Custom DNA Probes

Scorpions® Probes

Scorpions probes are highly sensitive, sequence-specific, bi-labeled fluorescent probe/primer hybrids designed for qPCR.


Choose Scorpions Probes for:

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

Because the probe and primer are incorporated into a single molecule, the reaction kinetics of this probe are extremely fast. The reaction leading to generation of a fluorescent signal is essentially instantaneous and occurs prior to any competing side reactions. This enables Scorpions probes to provide stronger signals, shorter reaction times and better discrimination than other conventional bi-molecular mechanisms. It also allows for more reliable probe design.

Benefits of Using Scorpions Probes include:

  • Increased specificity
  • Fast amplicon detection
  • Exceptional signal-to-noise (bi-probes typically yield stronger signal when compared to uni-probes)

Add LNA to Your Probe 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

How Uni-Probe Scorpions Probes Work

The Scorpions uni-probe consists of a single-stranded bi-labeled fluorescent probe sequence held in a hairpin-loop conformation with a 5' end reporter dye and an internal quencher dye directly linked to the 5' end of a PCR primer via a blocker. The blocker prevents the polymerase from extending the PCR primer.

At the beginning of the qPCR reaction, the polymerase extends the PCR primer and synthesizes the complementary strand of the specific target sequence. During the next cycle, the hairpin-loop unfolds and the loop-region of the probe hybridizes intramolecularly to the newly synthesized target sequence. Now that the reporter dye is no longer in close proximity to the quencher dye, fluorescence emission may take place. The fluorescent signal is detected by the qPCR instrument and is directly proportional to the amount of target DNA.

Product Features include:

  • Amounts: 1, 5, and 10 OD
  • Purification: HPLC
  • Sequence Lengths: 30 - 60 bases (Uni-probe) and 15 - 45 bases (Bi-probe)
  • Quality Control: 100% mass spectrometry
  • Format: Supplied dry in amber tubes
  • Custom formats available (normalization, special plates, etc.)

Sigma's probes are provided in a format to simplify your experimental planning.

Guaranteed Yields

OD Yield
Approx. No.
of nmoles
Approx. No.
of µg
Approx. No.
of Reactions*
1 2 32 400
5 10 160 2,000
10 20 320 4,000
*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).

The available fluorophore and quencher combinations are listed below. Scorpions Probes include a HEG (hexathylene glycol) blocker.


5' Fluorophore Internal Quencher
FLC, 6-FAM™, HEX™, TET™, TAMRA™, JOE™, ROX™, Cyanine 3, Cyanine 5, Cyanine 5.5, Texas Red®, Rhodamine, Rhodamine Green™, Rhodamine Red™, Oregon Green® 488, Oregon Green 500, Oregon Green 514 DABCYL dT, BHQ-1, BHQ-2, BHQ-3


5' Fluorophore Internal Quencher
FLC, 6-FAM, HEX, TET, TAMRA, JOE, ROX, Cyanine 3, Cyanine 5, Cyanine 5.5, Texas Red, Rhodamine, Rhodamine Green, Rhodamine Red, Oregon Green 488, Oregon Green 500, Oregon Green 514 TAMRA, DABYCL, BHQ-1, BHQ-2, BHQ-3

Sigma is a licensed supplier of a variety of dyes and quenchers and continually adds to its portfolio of new chemistries. For assistance in the design of your Scorpions Probes and assays, use our online design tool at


CleanAmp dNTPs