DNA bending induced by DNA (cytosine-5) methyltransferases

DNA bending induced by six DNA (cytosine-5) methyltransferases was studied using circular permutation gel mobility shift assay. The following bend ang les were obtained: M.BspRI (GG(m5)CC), 46-50 degrees; M.HaeIII (GG(m5)CC), 40-43 degrees; M.SinI (GGW(m5)CC), 34-37 degrees; M.Sau96I (GGN(m5)CC), 52- 57 degrees; M.HpaII (C(m5)CGG), 30 degrees; and M.HhaI (G(m5)CGC), 13 degre es. M.HaeIII was also tested with fragments carrying a methylated binding s ite, and it was found to induce a 32 degrees bend. A phase-sensitive gel mo bility shift assay, using a set of DNA fragments with a sequence-directed b end and a single methyltransferase binding site, indicated that M.HaeIII an d M.BspRI bend DNA toward the minor groove. The DNA curvature induced by M. HaeIII contrasts with the lack of DNA bend observed for a covalent M.HaeIII -DNA complex in an earlier X-ray study. Our results and data from other lab oratories show a correlation between the bending properties and the recogni tion specificities of (cytosine-5) methyltransferases: enzymes recognizing a cytosine 3' to the target cytosine tend to induce greater bends than enzy mes with guanine in this position. We suggest that the observed differences indicate different mechanisms employed by (cytosine-5) methyltransferases to stabilize the helix after the target base has flipped out.