Molecular beacons are structured probes that are highly sensitive, sequence specific, and are used for sequence detection in qPCR and in vitro studies. Molecular beacons can be used in a variety of applications including:
- SNP detection
- Allele discrimination
- Pathogen detection
- Multiplexing
- Viral load quantification
- Gene expression analysis
- Gene copy determination
- Endpoint genotyping
- in vitro quantification or detection
Benefits of Using Molecular Beacons are particularly useful because of the increased specificity and the probe is preserved during the reaction.
Add Locked Nucleic Acid to Your Probe
- Improve the thermal stability and hybridization specificity
- Obtain greater accuracy in SNP detection, allele discrimination and in vitro quantification or detection
- Achieve easier and more sensitive probe designs for problematic target sequences
How Molecular Beacons Work
A Molecular beacon is a single-stranded bi-labeled fluorescent probe held in a hairpin-loop conformation (around 20 to 25 nt) by complementary stem sequences (around 4 to 6 nt) at both ends of the probe. The 5’ and 3’ ends of the probe contain a reporter and a quencher molecule, respectively. The loop is a single-stranded DNA sequence complementary to the target sequence. The proximity of the reporter and quencher causes the quenching of the natural fluorescence emission of the reporter. The structure and mechanism of a molecular beacon is shown below.
Molecular beacons hybridize to their specific target sequence causing the hairpin-loop structure to open and separate the 5’ end reporter from the 3’ end quencher. As the quencher is no longer in proximity to the reporter, fluorescence emission takes place. The measured fluorescence signal is directly proportional to the amount of target DNA.
Design and Customize your qPCR Probes to best suit your application.
Spectral Properties Table
The most common fluorophore and quencher combinations are listed below:
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