Molecular Beacons


Beginning May 8, 2022, BHQ® (Black Hole Quencher®) 1 and 2 will no longer be available as a modification to Custom DNA Oligos and Custom qPCR Probes. The replacements will be BXQ™ (Block All Quencher™) 1 and 2. Information about the BXQ dark quenchers will be added from time-to-time to key oligo landing pages up until the date of change. As these key landing pages are updated, this message will be updated to provide links to the new information. If you have any questions, please contact your local company representative. Alternatively, to learn more about BXQ, please visit the manufacturer’s website:  BXQ | AAT Bioquest.

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 Applications

  • 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

  • Probe preserved during the reaction
  • Increased specificity


Add Locked Nucleic Acid to Your Probe

  • Increase 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.

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

  • 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.)

Our probes are provided in a format to simplify your experimental planning.


Guaranteed Yields

OD Yield
Approx. nmol Approx. 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 nmol 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)
EM (nm)
6-FAM™ 495 520 BHQ-1, DABCYL
JOE™ 529 555 BHQ-1, DABCYL
TET™ 521 536 BHQ-1, DABCYL
HEX™ 535 556 BHQ-1, DABCYL
Cyanine 3 549 566 BHQ-2, DABCYL
ROX™ 586 610 BHQ-2, DABCYL
TxRd (Sulforhodamine 101-X) 597 616 BHQ-2, DABCYL
Cyanine 5 646 669 BHQ-3, DABCYL
Cyanine 5.5 675 694 BHQ-3, DABCYL

Shipping Schedule

Quantity (OD) 1 3 5 10
Molecular Beacons with Standard Dyes 5 days 5 days 5 days 5 days
Locked Nucleic Acid Molecular Beacons with Standard Dyes 7 days 7 days 7 days 7 days
Molecular Beacons with Post-Synthesis Dyes, with/without Locked Nucleic Acid
7-10 days 7-10 days 7-10 days 7-10 days

*Delivery times may be longer due to international transit, customs clearance delays, etc. Large projects will be placed on a delivery schedule based upon project needs.