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Molecular Beacon probes

Product info

Molecular Beacon probes are dual-labelled probes that form a stem-loop (hairpin) structure, bringing the reporter and quencher into proximity. The loop region contains the sequence that hybridises to the target sequence, while the complementary sequences at both ends of the probe form the stem. These probes generate fluorescence under non-hydrolytic conditions via hybridisation to the target.

Molecular Beacon structure:

  • 5′ fluorophore: The reporter dye emits fluorescence when the probe is linearised and hybridised to the target, separating the dye and quencher.
  • 3′ quencher: When the probe is in its hairpin structure, the proximity of the quencher to the reporter prevents fluorescence emission.
  • Stem: The stem is a double-stranded region formed by binding the complementary sequences (5-7 nt) at both ends of the probe.
  • Loop: The loop is a 18-30 nt sequence that is complementary to the target sequence.

 

Key benefits:

  • Enhanced specificity: The stem-loop conformation confers high specificity, making molecular beacons ideal for SNP/mismatch discrimination.
  • High signal-to-noise: Superior fluorophore quenching due to the proximity and the direct energy transfer between reporter and quencher while in the closed hairpin conformation.
  • Melt curve analysis suitability: Because molecular beacons generate fluorescence under non-hydrolytic conditions by target hybridisation, post-PCR melt curve analysis can be performed.
 
Order Molecular Beacon probes

Select the best dye for your application

We offer molecular beacon probes labelled with a wide selection of dyes, enabling you to select options based on instrumentation and assay design. Quencher options for this probe type include Black Hole Quenchers (BHQ-1 and BHQ-2) and DABCYL dye.

5' fluorescent dye

Abs (nm)

Em (nm)

3' quencher
  FAM 495 520 BHQ-1, DABCYL
  TET 521 536 BHQ-1, DABCYL
  CAL Fluor Gold 540 522 544 BHQ-1, DABCYL
  CIV-550 530 550 BHQ-1, DABCYL
  JOE 529 555 BHQ-1, DABCYL
  HEX 535 556 BHQ-1, DABCYL
  CAL Fluor Orange 560 538 559 BHQ-1, DABCYL
  Quasar 570 548 566 BHQ-2, DABCYL
  Cy3 549 566 BHQ-2
  TAMRA 557 583 BHQ-2, DABCYL
  CAL Fluor Red 590 569 591 BHQ-2
  ROX 586 610 BHQ-2, DABCYL
  CAL Fluor Red 610 590 610 BHQ-2, DABCYL
  CAL Fluor Red 635 618 637 BHQ-2
  Cy5 646 669 BHQ-2
  Quasar 670 647 670 BHQ-2
  Quasar 705 690 705 BHQ-2

Use the spectral overlay tool to view compatible dyes for your instrument. Learn more

Order now

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  • Oligos for North America, South America, and APAC will be supplied out of our Petaluma, US manufacturing facility while oligos for EMEA will be supplied out of our Lystrup, Denmark manufacturing facility unless you have an agreement in place.
  • Our advertised turnaround time applies to orders received before 12PM for the local manufacturing site. Turnaround time is defined as the time of checkout until shipment.
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Are you trying to include RNA bases? RNA bases are not allowed in standard BHQ probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in BHQnova probes and so the R character will be treated as a DNA wobble instead (A/G). Please click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in standard BHQplus probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in standard MGB probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
RNA bases are not allowed in standard Molecular Beacons. Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Inosine modifications are not allowed in standard BHQ probes. Please order on the custom oligo form custom oligo form or click here for help.
Inosine modifications are not allowed in standard Nova probes. Please order on the custom oligo form custom oligo form or click here for help.
An invalid character has been entered into this sequence. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
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Illegal character(s) were entered. Please review your sequence information.
Internal modifications are not allowed in standard Molecular Beacons. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
Internal modifications are not allowed in standard BHQplus probes. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
Internal modifications are not allowed in standard MGB probes. For additional assistance, click here for help.
Internal modifications are not allowed in standard Nova probes. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
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This oligo contains a number of 'wobbles'. Please consider limiting this to one trinucleotide wobble and one dinucleotide wobble in two different locations or three dinucleotide wobbles in three different locations such that there is a maximum of 6 variants in a single oligonucleotide.
Inosine modifications must be included in brackets such as [I] or [i].
Internal modifications are not allowed in standard primers. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
No special modifications are allowed in BHQplus® probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
No special modifications are allowed in MGB probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
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This oligo contains a number of 'wobbles'. Please consider limiting this to one trinucleotide wobble and one dinucleotide wobble in two different locations or three dinucleotide wobbles in three different locations such that there is a maximum of 6 variants in a single oligonucleotide.
Inosine modifications must be included in brackets such as [I] or [i].
Internal modifications are not allowed in standard primers. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
No special modifications are allowed in BHQplus® probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
No special modifications are allowed in MGB probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
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Product listing

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Technical Specs

Molecular Beacon Probe specifications
Dyes FAM, TET, CAL Fluor gold 540, CIV-550, JOE, HEX, CAL Fluor Orange 560, Quasar 570, TAMRA, CAL Fluor Red 590, ROX, CAL Fluor Red 610, CAL Fluor Red 635, Cy5, Cy3, Quasar 670, Quasar 705
Quenchers BHQ-1, BHQ-2, DABCYL
Yield Dye dependent (see product listing)
Purification DUAL HPLC
Delivery format Dry or in solution (water, TrisHCl, T10E0.1, T10E1)
Quality control MS and UHPLC
Quality standard ISO 9001 or ISO 13485
Shelf life 12 months from date of manufacture

 

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