Scorpion Probe

What is Scorpion Probe?

Scorpion Probe Structure

Scorpion probes consist of probe sequences, primer sequences, and PCR terminators. The probe sequence is similar to that of a molecular beacon, with a fluorescent group at the 5' end and a quenching group at the 3' end, and exhibits a stem-loop structure. Unlike molecular beacons, scorpion probes have a specific primer that binds to the corresponding target nucleic acid. The amplification product is obtained by polymerization and extension under the action of Taq DNA polymerase, and the sequence of the carried probe can exactly hybridize with the complementary sequence in the specific product at the extended end.

The structure of the Scorpion probe. - BOC SciencesFigure 1. The structure of the Scorpion probe.

  • 3' Burster: In the hairpin structure of the Scorpion probe, the bursting agent and the fluorescent reporter group are in close proximity to each other and do not fluoresce.
  • 5' Fluorophore: When the Scorpion probe undergoes linearization and hybridizes to the target sequence, the reporter dye and the bursting agent separate and emit fluorescence.
  • Stem: A double-stranded region formed by the binding of complementary sequences at both ends of the Scorpion probe, typically 5-7 nt in length.
  • Loop: The loop is a sequence that is complementary to the target sequence with a length of typically 18-30 nt.
  • Primer Sequence: Target-specific PCR primers are covalently attached to the 3' end of the probe sequence by a closed portion, usually hexaethylene glycol (HEG)-modified.

Scorpion Probe Mechanism

As the amplification cycle progresses, the hairpin structure of the primer changes, where the ring structure is opened. This allows the internal sequences of the Scorpion probe to hybridize to the target sequence and separate the bursting agent from the fluorescent reporter molecule. Subsequently, the Scorpion probe fluoresces.

The mechanism of the Scorpion probe. - BOC SciencesFigure 2. The mechanism of the Scorpion probe.

BOC Sciences' Custom Scorpion Probe Service

Scorpion probes can be specifically designed for qPCR with the advantage of high sensitivity and sequence specificity. The unique properties of Scorpions primers enable reliable probe design with stronger signals, shorter reaction times and better discrimination than other bimolecular systems. As an RNA expert, BOC Sciences offers you a one-stop shop for Scorpion probe customization, including sequence design, synthesis to validation, which can be applied in the following directions.

Scorpion probes in testing experiment.

  • Genotyping Assay
  • Allele Testing
  • Multiplexing Analysis
  • Genomic Expression Analysis
  • Gene Copy Assay
  • Single Nucleotide Polymorphism(SNP) Analysis
  • Real-time PCR
  • Virus Detection

We offer customization of Scorpion probes with a variety of 5' dye and 3' bursting agent pairing options. You can choose the desired bursting agent and we'll come to you with a choice of fluorescent reporting dyes that can be matched. Or, conversely, you provide the fluorescent reporter dye requirements and we will advise you on the choice of bursting agent.

(1) 3' Bursting Agent Choosing List in BOC Sciences

BursterQuenching RangeQuenching MaxPCR BlockerPrice
BHQ-1480-580 nm535 nmHEGInquiry
BHQ-2550-650 nm579 nmHEGInquiry
BHQ-3550-650 nm672 nmHEGInquiry
BBQ-650550-750 nm650 nmHEGInquiry
ECLIPSE390-625 nm522 nmHEGInquiry
DABCYL380-550 nm452 nmHEGInquiry
TAMRA470-560 nm544 nmHEGInquiry

(2) 5' Dye Choosing List in BOC Sciences

ATTO-390(ex: 390 nm, em: 476 nm)ATTO-425(ex: 439nm, em: 485 nm)LCCyan500(ex: 439nm, em: 485 nm)
6-FAM(ex: 495 nm, em: 520 nm)Fluo(ex: 495 nm, em: 520 nm)FITC(ex: 490 nm, em: 525 nm)
ATTO-495(ex: 498 nm, em: 526 nm)TET(ex: 521 nm, em: 536 nm)ATT0-520(ex: 517nm, em: 538nm)
JOE(ex: 522 nm, em: 548 nm)Yakima Yellow(ex: 530 nm, em: 549 nm)HEX(ex: 535 nm, em: 556 nm)
ATTO-Rho6G(ex: 533 nm, em: 557 nm)Cy3(ex: 546 nm, em: 563 nm)TAMRA(ex: 564 nm, em: 579 nm)
ROX(ex: 576 nm, em: 601 nm)Texas Red(ex: 586 nm, em: 610 nm)LCRed610(ex: 590 nm, em: 610 nm)
ATTO-Rho13(ex: 603 nm, em: 627 nm)DY480XL(ex: 500 nm, em: 630 nm)ATTO-Rho14(ex: 625 nm, em: 646 nm)
LCRed640(ex: 625 nm, em: 640 nm)Cy5.5(ex: 683 nm, em:705 nm)IRD700(ex: 685 nm, em: 705 nm)

Advantages of BOC Sciences' Custom Scorpion Probe Service

  • Each oligonucleotide from BOC Sciences is quality checked by electrospray ionization mass spectrometry (ESI-MS), capillary electrophoresis (CE), and polyacrylamide gel electrophoresis (PAGE).
  • BOC Sciences has a specialized oligonucleotide synthesis platform that minimizes synthesis time and offers competitive pricing for large-scale synthesis.
  • BOC Sciences ensures that high purity and low background noise probes are made using fine purification techniques.
  • BOC Sciences' Scorpion probe has a wide range and potential of applications in the field of detection and diagnostics.

For additional probe designs, larger mole quantities, large orders, or other special requests, please feel free to contact us.

* Only for research. Not suitable for any diagnostic or therapeutic use.
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