Scorpions Primers are highly sensitive, sequence specific dual labeled, hairpin, uni-probes that combine a target specific PCR primer with a target specific DNA probing sequence in a single molecule design. This uni-molecular mechanism results in faster kinetic reaction and lead to instantaneous generation of a fluorescent signal in real-time qPCR without incurring any competing side reactions. These primers do not require enzymatic cleavage of the probe during PCR cycling. The unique properties of Scorpions Primers enable reliable probe design with stronger signals, shorter reaction times and better discrimination power than other bi-molecular systems. Scorpions probes offer valuable tools for rapid, real-time PCR, endpoint PCR, SNP detection and gene quantification.

All Bio-Synthesis's Scorpion Primers are available at a fixed price per oligonucleotide, within the following parameters:

  • DNA up 30-60 bases (Uni-probe) and 15-45 bases (Bi-probe)
  • 5' fluorophore, internal quencher and capped by HEG blockers
  • BNA are available
  • All HPLC purified
  • 100% QC by MALDI-TOF MS, analytical HPLC
  • Deliver lyophilized
  • TAT of 4-6 working days
  • Custom formulation available

Benefit of Using Scorpion Probes:

  • Increased specificity
  • Fast amplification detection
  • Exceptional signal-to-noise using bi-probe system

Scorpions Probe Applications:

  • Single type genotyping Assays
  • SNP detection
  • Allele discrimination
  • Multiplexing
  • Gene expression analysis
  • Gene copy determination
  • Pathogen detection
  • Viral load quantification

How Do Scorpion Probes Work?

Scorpion Primers and Probes

Design of Scorpion Probes:

  1. Amplicon Length: The primer pair should be designed to give an amplicon of approximately 100-200 bp.
  2. Secondary Structures: The designed primers should be tested for hairpins and secondary structures. Ideally the primers should have as little secondary structure as possible.
  3. Tm Criteria: The Tm's of the two primers should be similar. Also, the stem Tm should be 5-10oC higher than the probe Tm.
  4. Complementary Probe: The scorpion® should be written as the reverse complement of the target.
  5. Length Criteria: Probe sequences should ideally be about 17-27 bases Also, the probe target should be 11 bases or less from the 3' end of the scorpion®.
  6. Probe Stem: The stem sequence can be of 6 to 7 bases, mostly Cs and Gs, avoiding motifs. The 5' stem sequence should begin with a C as G may quench the FAM.
  7. Primer Probe Hybridization: There is always the possibility of the primer hybridizing to the probe element, this will lead to linearization of the probe in an amplification-independent manner causing significant, target-independent fluorescence.


  1. Pals, G., et al., Detection of a single base substitution in a single cell using the LightCycler. J. Biochem. Biophys. Methods, 47, 121-129 (2001)

Enhanced your Detection with BNA Enhanced Scorpions Primers for

  • Increased thermal stability and hybridization specificity
  • Greater accuracy in SNP detection and allele discrimination
  • Easier and more sensitive probe designs for problematic target sequences

Learn more about Bridged Nucleic Acids (BNAs).

Scorpion Probes for Real-time PCR and Genotyping

All scorpions primers include DNA probing sequences held in a stem-loop conformation with a 5' reporter dye and an internal quencher dye directly linked to the 5' end of a PCR primer via a hexathylene glycol blocker. These probes are HPLC purified and controlled by MALDI-TOF Mass Spectrometry and deliver in lyophilized format.

