UB Scientists Model DNA Reaction

University at Buffalo scientists are using the Center for Computational Research's high-performance computers to model the methylation reaction between DNA (double helix in the center) and the protein M,Hhal (colorful, twisted ribbons in center) in an aqueous solution (the small molecules scattered throughout). Uncontrolled DNA methylation is responsible for the development of some types of cancer.

Density Functional Theory calculations show that the reaction occurs only when a cytosine base from the DNA is bonded to an amino acid of the protein, after the cytosine is flipped out of the DNA helix. The calculation results have been confirmed by experiments using X-ray and nuclear magnetic resonance data.

Credit: M. Freindorf and T. Furlani, Center for Computational Research, T. Szyperski, Department of Chemistry, University at Buffalo; J. Kong, Q-Chem Inc.; visualization by Adam Koniak, Center for Computational Research, University at Buffalo