicine, University of São Paulo (protocol no 1310/09).
1. Collection of mice tissues
2. DNA extraction
Note: The DNA extraction method was modified from Loureiro et al. (2009)35 to allow the analyses of the lesions studied here.
3. DNA enzymatic hydrolysis
4. Solid phase extraction for analyses of 1, N6-εdAdo and 1, N2-εdGuo
5. Preparation of calibration curves
6. Preparation of DNA samples for method validation
7. HPLC-ESI-MS/MS analysis of 8-oxodGuo
Figure 2. System of two columns used for 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) analyses. A) Configuration used in the first 16 min and from 32 to 46 min of the chromatography; B) Configuration used in the interval 16 – 32 min, allowing further separation and peak narrowing in column B prior to elution to the ESI source of the mass spectrometer. This figure has been republished from Oliveira et al.34. Please click here to view a larger version of this figure.
8. HPLC-ESI-MS/MS analysis of 1, N 6 -εdAdo and 1, N 2 -εdGuo
ESI-MS/MS parameters | 8-oxodGuo | Etheno adducts |
Curtain Gas | 20 psi | 20 psi |
Nebulizing Gas | 55 | 50 |
Ion Source Gas | 50 psi | 40 psi |
Collision-induced Dissociation Gas | Medium | Medium |
Ion Spray Voltage | 5000 | 4500 |
ESI Probe Temperature | 450 | 450 |
Declustering Potential | 31 V, 8-oxodGuo | 41 V, 1,N6-εdAdo |
31 V, [15N5]8-oxodGuo | 41 V, [15N5]1,N6-εdAdo | |
45 V, 1,N2-εdGuo | ||
45V, [15N5]1,N2-εdGuo | ||
Collision Energy | 23 eV, 8-oxodGuo | 25 eV, 1,N6-εdAdo |
23 eV, [15N5]8-oxodGuo | 25 eV, [15N5]1,N6-εdAdo | |
27 eV, 1,N2-εdGuo | ||
27 eV, [15N5]1,N2-εdGuo | ||
Collision Cell Exit Potential | 16 V, 8-oxodGuo, | 8 V, 1,N6-εdAdo |
16 V, [15N5]8-oxodGuo | 8 V, [15N5]1,N6-εdAdo | |
16 V, 1,N2-εdGuo | ||
16 V, [15N5]1,N2-εdGuo | ||
Entrance Potential | 10 V | 10 V |
Table 1. Parameters used in the ESI-MS/MS equipment for detection of the DNA lesions. This table has been modified from Oliveira et al.34.
9. Quantification of normal 2'-deoxyribonucleosides by HPLC-UV
10. Quantification of the DNA lesions
The average DNA concentrations (± SD) obtained from mice liver (~ 1 g tissue), lung (~ 0.2 g tissue) and kidney (~ 0.4 g tissue) were, respectively, 5,068 ± 2,615, 4,369 ± 1,021, and 3,223 ± 723 µg/mL in the final volume of 200 µL. A representative chromatogram obtained by HPLC-DAD of the purified DNA is shown in Figure 3. The presence of the four 2'-deoxynucleosides, free from the RNA ribonucleosides, which elute immediately before the corresponding 2'-deoxynucleosides, demonstrates the DNA purity.
Representative chromatograms from HPLC-ESI-MS/MS analyses for quantification of 8-oxodGuo, 1,N6-εdAdo and 1,N2-εdGuo in mice tissue DNA samples are shown in Figures 4 to 6. The chromatogram obtained with UV detection in Figure 4 shows the four 2'-deoxynucleosides eluting from the first column until ~ 10 min, with a good separation from 8-oxodGuo, eliminating undesired interferences. The normal 2'-deoxynucleosides were not present in the analyses of 1,N6-εdAdo and 1,N2-εdGuo, as they were eliminated in the solid phase extraction procedure. Mass spectra of the standards used in this work are shown in Figure 7.
Typical linear calibration curves for quantification of 8-oxodGuo, 1,N6-εdAdo and 1,N2-εdGuo are shown in Figure 834. The methods were accurate and precise, as presented in Table 234. The inter-day precision calculated for DNA aliquots supplemented with 367 fmol of 8-oxodGuo was 16.97%, supplemented with 10 fmol of 1,N2-εdGuo was 14.01%, and supplemented with 1 fmol of 1,N6-εdAdo was 16.66%. The limits of quantification (S/N = 10) for the standards injected on-column were 25 fmol for 8-oxodGuo, 0.3 fmol for 1,N6-εdAdo, and 1 fmol for 1,N2-εdGuo34.
