The author granted permission for the digitization of this paper. It was submitted by CD.The nucleic acid bases in DNA rely on hydrogen-bonding to maintain the structure that defines their function. When a hydrogen atom of a nucleic acid base is substituted by a methyl group, the resulting change in sterics disrupts intrahelical and interstrand bonding, thus altering DNA structure and function. Substitutions on cytosine, as in the case of 5-methylcytosine and hydroxymethylcytosine, are the only known modified nucleic acid bases that exist in eukaryotes, and both interfere with transcription of DNA. Methylation of benzene and cytosine was modeled with and without an additional aromatic molecule in a sandwiched conformation using HCTH/6-31+g*. This additional pi-stacked molecule models both intercalation and the natural DNA environment. The methylation reaction was studied via two mechanisms; a Friedel-Crafts alkylation and the mechanism used in the methyltransferase enzyme. Structures and energies were calculated for reactants, transition states, and products. Results showed that the presence of the stacked aromatic ring increased the enthalpy of reaction and lowered the activation energy.This paper was read and approved by Drs. Mauricio Cafiero, Larryn Peterson, Carolyn Jaslow, and Darlene Loprete.