DNA methylation patterns play an important role in determining gene expression patterns. These patterns are of particular interest in embryonic development and in cancer cells, which often exhibit abnormal methylation patterns. The ability to control the activity and specificity of DNA methyltransferases would have applications in the study of DNA methylation in cells, would offer an avenue to control gene expression epigenetically and potentially would allow the correction of abnormal methylation patterns for therapeutic purposes. Most known DNA methyltransferases are encoded in a single polypeptide chain. DNA methyltransferases in which the activity is encoded by heterodimerizing peptides, offer unique platform for engineering DNA methyltransferases with novel properties. The C5-methylcytosine methyltransferases M. AquI and M. EcoHK31I each have alpha and beta peptide chains that associate to create a functional enzyme. Methylation is not possible without the association of the two fragments. Truncated version of these fragments exhibit decreased association in vitro. We have used an in vivo method to determine if the fragment's association is more or less sensitive to these truncations in the cellular environment. The results have implications for engineering control over the association of these fragments for live cell applications.