The methods were applied to the quantification of 8-oxodGuo, 1,N2-εdGuo and 1,N6-εdAdo in lung, liver, and kidney DNA samples of A/J mice tissues exposed whole body to ambient air enriched in PM2.5, compared to those exposed to in situ ambient air as the study control34. The levels found are shown in Table 3, and indicate the induction of DNA lesions in lung, liver and kidney by PM2.5 exposure34.
Figure 3. Chromatogram of the hydrolysate of a DNA sample extracted from mouse lung. The chromatogram was obtained at 260 nm from the HPLC-DAD system. The four 2'-deoxynucleosides are indicated: dC, 2'-deoxycytidine; dA, 2'-deoxyadenosine; dG, 2'-deoxyguanosine; dT, 2'-deoxythymidine. Please click here to view a larger version of this figure.
Figure 4. Representative chromatograms showing the detection of 8-oxo-7,8-dihydro-2´-deoxyguanosine (8-oxodGuo) and the internal standard [15N5]8-oxodGuo by HPLC-ESI-MS/MS, as well as the normal 2'-deoxynucleosides eluting from the first column and diverted to DAD detection (λ = 260 nm) and waste. The DNA sample was extracted from mouse lung. The analyses by HPLC-ESI-MS/MS were performed with multiple reaction monitoring (MRM) using the fragmentations specified in the images. Please click here to view a larger version of this figure.
Figure 5. Representative chromatograms showing the detection of 1,N6-etheno-2´-deoxyadenosine (1,N6–εdAdo) and the internal standard [15N5]1,N6-εdAdo by HPLC-ESI-MS/MS. The DNA sample was extracted from mouse kidney. The analyses were performed with multiple reaction monitoring (MRM) using the fragmentations specified in the images. Please click here to view a larger version of this figure.
Figure 6. Representative chromatograms showing the detection of 1,N2-etheno-2´-deoxyguanosine (1,N2–εdGuo) and the internal standard [15N5]1,N2-εdGuo by HPLC-ESI-MS/MS. The DNA sample was extracted from mouse liver. The analyses were performed with multiple reaction monitoring (MRM) using the fragmentations specified in the images. Please click here to view a larger version of this figure.
Figure 7. Mass spectra of the standards used in this work. The spectra were obtained in MS2 using the collision energy of 20 eV to fragment the [M+H]+ ions. Please click here to view a larger version of this figure.
Figure 8. Calibration curves obtained by HPLC-ESI-MS/MS for quantification of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo), 1,N2-etheno-2´-deoxyguanosine (1,N2–εdGuo) and 1,N6-etheno-2´-deoxyadenosine (1,N6–εdAdo). Relative Area means the area ratios between the lesion and its respective [15N5] internal standard. This figure has been modified from Oliveira et al.34. Please click here to view a larger version of this figure.
ESI-MS/MS parameters | 8-oxodGuo | Etheno adducts |
Curtain Gas | 20 psi | 20 psi |
Nebulizing Gas | 55 | 50 |
Ion Source Gas | 50 psi | 40 psi |
Collision-induced Dissociation Gas | Medium | Medium |
Ion Spray Voltage | 5000 | 4500 |
ESI Probe Temperature | 450 | 450 |
Declustering Potential | 31 V, 8-oxodGuo | 41 V, 1,N6-εdAdo |
31 V, [15N5]8-oxodGuo | 41 V, [15N5]1,N6-εdAdo | |
45 V, 1,N2-εdGuo | ||
45V, [15N5]1,N2-εdGuo | ||
Collision Energy | 23 eV, 8-oxodGuo | 25 eV, 1,N6-εdAdo |
23 eV, [15N5]8-oxodGuo | 25 eV, [15N5]1,N6-εdAdo | |
27 eV, 1,N2-εdGuo | ||
27 eV, [15N5]1,N2-εdGuo | ||
Collision Cell Exit Potential | 16 V, 8-oxodGuo, | 8 V, 1,N6-εdAdo |
16 V, [15N5]8-oxodGuo | 8 V, [15N5]1,N6-εdAdo | |
16 V, 1,N2-εdGuo | ||
16 V, [15N5]1,N2-εdGuo | ||
Entrance Potential | 10 V | 10 V |
Table 1. Parameters used in the ESI-MS/MS equipment for detection of the DNA lesions. This table has been modified from Oliveira et al.34.
