In this assay, an oligonucleotide probe (molecular beacon) is used, which consists of the target SNP sequence, with its two ends being complementary to each other. The two ends of the' oligonucleotide are labelled just like the oligonucleotide probe used in TaqMan assay.
The probe, when fails to form a duplex with the template DNA, generates a hairpin structure due to self-annealing of its two ends, thus quenching the reporter.
But when the probe anneals with the template, it gets linearized, thus separating the reporter from quencher and permitting fluorescence signal.
The fluorescence signals, both in TaqMan and molecular beacon can be detected by appropriate sensing devices.
Use of Molecular Beacon as a probe for Detection
1. Molecular Beacon (Non-fluorescent due to hairpin structure)
