Nanocluster Beacons for Detection of a Single N6-Methyladenine Epigenetic Modification

NanoCluster Beacons (NCBs) are a new type of activatable molecular probes that are low cost, easy to prepare and have high fluorescence enhancement ratios. NCBs employ DNA-templated, few-atom silver nanoclusters (DNA/Ag NCs, with about 2∼20 silver atoms per cluster) as reporters which can significantly “light up” through interactions with a nearby DNA sequence (called an enhancer). Taking advantage of this fluorescence tunability by altering the surrounding ligands, a property that is not commonly seen among existing reporters, NCB soon evolved to a multicolor probe, termed chameleon NanoCluster Beacon (cNCB), for single-nucleotide polymorphism (SNP) detection. Here we bring the NCB detection to the next level by designing a new NCB specifically for N6-methyladenine (hereafter denoted as m6A) detection. m6A is a methylation modification abundant in prokaryotic genomes, and also found in lower eukaryotes and higher plants. So far detection of m6A relies on methods such as TLC, HPLC, MS, and enzymatic reactions, which are often laborious, expensive, with low specificity and varying reactivity. Whereas high-resolution melting analysis is able to detect a single m6A modification within a target DNA via the destabilizing effect of m6A, HRM cannot pinpoint the location of m6A in the sequence. A simple and cost-effective way to identify single m6A at any specific sites is therefore highly desired. Here, we developed a robust, simple, enzyme-free and hybridization-based method for m6A detection with “pinpoint specificity”, using a new type of silver cluster-based DNA probe which we term methyladenine-specific NanoCluster Beacon (maNCB). To date, there is no hybridization technique that has the potential to reach these remarkable results.Y.-A. Chen, J.M. Obliosca, Y.-L. Liu, C. Liu, M.L. Gwozdz, and H.-C. Yeh, “NanoCluster Beacons enable detection of a single N6-methyladenine,” JACS, http://dx.doi.org/10.1021/jacs.5b06038, 2015.