DNA methylation may play a key role in some biological processes, as in DNA replication, transcription and recombination, gene expression, cell differentiation, and development. However, the experimental facts were elusive up to now. Using results calculated from quantum mechanics (at the electron level) we have solved some problems which existed concerning the relationship of DNA methylation and gene transcription and mutation. We think that the methylation of cytosine in eukaryotes does not lead directly to gene mutation, on the contrary, it can inhibit transcription.