Aptamer Beacons for the Direct Detection of Proteins

We have designed a new class of molecules, which we term aptamer beacons, for detecting a wide range of ligands. Similar to molecular beacons, aptamer beacons can adopt two or more conformations, one of which allows ligand binding. A fluorescence-quenching pair is used to report changes in conformation induced by ligand binding. An anti-thrombin aptamer was engineered into an aptamer beacon by adding nucleotides to the 5′-end which are complementary to nucleotides at the 3′-end of the aptamer. In the absence of thrombin, the added nucleotides will form a duplex with the 3′-end, forcing the aptamer beacon into a stem-loop structure. In the presence of thrombin, the aptamer beacon forms the ligand-binding structure. This conformational change causes a change in the distance between a fluorophore attached to the 5′-end and a quencher attached to the 3′-end. Aptamer beacon can be a sensitive tool for detecting proteins and other chemical compounds.