O6-Methylguanine in place of guanine causes asymmetric single-strand cleavage of DNA by some restriction enzymes

The interactions of restriction enzymes with their cognate DNA recognition sequences present a model for protein-DNA interactions. We have investigated the effect of O6-methylguanine on restriction enzyme cleavage of DNA; O6-methylguanine is a carcinogenic lesion and a structural analogue of the biological restriction inhibitor N6-methyladenine. O6-Methylguanine was synthesized into oligonucleotides at unique positions. The oligonucleotides were purified and analyzed by high-pressure liquid chromatography to assure that, within the limits of our detection, O6-methylguanine was the only modified base present. These oligonucleotides were annealed with their complement so that cytosine, and in one case thymine, opposed O6-methylguanine. DNA cleavage by restriction enzymes that recognize a unique DNA sequence, HpaII, HhaI, HinPI, NaeI, NarI, PvuII, and XhoI, was inhibited by a single O6-methylguanine in place of guanine (adenine for PvuII) within the appropriate recognition sequences. However, only the modified strand was nicked by HpaII, NaeI, and XhoI with O6-methylguanine at certain positions, indicating asymmetric strand cleavage. For all the restriction enzymes studied but AhaII, BanI, and NarI, lack of double- or single-strand cleavage correlated with inability of the O6-methylguanine-containing recognition sequence to measurably bind enzyme. None of the restriction enzymes studied were inhibited by O6-methylguanine outside their cognate recognition sequences.