DNA methyltransferases modify specific cytosines and adenines within 2- 6 bp recognition sequences. We used scanning force microscopy and gel shift analysis to show that M.HhaI, a cytosine C5 DNA methyltransferase, causes only a 2° bend upon binding its recognition site. Our results are consistent with prior crystallographic analysis showing that the enzyme stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed. In contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average bend angle of approximately 52°. This distortion of DNA conformation by M.EcoRI is shown to be important for sequence-specific binding.