High-Throughput Bead-Based Identification of Structure-Switching Aptamer Beacons

We describe a new platform to identify structure‐switching DNA beacon aptamers, which detect small molecules in a specific manner. By clonally amplifying a DNA library designed to fluoresce in response to binding events onto microbeads, aptamer beacons can be selected by stringent fluorescence‐assisted sorting. We validated this method by isolating known and novel anti‐steroid aptamers from two separate DNA libraries that were structurally enriched with three‐way junctions. Importantly, aptamers were retrieved in only a few (three) rounds of selection by this approach and did not require further optimization, significantly streamlining the process of beacon development. Using a new platform, we were able to isolate DNA beacon aptamers that fluoresce in the presence of a given small molecule by an in vitro selection scheme that includes bead‐based emulsion PCR (ePCR) and FACS. This method represents a streamlined method for aptamer beacon development.