Single-molecule Fluorescence Study for the Effects of DNA Methylation on the Association and Dissociation Kinetics of Restriction Endonuclase and DNA

Abstract

DNA methylation plays a great role both in eukaryotic and prokaryotic cells. In eukaryotes, it suppresses gene regulation, whereas in prokaryotes, specifically in bacteria, it protects the cell from invasion of foreign genes. Many studies have been carried out for the effect of DNA methylation at the ensemble level, but in this study, we investigated the effect of DNA methylation on DNA-protein interaction by single-molecule fluorescence to understand the interaction at the molecular level. We measured the association and dissociation rates of native as well as methylated DNA and found that the values converge to the corresponding ensemble rates. We were able to differentiate the kinetics of association, and dissociation and found that our result was consistent with the fact that DNA methylation interrupts the DNA- protein interaction, especially at a specific kinetic step.