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Molecular Beacons

Highest specificity with Molecular Beacons

Molecular Beacons are hairpin shaped hybridisation probes with a 3‘ fluorescent dye and 5‘ quencher. This sequence structure makes Molecular Beacons highly specific and is therefore often used in clinical or diagnostic assays.

Product specifications:

  • Available synthesis scales: 50 nmole - 1.0 µmole
  • Probe lengths: 5-40 bases (wobbles non-defined ratio possible)
  • HPLC purified by default
  • TAT: 3–5 working days (1.0 µmole scale takes longer)
  • Delivery format: dried or liquid at selected concentration
  • QC report incl. ESI

A ready-to-use qPCR probe dilution buffer (10 mM Tris-HCl; 1 mM EDTA; pH 8) is provided along with all probes (1 ml for up to 3 probes).


Molecular Beacons are ordered from the custom DNA order page by selecting the desired 5' and 3' modifications (dye-quencher combo). Go to custom order page.

Available dye-quencher combinations:

5' Reporter Abs [nm] Em [nm] 3' Quencher
495 520 TAM, BHQ1, DAB, Eclip
TET [5TET] 521 536 DAB
JOE [JOE] 520 548 TAM
HEX [5HEX] 535 556 BHQ1, DAB
Cyanine3 [Cy3] 552 570 BHQ2, DAB
ROX [ROX] 575 602 BHQ2
Texas Red [TxRed] 583 603 BHQ2
Cyanine5 [Cy5]
649 670 BHQ2, BBQ650

Principle of molecular beacons

Molecular beacons contain a fluorescent reporter and a quencher at their 5' and 3' ends, respectively.

The sequence of these probes is designed to allow the formation of a hairpin structure in which the fluorescent dye and the quencher are in close proximity.

A molecular beacon specific for the sequence of interest is used in PCR. The probe is designed to anneal between the PCR primers.

When the probe hybridises to its target sequence in the PCR annealing step, the loop opens and the fluorescent reporter and quencher are separated, resulting in a fluorescent signal upon excitation. The amount of signal is proportional to the amount of target sequence, and is measured in real time to allow quantification of the amount of target sequence.



Additional Probe Options

Dual Labeled Probes

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LNA Probes

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MGB Probes

Order MGB Probes

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