Basal level | Added | Detected | Detected(-) Basal | Accuracy | CV | ||||
Average ± SD (fmol) | fmol | Average ± SD (fmol) | Average (fmol) | % | % | ||||
8-oxodGuo | |||||||||
373.00 | ± | 2.71 | 0 | 372.79 | ± | 50.6 | – | – | 13.57 |
373.98 | ± | 4.86 | 367 | 755.41 | ± | 107.92 | 381 | 103.93 | 14.29 |
374.84 | ± | 5.19 | 734 | 1069.57 | ± | 108.51 | 695 | 94.65 | 10.14 |
357.94 | ± | 15.05 | 1469 | 1671.67 | ± | 44.27 | 1314 | 89.43 | 2.65 |
371.07 | ± | 2.43 | 2204 | 2272.01 | ± | 40.2 | 1901 | 86.25 | 1.77 |
1,N2-εdGuo | |||||||||
0.54 | ± | 0.01 | 0 | 0.54 | ± | 0.09 | – | – | 16.88 |
0.54 | ± | 0.01 | 1 | 1.47 | ± | 0.16 | 0.93 | 93.39 | 11.17 |
0.55 | ± | 0.01 | 5 | 5.30 | ± | 0.72 | 4.76 | 95.11 | 13.50 |
0.53 | ± | 0.01 | 10 | 10.60 | ± | 0.39 | 10.06 | 100.63 | 3.67 |
0.54 | ± | 0.01 | 20 | 20.20 | ± | 0.93 | 19.66 | 98.29 | 4.60 |
1,N6-εdAdo | |||||||||
2.08 | ± | 0.10 | 0 | 2.29 | ± | 0.39 | – | – | 17.05 |
2.05 | ± | 0.04 | 1 | 3.06 | ± | 0.47 | 1.01 | 100.89 | 15.31 |
1.99 | ± | 0.06 | 5 | 7.87 | ± | 1.66 | 5.88 | 117.60 | 21.10 |
2.03 | ± | 0.07 | 10 | 12.43 | ± | 1.25 | 10.41 | 104.06 | 10.06 |
1.97 | ± | 0.03 | 20 | 22.42 | ± | 3.89 | 20.46 | 102.29 | 17.34 |
Table 2. Method accuracy and coefficient of variation (CV) for quantification of 8-oxodGuo, 1,N2–εdGuo and 1,N6-εdAdo in DNA. This table has been modified from Oliveira et al.34.
Ambient Air | PM2.5 | N | P value | |||||
Average ± SEM | Average ± SEM | |||||||
Lung | ||||||||
8-oxodGuo/108 dGuo | 2124 | ± | 56.96 | 2466 | ± | 93.10 | 6 | 0.01 |
1,N2-εdGuo/108 dGuo | ND | ND | – | – | ||||
1,N6-εdAdo/108 dAdo | 1.41 | ± | 0.23 | 1.44 | ± | 0.13 | 7 | NS |
Liver | ||||||||
8-oxodGuo/108 dGuo | 2848 | ± | 183.5 | 2949 | ± | 223.8 | 6; 5 | NS |
1,N2-εdGuo/108 dGuo | 7.79 | ± | 2.49 | 24.94 | ± | 5.21 | 4 | 0.02 |
1,N6-εdAdo/108 dAdo | 2.82 | ± | 0.30 | 2.18 | ± | 0.25 | 6 | NS |
Kidney | ||||||||
8-oxodGuo/108 dGuo | 1854 | ± | 87.13 | 2363 | ± | 157.0 | 6 | 0.02 |
1,N2-εdGuo/108 dGuo | ND | ND | – | – | ||||
1,N6-εdAdo/108 dAdo | 1.09 | ± | 0.15 | 1.52 | ± | 0.12 | 7 | 0.04 |
(NS, Not Significant; ND, Not Detected) |
Table 3. Levels of the DNA lesions in A/J mice tissue samples. The mice were exposed to ambient air and to ambient air enriched in PM2.5 (PM2.5 concentrated 30 times). Means between the two groups (ambient air and PM2.5) were compared using t test. Results were considered statistically significant when P value was less than 0.05. This table has been modified from Oliveira et al.34.
