A molecular beacon is a fluorescent probe molecule that is designed to fluoresce only when it binds to a specific DNA target sequence. The probe contains both a fluorescent group, or fluorophore, and a quenching group at opposite ends of a DNA sequence of 20 to 30 bases. The central region of the probe is complementary to the target sequence. The terminal half dozen bases at each end of the probe are complementary and form a short double-stranded region as shown in Fig. 21.37. In the stem and loop conformation the quenching group is next to the fluorophore and so prevents fluorescence. When the molecular beacon binds to the target sequence it is linearized. This separates the quenching group from the fluorophore, which is now free to fluoresce. Care is needed to avoid disrupting the short stem structure. For example, high temperatures will cause unpairing and give a false positive response.
fluorophore A fluorescent chemical group molecular beacon A fluorescent probe molecule that contains both a fluorophore and a quenching group and that fluoresces only when it binds to a specific DNA target sequence
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