The in vitro methylation of DNA by a minor groove binding methyl sulfonate ester

The preparation of sequence and groove specific DNA methylating agents based on N-methylpyrrolecarboxamide subunits appended with an O-methyl sulfonate ester functionality (MeOSO(2)(CH2)(2)-Lex) has previously been described [Zhang, Y., Chen, F.-X., Mehta, P., and Gold, B. (1993) Biochemistry 32, 7954-7965]. In contrast to simple methyl sulfonate esters, e.g., methyl methanesulfonate (MMS), which predominantly methylate at 7-guanine, MeOSO(2)(CH2)(2)-Lex affords N3-methyladenine (3-MeAde) as its major adduct. Using competitive ELISA determinations, the methylation at major and minor groove sites in calf thymus DNA by MeOSO(2)(CH2)(2)-Lex has been precisely quantitated. The yields of N7-methylguanine (7-MeGua), 3-MeAde, and O-6-methyldeoxyguanosine (B-Me-dGuo) are 0.424, 3.195, and 0.0027 mmol of adduct/mol of DNA, respectively, using 10 mu M MeOSO(2)(CH2)(2)-Lex and 100 mu M DNA. This compares to 0.773, 0.072, and 0.0033 mmol of adduct/mol of DNA for 7-MeGua, S-MeAde, and 6-Me-dGuo, respectively, using MMS. The increase in the yield of 3-MeAde due to the minor groove equilibrium binding properties of MeOSO(2)(CH2)(2)-Lex is similar to 40-fold relative to MMS.