In addition to Taqman probes, molecular beacons are widely used in probe design.

Molecular beacons are short oligonucleotide probes capable of forming a hairpin structure. They are labeled with a fluorescent dye at the 5' end and a quencher (Dabcyl) at the 3' end. The bases in the loop of the probe are complementary to the target gene sequence, while the ends of the hairpin form a stem with complementary bases. In the absence of the target molecule, the fluorescence and quencher groups of the molecular beacon are in close proximity, resulting in quenching of the fluorescence. When the probe binds to the target sequence, the reporter and quencher groups separate, resulting in a fluorescent signal. The unique hairpin structure of molecular beacons enables them to exhibit highly specific recognition of target sequences. Therefore, they have been widely used in clinical diagnosis, gene detection, environmental monitoring, live-cell imaging, gene chips, and biosensing applications.