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.

Choose Molecular Beacons for:

  • 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 include:

  • Probe preserved during the reaction
  • Increased specificity

Add LNA to Your Probe for:

  • Increased thermal stability and hybridization specificity
  • Greater accuracy in SNP detection, allele discrimination and in vitro quantification or detection
  • 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 close 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.

How Molecular Beacons Work

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.

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.

Guaranteed Yields

Guaranteed
OD Yield
Approx. No.
of nmoles
Approx. No.
of µg
Approx. No.
of Reactions*
1 3 32 600
3 9 96 1,800
5 15 160 3,000
10 30 320 6,000

*Estimate is based on 3 nmoles or 32 µg for 1 OD and 200 nM in 25 µl reaction (5.0 pmol/reaction). Estimate is based on an average sequence length of 30 bases.

The most common fluorophore and quencher combinations are listed below:

Spectral Properties Table

Dye Max.
EX (nm)
Max.
EM (nm)
Compatible
Quencher
6-FAM™ 494 515 BHQ-1, DABCYL
Fluorescein 495 520 BHQ-1, DABCYL
JOE™ 520 548 BHQ-1, DABCYL
TET™ 521 536 BHQ-1, DABCYL
HEX™ 535 555 BHQ-1, DABCYL
Cyanine 3 550 570 BHQ-2, DABCYL
ROX™ 573 602 BHQ-2, DABCYL
Texas Red® 583 603 BHQ-2, DABCYL
Cyanine 5 651 674 BHQ-3, DABCYL
Cyanine 5.5 675 694 BHQ-3, DABCYL

Materials