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.