A major problem found in the 8-oxodGuo analyses by HPLC methods is the possible induction of its formation during the workup procedures of DNA extraction, DNA hydrolysis, and concentration of DNA hydrolysates22,38. In order to minimize the problem of 8-oxodGuo artifactual formation, it is recommended the addition of deferoxamine to all DNA extraction, storage and hydrolysis solutions, the use of the sodium iodide chaotropic method and avoidance of phenol in DNA extraction, as well as the use of DNA amounts close to 100 µg in the hydrolysis procedure to minimize the contribution of spurious oxidation to the final result39. We took into account the recommendations cited above, except the use of the sodium iodide chaotropic method for DNA extraction. Instead, for simplicity, we used commercial solutions for DNA extraction, adding deferoxamine to them before use. In addition, the obtained DNA hydrolysates were directly injected into a first column of the HPLC-ESI-MS/MS system for a previous separation of 8-oxodGuo from the normal nucleosides. Immediately before the elution of 8-oxodGuo, a switching valve was used to divert the first column eluent to a second column where further separation and peak narrowing were achieved. This approach allowed adequate sensitivity for 8-oxodGuo quantification free from interferences. The most similar approach for quantification of 8-oxodGuo in DNA was described by Chao and coworkers22, who used a trap column for sample cleanup and 8-oxodGuo retention prior to sample elution into the analytical column, using a switching valve between the columns. Alternatively, a concentration step of 8-oxodGuo collected from fractions eluted from HPLC separations of DNA hydrolysates prior to HPLC-ESI-MS/MS analyses was performed15, which is much more laborious.
Reported basal levels of 8-oxodGuo in rodent lung tissue, based on HPLC analyses, range from 180 – 450/108 dGuo23,39,41,42,43, 1,340 – 2,120/108 dGuo44, or approximately 3,000/108 dGuo45,46, with the lowest values obtained from DNA extraction methods by using sodium iodide. The mean 8-oxodGuo level found here in the lung of mice exposed to ambient air was 2,124/108 dGuo. The level increased to 2,466/108 dGuo in the animals exposed to ambient air enriched in PM2.5 (Table 3)34. It is possible that the sensitivity for detection of differences between groups could be improved by extracting the DNA with the sodium iodide chaotropic method. In the present study, the mean 8-oxodGuo levels found in control mice lung, kidney, and liver DNA were, respectively, 2.0, 1.8, and 2.7 times higher than the median basal level (1,047/108 dGuo) obtained by the European Standards Committee on Oxidative DNA Damage (ESCODD) in an inter-laboratory assessment of 8-oxodGuo in DNA extracted from standard samples of pig liver38.
The main limitation for detection of 1,N6-εdAdo and 1,N2-εdGuo in DNA is the method sensitivity, as these lesions occur at very low levels. The lowest levels of 1,N2-dGuo in DNA, quantified by HPLC-ESI-MS/MS, were in the range of 0.87 – 4 lesions per 108 dGuo in a human cell line and rat tissues25,47. One way to improve the sensitivity and selectivity for their quantification is to concentrate them from large samples of DNA hydrolysates, using solid phase extraction. This cleanup step solves chromatographic troubles that could arise from injections of more than 100 µg DNA hydrolysates into HPLC analytical columns. We used this approach in the validated method presented here.The levels of 1,N6-εdAdo detected in this study34 fall within the range obtained in studies employing ultrasensitive immunoaffinity/32P-postlabeling48,49,50,51 and are lower than those described by other groups employing HPLC-ESI-MS/MS21,23,24. Similarly, the 1,N2-εdGuo levels quantified here34 are consistent with the lowest levels reported by Garcia25 and Angeli26 by using HPLC-ESI-MS/MS.
HPLC-ESI-MS/MS systems with higher sensitivity than the equipment used in this study are available. The use of such systems allows the analyses of smaller amounts of DNA, which broadens the applications of the methods presented here for situations in which tissue availability is a limitation. The methods presented here may be adapted for the quantification of other modified deoxynucleosides, depending on the availability of their standards and isotopic standards. Adjustment of the chromatographic conditions would be necessary in order to obtain sharp peaks of all molecules included in the analyses.
