Molecular Beacons are a type dual-labeled FRET probes incorporating a quencher and a fluorophore reporter molecule. They differ from traditional dual-labeled probes, due to the incorporation of a short (~5 b.p.) complementary stem sequence at the 3' and 5' ends.
These complementary sequences hybridize to form a “stem-loop” structure which holds the reporter and quencher close together in space. This alternate conformation makes Molecular Beacons more discriminatory, allowing them to resolve different target sequences differing by a single nucleotide. Molecular Beacons also differ from traditional dual-labeled probes because they do not rely on probe hydrolysis from the 5' exonuclease activity of Taq polymerase to generate its fluorescence, therefore, a post-PCR melt curve is possible.
Just like standard Dual-labeled BHQ® probes it is possible to multiplex assays using Molecular Beacons. Multiplexing allows for the detection of several targets simultaneously using multiple spectrally resolved fluorescent probes.
Molecular Beacons are sold under license from the Public Health Research Institute, Newark, NJ. For information on designing Molecular Beacons please refer to The Public Health Research Institute's Molecular Beacons website.