Simultaneous quantification of methylated purines in DNA by isotope dilution LC-MS/MS coupled with automated solid-phase extraction

Since methylation at the N-7 and O6 positions of guanine and the N-3 position of adenine in DNA are the predominant reaction sites, N7-methylguanine (N7-MeG), O6-methylguanine (O6-MeG), and N3-methyladenine (N3-MeA) have been suggested as good biomarkers for assessing exposure to methylating agents. Here, we report the development of a sensitive and selective assay based on liquid chromatography–tandem mass spectrometry (LC-MS/MS) to simultaneously measure N7-MeG, O6-MeG, and N3-MeA in DNA hydrolysates. With the use of isotope internal standards (15N5-N7-MeG, d3-O6-MeG, and d3-N3-MeA) and online solid-phase extraction, DNA hydrolysates can be directly analyzed within 12 min without prior sample purification. The limits of detection were 0.02, 0.002, and 0.01 ng/mL on-column (6.1, 0.6, and 3.4 fmol) for N7-MeG, O6-MeG, and N3-MeA, respectively. Inter- and intraday imprecision (CV) were 3.6–9.6% and 2.7–13.6%, respectively. Mean recoveries were 96–109%. This method was then applied to quantitate the amounts of methylated purines in calf thymus DNA treated with methyl methanesulfonate (MMS). The levels of N7-MeG, O6-MeG, and N3-MeA in calf thymus DNA increase with MMS concentration and incubation time. The ratio of relative yields of N7-MeG, O6-MeG, and N3-MeA in MMS-treated DNA was found to be 1.00:0.0032:0.119, respectively. This LC-MS/MS assay provides the sensitivity and high throughput required to evaluate the extent of methylated lesions in DNA induced by methylating agents.