Mechanistic study on DNA mutation of the cytosine methylation reaction at C5 position

DNA methylation is a crucial epigenetic mark connected to conventionally changing the DNA bases, typically by adding methyl groups into DNA bases. Methylation of cytosine at the C5 position (5-methylcytosine) occurs mostly in the context of cytosine-phosphate-guanine dinucleotides, the methylation of which has important impacts on gene regulation and expression. How-ever, the mechanistic details of this reaction are still debatable concerning the concertedness of the key reaction steps and the roles played by the base that abstracts the proton in the b-elimination and water molecules at the active site. To gain a deeper insight into the formation of 5-mehtylcytosine, an extensive density functional theory (DFT) study was performed with the B3LYP functional in conjunction with different basis sets. Our study has clearly established the mechanistic details of this methylation approach, based on which the roles of conserved active site residues, such as glutamic acid and waters, are well understood. Our results show that the reaction of 5-methylcytosine follows a concerted mechanism in which water molecules are critically involved. Moreover, arginine and alanine give more significant catalytic effects than glutamic acid on the 5-methylcytosine process. Considering the effect of Alanine, Arginine, and one water bridging molecule, the activation energy is 31 kJ mol(-1) calculated at B3LYP/6-31G(d) level of theory. (C) 2022 The Authors. Published by Elsevier B.V. on behalf of King Saud University.

Automated summary

DNA methylation is an important epigenetic mark that regulates gene expression. This study investigated the mechanistic details of the formation of 5-methylcytosine and identified the roles of active site residues and water molecules in the reaction. The results showed that the reaction follows a concerted mechanism involving the participation of water molecules, and alanine and arginine have significant catalytic effects on the process.