A molecular beacon is a probe containing a 3' quencher dye and a fluorescent 5' reporter dye. A molecular beacon is designed to form a hairpin in free solution by introducing complementary arm sequences that flank the probe sequence. The loop of the structure is the probe itself designed to be complementary to a very specific sequence in the template strand. Any time the beacon is in this hairpin conformation, the reporter dye will be quenched. Any time a beacon is hybridized it will fluoresce. During primer extension, the beacon will dissociate from the strand and revert to the favourable hairpin structure. If designed properly, the molecular beacon assay is extremely sensitive.