Please browse our selection below to find a suitable dye and quencher combination, or you may contact us

Guarantee Delivered Quantity (nmol)*
Guaranteed OD260 Estimate No. of nmol* Estimate No. of µg Estimate No. of Reactions max. Length
1 2 32 400 60 mer
5 10 160 2,000 60 mer
10 20 320 4,000 60 mer
20 40 640 8,000 60 mer

* including dual HPLC and Mass Check

For probe design, larger molar amounts, large volume orders or other special requests, please contact us at info@biosyn.com

Uni-Probe: 5' Flurophore Internal Quenchers Blocker
6-FAMTM, TET, JOE, HEX, Cy3, (Tamra)*, (Cy3.5)*, (Rox)*, (Texas Red)* Dabcyl, dT HEG
6-FAMTM, HEXTM, TETTM, JOETM, Oregon Green 514, Bodipy R6G-X, Cy3, Rodamine Red-X, TAMRA BHQ1 HEG
HEX, TAMRATM, Texas Red®, ROXTM, Cy3, Cy3.5, Texas Red-X, Bodipy TR-X, LightCycler 630, Rhodamine RedTM, (CY5)* BHQ1 HEG
Cy5, Cy5.5. BHQ3 HEG

* Dyes indicated in parentheses are reporter groups that quench with less than optimal efficiency but can still be used in probes having hairpin design.

*Estimate is based on 2 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 50 bases (uni-probe).


In order to ensure that there is no background fluorescence, 100% of the dual labeled probes are purified by single or dual rp-HPLC and ie-HPLC as a standard protocol for all dual–labeled probes which give 90-97% purity. Depending on the type of the probes, one or two purification may performed to ensure the highest purity level

Quality Control

All dual labeled probes are quality checked by MALDI-TOP Mass spectrometry , analytical HPLC and analyze by Fluorometric Scan (ABS/EM) . In addition, the signal-to-background ratio is measured against a target sequence for all molecular beacons.

Delivery times

3-5 Working days



Shipping conditions

Room temperature

Storage conditions  

-20 oC to -70 oC

Oligonucleotides are stable in solution at 4oC for up to 2 weeks. Properly reconstituted material stored at -20oC should be stable for at least 6 months. Lyophilized DNA (when kept at -20oC) in a nuclease-free environment should be stable for year


Quality control:

Every oligo is quality checked by MALDI-TOF mass spectrometry, electrospray ionization mass spectrometry (ESI-MS), capillary electrophoresis (CE), and/or polyacrylamide gel electrophoresis (PAGE).


Fully deprotected and desalted. Purified by PAGE or RP-HPLC


LightCycler probes 15 to 40 mers (optimal length: 20 to 30 mers)
Dual-labeled fluorogenic probes: 15 to 40 mers
Molecular Beacons 15 to 40 mers
Scorpions probes 30 to 60 mers (uni-probe)
15 to 45 mers (bi-probe)
Plexor up to 30 mers


Phosphodiester bond


Delivered as dried-down product in opaque tubes

Turn-around time:

Turn-around time
LightCycler probes 4 to 5 working days
Dual-labeled fluorogenic probes: 5 to 6 working days
Molecular Beacons 5 to 6 working days
Scorpions probes 7 to 10 working days

Turn-around time is dependent upon successful QC validation and does not include shipping time.

Storage and stability:

See information on our oligos: storage recommendations


Shipped by mail or express delivery, dry, in individual, opaque tubes

Technical Documentation:

Oligonucleotides are delivered with an Oligonucleotide Technical Data Sheet, which includes oligonucleotide name, sequence, concentration, precise quantity in OD and nmols, Tm, MW, length, extinction coefficient and purification data.

Additional Services:

  • Probe design services
  • High-throughput screening formats (microplates, etc)
  • Aliquoting

Additional services may increase turn-around time


Please contact your local Bio-Synthesis representative


On-line (contact us), by email (info@biosyn.com) or fax

Ordering & Contact Information

  • Please contact us for additional information or send an email to info@biosyn.com.
  • You may also request an online quote.
  • To contact us by phone, please Call 972-420-8505 (USA) 800-227-0627 (INTL.) or Fax 972.420.0442
  • Orders may be placed using a purchase order (PO) or by credit card through our secure online ordering system.
  • When using a credit card ( creditcard ) it will be billed under "Bio-Synthesis, Inc."