The authors have nothing to disclose.
FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, Proc. 2012/22190-3 and 2012/08616-8), CNPq (Proc. 454214/2014-6 and 429184/2016-6), CAPES, PRPUSP (Pró-Reitoria de Pesquisa da Universidade de São Paulo), INCT INAIRA (MCT/CNPq/FNDCT/CAPES/FAPEMIG/FAPERJ/FAPESP; Proc. 573813/2008-6), INCT Redoxoma (FAPESP/CNPq/CAPES; Proc. 573530/2008-4), NAP Redoxoma (PRPUSP; Proc. 2011.1.9352.1.8) and CEPID Redoxoma (FAPESP; Proc. 2013/07937-8). T. F. Oliveira and A. A. F. Oliveira received scholarships from FAPESP (Proc. 2012/21636-8, 2011/09891-0, 2012/08617-4) and CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior). M. H. G. Medeiros, P. Di Mascio, P. H. N. Saldiva, and A. P. M. Loureiro received fellowships from CNPq.
Some figures and tables present in this work were originally published in Oliveira A.A.F. et al. Genotoxic and epigenotoxic effects in mice exposed to concentrated ambient fine particulate matter (PM2.5) from São Paulo city, Brazil. Particle and Fibre Toxicology. 15, 40 (2018).
[15N5]-2’-deoxyadenosine | Cambridge Isotope Laboratories | NLM-3895-25 | |
[15N5]-2’-deoxyguanosine | Cambridge Isotope Laboratories | NLM-3899-CA-10 | |
acetonitrile | Carlo Erba Reagents | 412413000 | |
alkaline phosphatase from bovine intestinal mucosa | Sigma | P5521 | |
ammonium acetate | Merck | 101116 | |
calf thymus DNA | Sigma | D1501 | |
cell lysis solution | QIAGEN | 158908 | |
chloroform | Carlo Erba Reagents | 412653 | |
deferoxamine | Sigma | D9533 | |
deoxyribonuclease I (DNase I) | Bio Basic Inc | DD0649 | |
ethanol | Carlo Erba Reagents | 414542 | |
formic acid | Sigma-Aldrich | F0507 | |
HPLC-ESI-MS/MS system | HPLC: Agilent 1200 series ESI-MS/MS: Applied Biosystems/MDS Sciex Instruments | HPLC: binary pump (G1312B), isocratic pump (G1310A), column oven with a column switching valve (G1316B), diode array detector (G1315C), auto sampler (G1367C). ESI-MS/MS: Linear Quadrupole Ion Trap mass spectrometer, Model 4000 QTRAP. | |
HPLC/DAD system | Shimadzu | Two pumps (LC-20AT), photo diode array detector (DAD-20AV), auto-injector (Proeminence SIL-20AC), column oven (CTO-10AS/VP) | |
HPLC column (50 x 2.0 mm i.d., 2.5 µm, C18) | Phenomenex | 00B-4446-B0 | |
HPLC column (150 x 2.0 mm i.d., 3.0 µm, C18) | Phenomenex | 00F-4251-B0 | |
HPLC column (250 x 4.6 mm i.d., 5.0 µm, C18) | Phenomenex | 00G-4252-E0 | |
HPLC C18 security guard cartridge (4.0 x 3.0 mm i.d.) | Phenomenex | AJO-4287 | |
isoamyl alcohol | Sigma-Aldrich | M32658 | |
isopropyl alcohol (isopropanol) | Carlo Erba Reagents | A412790010 | |
ketamine | Ceva | Commercial name: Dopalen | |
magnesium chloride | Carlo Erba Reagents | 349377 | |
magnesium chloride | Sigma | M2393 | |
methanol | Carlo Erba Reagents | L022909K7 | |
phosphodiesterase I from Crotalus atrox | Sigma | P4506 | |
protein precipitation solution | QIAGEN | 158912 | |
proteinase K | Sigma-Aldrich | P2308 | |
ribonuclease A | Sigma | R5000 | |
sodium chloride | Sigma-Aldrich | S9625 | |
SPE-C18 (Strata-X) | Phenomenex | 8B-S100-TAK | |
tris(hydroxymethyl)-aminomethane | Carlo Erba Reagents | 489983 | |
xylazine | Syntec do Brasil | Commercial name: Xilazin |