A DNA as a Substrate and an Enzyme: Direct Profiling of Methyltransferase Activity by Cytosine Methylation of a DNAzyme.

Abstract

Inhibiting DNA methyltransferase (MTase) activity is crucial for cancer treatment. Evaluating drug candidates as inhibitors of MTase requires the measurement of its activity. However, direct profiling of MTase activity remains an analytical challenge, since a complicated hydrolysis step using methylation-sensitive restriction enzymes (msRE) was inevitable in almost all previously reported methods. Taking advantage that DNA is the substrate of MTase and certain DNA sequences, known as DNAzymes, can also have enzyme-like activities, we herein developed an enzyme-free and label-free route for direct assaying MTase activity. Specifically, adding a cytosine at the meta-position of a peroxidase-mimicking DNAzyme can improve the catalytic activity of DNAzyme up to 5-fold. After methylation of the cytosine cap, the activity is further doubled. Based on these findings, direct assaying of MTase inhibitors was performed without the extra and complicated hydrolysis step. These new findings provide a helpful tool for screening drugs for cancer therapy. The idea of using the same DNA as a substrate and an enzyme could be a general way for assaying other enzymes.