NanoCluster Beacons Enable Detection of a Single N6-Methyladenine

While N6-methyladenine (m6A) is a common modification in prokaryotic and lower eukaryotic genomes and has many biological functions, there is no simple and cost-effective way to identify a single N6-methyladenine in a nucleic acid target. Here we introduce a robust, simple, enzyme-free and hybridization-based method using a new silver cluster probe, termed methyladenine-specific NanoCluster Beacon (maNCB), which can detect single m6A in DNA targets based on the fluorescence emission spectra of silver clusters. Not only can maNCB identify m6A at the single-base level but it also can quantify the extent of adenine methylation in heterogeneous samples. Our method is superior to high-resolution melting analysis as we can pinpoint the location of m6A in the target.