Molecular Beacons

Molecular Beacons are structured probes that are highly sensitive, sequence specific, and are used for sequence detection in qPCR and in vitro studies.

• When to Choose Molecular Beacons
• Benefits of Using Molecular Beacons
• Add LNA^® to Your Probe
• How Molecular Beacons Work
• Product Features
• Guaranteed Yields

Choose Molecular Beacons for:

• SNP detection
• Allele discrimination
• Pathogen detection
• Multiplexing
• Viral load quantification
• Gene expression analysis
• Gene copy determination
• End point genotyping
• in vitro quantification or detection

Benefits of Using Molecular Beacons include:

• Increased specificity
• Probe preserved during the reaction

Add LNA to Your Probe for:

• Increased thermal stability and hybridization specificity
• Greater accuracy in SNP detection and allele discrimination
• 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 dye and a quencher molecule, respectively. The loop is a single-stranded DNA sequence complementary to the target sequence. The close proximity of the reporter and quencher causes the quenching of the natural fluorescence emission of the reporter dye. 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 dye from the 3' end quencher. As the quencher is no longer in proximity to the reporter dye, fluorescence emission takes place. The measured fluorescence signal is directly proportional to the amount of target DNA.

Product Features include:

• Amounts: 1, 3, 5, and 10 OD
• Purification: HPLC
• Sequence Lengths: 15 - 40 bases
• Quality Control: 100% mass spectrometry
• Format: Supplied dry in amber tubes
• Custom formats available (normalizations, special plates, etc.)

Sigma's probes are provided in a format to simplify your experimental planning.

The most common fluorophore and quencher combinations are listed below:

Sigma is a licensed supplier of a variety of dyes and quenchers and continually adds to its portfolio of new chemistries. For assistance in the design of your Molecular Beacons and assays, use our online design tool at sigma.com/probedesignonline.

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