Molecular Beacon Probes
Molecular Beacons are hairpin-shaped oligonucleotide probes. The 5′ end of the molecular beacon is labeled with a fluorophore (e.g., FAM, HEX), and the 3′ end is labeled with a quencher (e.g., DABCYL, BHQ). In the absence of a target, the proximity of the quencher suppresses the fluorescence of the fluorophore. When the probe binds to the target sequence, the hairpin opens, separating the fluorophore and quencher and resulting in fluorescence emission. The stem-loop structure of molecular beacons keeps them in a hairpin conformation when unbound. This conformation prevents the interaction of the fluorophore with the surrounding environment, minimizing background fluorescence.
Molecular beacons offer high specificity and enable the quantification of viral RNA or DNA in a sample by providing real-time fluorescence signals proportional to the amount of amplified nucleic acid during PCR. Molecular beacons can be employed for genotyping and mutation analysis of viral genomes. The sequence specificity of the beacon allows discrimination between different viral strains or the identification of specific mutations.
The principles of molecular beacon probes, with their stem-loop structure and real-time monitoring capabilities, make them versatile tools for the detection and analysis of viruses, contributing to various applications in molecular diagnostics and research.