Molecular beacons

Molecular beacon


Molecular beacons are highly sensitive, structured probes. They are used for sequence-specific detection in quantitative Real-Time PCR. Ideal for discriminating single nucleotide polymorphisms (SNPs).


Molecular beacons for Real-Time PCR can be ordered in our webshop or by email. Download our excel orderform for ordering by email or use it to upload multiple probes in our webshop.

Order your primes and probes delivered premixed according to your specifications. All fluorophore -quencher combinations are possible, ideal for Real-Time PCR applications.

With our oligo prepaid service we make oligo ordering easy. Credit can be easily transferred to your account. Oligos can then be ordered immediately, eliminating possible delays due to purchase authorization. Please contact Biolegio for more information.

You can fit your Real-Time PCR probe with numerous fluorophores and quenchers from an extensive list of modifications. 

>view fluorophores            >view quenchers

Quencher and dye compatibility

Molecular Beacons are synthesized with a quencher at the 3'-site and a fluorophore at the 5'-site. The most frequently used quencher at this moment is Dabcyl. However, there are other quenchers available. As a fluorophore you can choose between different dyes. The most commonly dyes used are FAM, HEX, TET, TAMRA, Cy3 and Cy5. 

Please follow the link below for a compatibility figure. For multiplexing applications use fluorophores with the least amount of spectral overlap.

>Fluorophores vs Quenchers compatibility

How can I fit modifications to my custom Real-Time PCR probe?

Select the modifications of your choice in our webshop or in our excel ordering sheet. In the webshop you can have instant pricing insight. Select 'TDP probe' in the orderform as the chemistry used for ordering Twice Dyed Probes probes.

How can I add mixed bases to my oligo?

Use the standard code letters for mixed bases / wobbles

All Real-Time PCR probes are delivered HPLC purified, this is included in the price. 

>more about purification

Real-Time PCR probe scale and length

Biolegio three different synthesis scales for Real-Time PCR probes oligos: 40 nmol, 200 nmol and 1000 nmol. Prices include synthesis of maximum 40 nucleotides.

Yield Real-Time PCR probes

40 nmol scale:    approx. 8 nmol min. yield
200 nmol scale:   approx. 20 nmol min. yield
1000 nmol scale: approx. 60 nmol min. yield


Biolegio has three synthesis protocols: 'Economy' , 'High Purity' and 'B-pure'. The used protocol depends on the length of the oligo. This means that the protocols have been optimized for certain oligo lengths. 

  • Economy protocol is used for oligos between 2 and 49 bases.
  • High purity protocol is used for oligos between 49 and 79 bases. 
  • All DNA oligos longer than 80 bases are synthesized on our B-pure synthesis protocol.

Each protocol delivers the highest possible coupling efficiency for the specified range. 

Your Real-Time PCR probe can be shipped dry or dissolved or mixed. Standard probes are delivered dissolved in a tube in a concentration of 100 pmol/μl.

Available buffers
  • H20 buffer
  • LoTE buffer
  • TE buffer
Your primers and probes delivered as a ready-to-use assay?

Probes can be delivered in any format, concentration or combination. Have a look at our oligo dispensing service for more information about this topic.

All your DNA oligos are delivered with a specification sheet including GC-content, molecular weight, melting temperature (Tm), OD value, sequence and quantity in μgram and nmol. 

A stringent quality control system ensures that you can expect the quality of our oligonucleotides to be of the highest standard. Before the synthesis, all chemicals are checked to meet our quality standards. During the fully automated oligo synthesis, all steps of the synthesis are monitored by multiple control functions on our DNA synthesizers. This way we can assure the coupling efficiency of the synthesis to meet our demands.

Synthesis is followed by further quality controls to guarantee the quality of the oligos. All oligos are routinely analyzed by optical density (OD) measurement. In addition, oligos are randomly analyzed by gel electrophoresis and Liquid Chromatography Mass Spectrometry (LCMS). If an oligo does not meet our requirement it’s resynthesized. The result of our stringent QC process is a product of the highest standard. All oligos are delivered with our product specification sheet, which includes: % GC content, yield in nmol and μgram, OD, melting temperature and molecular weight (MW).


ISO quality management

ISO 9001             


ISO is an independent, non-governmental membership organisation and the worlds largest developer of voluntary international standards. Biolegio’s manufacturing facility is ISO 9001:2008 and ISO 13485:2003 certified. Achieving these certificates ensures good, reliable and safe products as a result of strong product quality and manufacturing procedures and an ongoing development of our quality management system. This ongoing development empowers us to continuously strengthen our ability to identify and exceed the needs and expectations of our customers.