Self-reporting real-time PCR probes that combine primer and probe function into a single molecule for rapid, highly specific fluorescence detection.
Scorpions® primers are intramolecular qPCR probes designed for fast signal kinetics, strong allele discrimination, and low background fluorescence
Primers are specialized self-reporting real-time PCR probes that integrate a PCR primer and probe sequence into a single oligonucleotide. The probe region is typically held in a stem-loop structure containing a fluorophore and quencher, while a PCR-blocking moiety prevents polymerase extension into the probe region.
After primer extension, the probe sequence hybridizes back to the newly synthesized target strand within the same molecule. This intramolecular probing mechanism separates the fluorophore from the quencher and produces fluorescence signal during amplification.
Because the probe is physically linked to the primer, Scorpions® technology can provide rapid signal generation, high specificity, and low background fluorescence for demanding qPCR and genotyping workflows.
Scorpions® intramolecular mechanism. The probe is linked to the primer, enabling rapid hybridization to the newly synthesized strand and fast fluorescence generation without probe diffusion or cleavage.
Bio-Synthesis offers fixed-price Scorpions® primer/probe synthesis for real-time PCR and genotyping applications. Scorpions® primers include a DNA probing sequence held in a stem-loop conformation with a 5′ reporter dye, an internal quencher, and an HEG blocker linking the probe to the PCR primer.
Standard Scorpions® primers are HPLC purified, QC checked by MALDI-TOF MS and analytical HPLC, delivered lyophilized, and are typically supplied in 4–6 working days.
*Includes dual HPLC purification and mass check.
Some reporter dyes may quench with less-than-optimal efficiency but can still be used in properly designed hairpin probes.
Scorpions® primers are commonly compared with TaqMan® probes and Molecular Beacons in real-time PCR applications. The key difference lies in the detection mechanism, which directly impacts signal speed, specificity, and assay performance.
Intramolecular hybridization reduces probe diffusion limitations and produces fluorescence earlier in PCR cycles.
Excellent for SNP genotyping, mutation detection, and allele discrimination assays.
The hairpin structure keeps fluorophore and quencher close until target-dependent activation.
Primer and probe are integrated into one molecule, simplifying assay design.
Reliable for low-copy targets, rapid cycling, and high-sensitivity applications.
Flexible fluorophores, quenchers, blockers, purification, and QC options tailored to your assay.
Successful Scorpions® probe performance depends on careful coordination between primer design, probe sequence, stem-loop stability, fluorophore–quencher pairing, and PCR-blocking chemistry.
Bio-Synthesis provides custom Scorpions® primer and probe synthesis with options for fluorophore–quencher selection, PCR blocker incorporation, purification, and analytical QC documentation.
Single-molecule Scorpions® designs incorporating primer, probe, stem-loop, fluorophore, quencher, and blocker elements.
Common fluorophore and quencher combinations can be selected based on assay platform and spectral requirements.
HPLC, PAGE, or custom purification strategies can be selected based on length, label complexity, and application.
Mass confirmation, HPLC purity, and supporting analytical documentation can be provided depending on project scope.
Support for research, assay development, validation lots, and recurring production requirements.
Discuss design, feasibility, fluorescence channels, synthesis complexity, and delivery requirements with our team.
Scorpions® primers are self-reporting real-time PCR probes that combine a PCR primer and probe sequence into one molecule. They generate fluorescence after primer extension when the probe hybridizes intramolecularly to the new target strand.
Scorpions® primers use intramolecular hybridization, while TaqMan® probes are separate probes that generate signal through nuclease cleavage during PCR.
Scorpions® are useful when rapid signal generation, low background, and strong mismatch discrimination are important, such as SNP genotyping, mutation detection, and allele discrimination.
Yes. Scorpions® designs are well suited for SNP genotyping because the probe can be positioned to strongly discriminate matched and mismatched targets.
Yes. Bio-Synthesis provides custom Scorpions® primer synthesis with fluorophore, quencher, PCR blocker, purification, and QC options.
Send the target sequence, desired primer/probe design if available, mutation or SNP position, fluorophore/quencher preference, purification requirement, quantity, and intended application.
For the fastest review, send your target sequence, desired Scorpions® design, mutation or SNP position, fluorophore/quencher requirements, quantity, purification preference, and intended application.
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