Development of a Fluorogenic Probe Based on a DNA Staining Dye for Continuous Monitoring of the Histone Deacetylase Reaction

We designed a simple, rapid, and continuous method for the detection of the activity of histone deacetylases (HDACs), which are key enzymes involved in epigenetic gene regulation, using a DNA-based fluorogenic probe. We designed and synthesized a fluorogenic probe, BOXTO-GK­(Ac)­G, which is a DNA staining dye–peptide conjugate containing an acetylated lysine. The DNA-dependent fluorescence of BOXTO-GK­(Ac)­G was greatly enhanced upon deacetylation of the acetylated lysine moiety, owing to the increased DNA binding ability of the probe. The HDAC reaction was detected through a simple procedure that combined this probe with DNA. Our detection system monitored the enzymatic reaction in real time and could be applied to the inhibition assay. These findings demonstrated that our system might be a useful tool for the analysis of HDAC function and for the evaluation of the inhibitor potencies of drug candidates that target HDACs.