Disruption of the target G-C base-pair by the HhaI methyltransferase

HhaI MTase binds DNA duplexes containing mismatches at the target base position with higher affinity than that observed for the canonical substrate. The stability of these MTase-DNA complexes inversely correlates with the strength of the base pair that is disrupted upon interaction. This finding may offer a general tool to detect other enzymes that flip bases out of the DNA helix.