Molecular beacon probes are a sequence of nucleotides that can be used to fluorescently detect the presence of a specific sequence of DNA or RNA. The molecular beacon is designed so that a a small number of nucleotide bases (between five and seven) at the sequence terminals are complementary to each other and get paired forming what is called the stem. The formation of the stem creates a loop of the unpaired bases, which is termed the stem loop or hairpin loop. Finally at one end of the nucleotide sequence there is a covalently attached fluorophore and a fluorescence quencher at the other end of the sequence. When the molecular beacon is in this hairpin form, the quencher heavily diminishes the fluorophore fluorescence through Förster Resonance Energy Transfer (FRET) quenching. In this application note, nanomolar concentrations of complementary DNA were quantified using a molecular beacon while controlling the temperature of incubation and measuring the sample emission with a spectrofluorometer.
