Base methylation and local DNA helix stability. Effect on the kinetics of cruciform extrusion

We have studied the effect of base methylation on the rate of cruciform extrusion. A number of inverted repeats with central restriction sites were methylated at N6-adenine and C-5-cytosine, and rate constants for cruciform extrusion at 37 degrees C were measured. The effect of A-methylation at two bases was to enhance the rate for extrusion by nearly fourfold, while C-methylation lead to reduced extrusion rates, by factors of 1.7 and 2.7. The bkb inverted repeat, which has a central GGATCC sequence, was independently and simultaneously methylated at adenine and cytosine. It was found that the effects of the two kinds of modification could be treated effectively independently. The results reveal the local helical destabilization and stabilization due to A and C-methylation, respectively.