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.
Figure 1. The structure of the Scorpion probe.
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.
Figure 2. The mechanism of the Scorpion probe.
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.
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.
| Burster | Quenching Range | Quenching Max | PCR Blocker | Price |
| BHQ-1 | 480-580 nm | 535 nm | HEG | Inquiry |
| BHQ-2 | 550-650 nm | 579 nm | HEG | Inquiry |
| BHQ-3 | 550-650 nm | 672 nm | HEG | Inquiry |
| BBQ-650 | 550-750 nm | 650 nm | HEG | Inquiry |
| ECLIPSE | 390-625 nm | 522 nm | HEG | Inquiry |
| DABCYL | 380-550 nm | 452 nm | HEG | Inquiry |
| TAMRA | 470-560 nm | 544 nm | HEG | Inquiry |
| 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) |
For additional probe designs, larger mole quantities, large orders, or other special requests, please feel free to contact us.
Scorpion probes integrate both primer and detection functions in a single molecule, featuring a stem-loop structure with covalently linked primer sequences that enable intramolecular detection during amplification.
The stem-loop structure maintains close proximity between fluorophore and quencher until target binding occurs, minimizing background fluorescence while ensuring specific signal generation only upon successful hybridization.
Stem length typically ranges from 5-7 nucleotides, balanced to maintain stable hairpin structure while allowing efficient unfolding during target hybridization for optimal signal-to-noise ratio.
SNP analysis, genotyping assays, and multiplex detection systems particularly benefit from Scorpion probes due to their high specificity and single-molecule detection mechanism.
Selection is based on spectral overlap characteristics, with common pairs including FAM-BHQ1 for green channels and ROX-BHQ2 for red channels, matched to instrument detection capabilities.
