The precise molecular recognition event of nucleic acid hybridization is fundamental to molecular biology. Traditionally, probes are tagged with fluorescent or radioactive labels and hybridized to a sample. Unbound probe is removed via a dilution or digestion step. This allows the investigator to quantify the amount of bound probe but simultaneously disrupts the equilibrium state of the hybridization, preventing the use of this technique in real-time or in vivo.

Molecular beacons, single-stranded oligonucleotides that have a fluorescent "reporter" group at one end and a fluorescence "quencher" at the other, do not suffer from these shortcomings.1 When free in solution, a beacon's complementary arms bind to each other, forming an internal hairpin that brings the reporter and quencher groups together and dousing fluorescence. When the probe meets its target, it unfolds and forms a stable hybrid, and the reporter dye emits a fluorescent signal. Because the dilution or digestion step...

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