Epigenetic modifications are significant processes controlling gene expression. Since their discovery by C. H. Waddington, several multisubject research proceeded and allowed investigation of how biochemical regulations can influence gene transcription. The main epigenetic modification is DNA methylation. This catalytic process of attaching methyl groups to nucleobases (mostly cytosine) is fundamental for the regulation of gene expression and chromatin accessibility. Methylated parts of the genome, which are mostly gene promoters and enhancers, are silenced due to specific biological mechanisms. Scientists postulate that aberrant DNA methylation and other epigenetic modifications can contribute to the development of diverse pathologies such as Alzheimer's disease, epilepsy, Schizophrenia, tumorigenesis, and atherosclerosis. Due to these discoveries, it is important to characterize in detail the mechanism of epigenetic modifications to develop new possible ways of treatment. In this work, we presented complex studies of DNA methylation mechanism including dynamic and energetic analysis of the reaction system. A cluster chemical approach was used to model the active site of enzyme catalyzing methylation - DNMT1 (DNA methyltransferase 1). The created model was subjected to quantum chemical calculations. Geometry optimization was performed with ADF software, providing an energetic characterization of the studied process. Dynamic properties of the enzyme model were described due to molecular dynamics (MD) procedures performed with CP2K software. MD calculations were focused on the observation and description of proton transfer between glutamate acid and cytosine, which is considered the main enzyme-substrate interaction leading to the creation of 5-methylcytosine 5mC (product of the studied reaction) and covalent bonding between enzymes cysteine and nucleobase. This research provides a comprehensive understanding of the DNA methylation mechanism and may contribute to the invention of new drugs and modern ways of treatment.