AAT Bioquest

What are molecular beacons used for?

Posted August 29, 2023


Molecular beacons are used in a wide variety of applications such as SNP detection, gene copy determination, pathogen detection, multiplexing, viral load quantification, and endpoint genotyping. Molecular beacons use PCR for the high-throughput screening of SNPs in homogeneous assays. Viral load assays utilizing homogeneous detection with MB include NucliSense EasyQ HIV-1 assay. Molecular beacons may use MB-based junction probes to achieve rapid, and highly sensitive detection of sequence-specific oligonucleotides and a strong SNP identifying capability. Real time PCR experiments in which multiple molecular beacons with different colored fluorophores are also utilized to detect multiple targets in the same tube. MBs are also adapted to be used in microarray analysis for detection of gene sequences relative to specific disease states. Thus, it is suitable for simultaneous detection of hundreds of DNA target sequences in one test run using a series of beacons. MBs are also used alongside nucleic acid sequence based amplification (NASBA) assays to provide a real-time analysis tool, which functions faster than the RT-PCR technique. This offers several advantages as there is a low probability of pollution and the isothermy of the reaction. Additionally, NASBA is used for pathogen detection.   

Additional resources

Molecular Beacon

Real-Time PCR (qPCR)

Tide Fluor™ 1 acid [TF1 acid] *Superior replacement for EDANS*