Nucleic acid-based fluorescence sensors for detecting proteins

We report here development of a rapid, homogeneous, aptamer-based fluorescence assay (molecular beacons) for detecting proteins. The assay involves protein-induced coassociation of two aptamers recognizing two distinct epitopes of the protein. The aptamers contain short fluorophore-labeled complementary signaling oligonucleotides attached to the aptamer by non-DNA linker. Coassociation of the two aptarners with the protein results in bringing the two signaling oligonucleotides into proximity, producing a large change of fluorescence resonance energy transfer between the fluorophores. We used thrombin as a model system to provide proof-ofprinciple evidence validating this molecular beacon design. Thrombin beacon was capable of detecting the protein with high selectivity (also in complex biological mixtures), picomolar sensitivity, and high signal-to-background ratio. This is a homogeneous assay requiring no sample manipulation. Since the design of molecular beacons described here is not limited to any specific protein, it will be possible to develop these beacons to detect a variety of target proteins of biomedical importance.