Our custom Scorpion probe synthesis services support biotechnology companies, assay developers, academic laboratories, and molecular assay development teams that need fast, sequence-specific fluorescent oligonucleotides for qPCR and related amplification workflows. A Scorpion probe combines a PCR primer and a stem-loop probe in a single construct, with a fluorophore, quencher, and polymerase-blocking linker arranged to produce intramolecular signal generation after amplification. Because assay performance depends on the interaction between primer placement, loop sequence, stem stability, blocker selection, and instrument channel compatibility, successful projects require more than routine oligonucleotide ordering.
Our platform integrates target review, Scorpion construct design, custom synthesis, purification planning, analytical characterization, and application-focused technical support. We help clients move from sequence concept to fit-for-purpose Scorpion probe delivery for SNP genotyping, allele discrimination, multiplex qPCR, gene expression studies, and assay redevelopment, while also supporting broader diagnostic probes & oligos programs for research and assay development.
The structure of the Scorpion probe.
Weak Allele Discrimination: Scorpion probes are often selected when teams need sharper mismatch recognition than standard probe formats can deliver. We review target position, probe length, primer relationship, and stem-loop behavior to improve discrimination of closely related variants in genotyping and mutation analysis workflows.
Background Signal and Spectral Crosstalk: High baseline fluorescence, poor quencher matching, or instrument-channel overlap can reduce assay confidence. Our service supports fluorophore-quencher pairing, multiplex channel planning, and construct architecture review to reduce background and improve signal separation.
Primer-Probe Structural Conflict: Because the primer and probe are physically linked, poorly balanced Scorpion designs can suffer from self-annealing, inefficient opening, or read-through risks if blocker selection is weak. We evaluate stem composition, loop complementarity, blocker placement, and primer behavior before synthesis to reduce avoidable redesign cycles.
Difficult Multiplex Translation: Moving from a single-target concept to a multiplex qPCR panel introduces challenges in dye spacing, Tm balancing, and amplicon coordination. We help align construct design and labeling strategy with instrument capabilities so multiplex projects are planned with fewer downstream compromises.
Redevelopment of Underperforming Assays: Many customers approach Scorpion chemistry after problems with slow signal generation, weak SNP calls, or unstable probe behavior in other qPCR formats. Our team supports comparative redesign planning, including review against TaqMan probes, molecular beacon probes, and dual-labeled probes, so the final construct is chosen for the actual assay problem rather than by habit.
Figure 2. The mechanism of the Scorpion probe.
Our Scorpion probe service is designed for customers who need coordinated support across sequence design, structural engineering, synthesis, and analytical review. We work with both new assay builds and rescue projects where an existing probe format is failing to provide the required speed, specificity, or multiplex compatibility.
The result is a service model that connects probe chemistry decisions directly to assay performance expectations, procurement requirements, and downstream experimental workflows.
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) |
This comparison table helps project teams decide when Scorpion chemistry is the right fit and when another probe architecture may be more practical based on assay speed, mismatch sensitivity, multiplex demands, and design flexibility.
| Probe Format | Core Detection Principle | Best Project Fit | Main Design Considerations | Typical Reason to Choose |
| Scorpion Probe | Primer and probe are linked in one construct, enabling intramolecular signal generation after amplification | Rapid qPCR readout, SNP discrimination, allele calling, and assay formats where fast signal development matters | Primer-probe geometry, stem-loop balance, blocker performance, and dye-channel compatibility | Strong specificity and fast signaling in demanding qPCR workflows |
| TaqMan Probe | Separate hydrolysis probe generates signal after cleavage during amplification | Broad qPCR adoption, routine quantification, and workflows that prioritize design familiarity | Cleavage efficiency, probe position, reporter-quencher pairing, and multiplex planning | Widely used format with straightforward assay transfer across many platforms |
| Molecular Beacon | Hairpin probe fluoresces when hybridization opens the stem-loop structure | High-specificity hybridization assays and workflows that benefit from non-hydrolytic signaling | Hairpin stability, target accessibility, and risk of slower bimolecular interaction | Useful when a standalone probe architecture is preferred over a linked primer-probe system |
| Dual-Labeled Probe | Linear probe uses reporter and quencher without Scorpion-style stem-loop architecture | Standard real-time PCR projects that need flexible probe placement and broad instrument compatibility | Probe length, Tm alignment, dye choice, and background control | Practical option for routine assay builds and broad multiplex adoption |
| MGB Probe | Minor groove binder raises target affinity, allowing shorter probes with stronger binding | Short targets, high-specificity variant detection, and assays with constrained design windows | Probe length, MGB placement, sequence context, and synthesis complexity | Better fit when short probe length is the main technical requirement |
Scorpion projects succeed when sequence design, probe architecture, and analytical planning are reviewed together rather than as isolated tasks. The matrix below summarizes the main technical checkpoints we use to de-risk synthesis and improve downstream assay usability.
| Review Area | Why It Matters | What We Evaluate | Typical Deliverable | Stage Alignment |
| Target Region & Amplicon Layout | Signal behavior depends on where the primer sits and how close the probe target is to the extension product | Amplicon size, primer direction, probe-binding location, and variant placement | Recommended assay geometry and prioritized target windows | Project initiation |
| Primer-Probe Orientation | Poor orientation can reduce opening efficiency or generate unproductive structures | Linked construct direction, primer compatibility, and risk of probe-primer interference | Annotated construct schematic and sequence notes | Design phase |
| Stem-Loop Thermodynamics | The stem must remain closed before target binding but still open efficiently during assay cycling | Stem composition, loop length, hybridization balance, and expected structural behavior | Refined stem-loop configuration for synthesis | Design phase |
| Blocker & Linker Strategy | Inadequate blocker design can allow polymerase read-through or unwanted signal behavior | Spacer choice, linker placement, and compatibility with the full construct architecture | Recommended blocker concept and modification map | Design / pre-synthesis |
| Dye-Quencher Matching | Channel mismatch and weak quenching can create baseline noise or reduce multiplex clarity | Fluorophore-quencher pairing, instrument optics, and singleplex versus multiplex demands | Labeling plan and channel allocation guide | Design / pre-synthesis |
| