Abstract: Tripartite molecular beacons (TMBs), are disclosed that are readily adaptable to high throughput applications. Each tripartite molecular beacon comprises three oligonucleotide components. The first oligonucleotide forms a hairpin stem and loop structure and the second and third oligonucleotides each comprise a sequence complementary to opposite strands of the hairpin stem. The second oligonucleotide has a fluorophore attached thereto and the third oligonucleotide has a quencher attached thereto.

Abstract: Aptamer based fluorescent reporters that function based on a switch from DNA/DNA duplex conformation to DNA/target conformation are provided. The DNA/DNA duplex is formed between the aptamer DNA sequence and an oligonucleotide carrying a reporter moiety. When the aptamer target is present, the aptamer assumes a tertiary structure for binding to the target. The formation of the tertiary structure forces the dissociation of the duplex structure and a signal is generated. The signal is preferably a fluorescent signal due to spatial separation of a fluorophore/quencher pair.