Molecular Beacons

Molecular Beacons are structured probes that are highly sensitive, sequence-specific and used for sequence detection in real-time 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:

• End-point genotyping
• In vitro quantification or detection studies
• Multiplexing
• SNP detection
• Allelic discrimination
• Pathogen 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 gene quantitation and allelic discrimination
• Easier and more sensitive probe designs for problematic target sequences

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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 dye, respectively. The loop is a single-stranded DNA sequence complementary to the target sequence. The close proximity of the reporter and quencher dyes 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 dye. As the quencher dye 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:

• Available in lengths of 15–40 bases
• Simple pricing – HPLC purification and base charges are included
• Stringent quality control including electrospray mass spectroscopy
• Shipped within 5–6 business days for 6-FAM™, HEX™, or TET™ labeled
• Shipped in an amber tube to protect dye integrity
• Custom formats available (normalization, special plates, etc.)

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

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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 probe and/or assays, submit your request at sigma.com/designmyprobe.

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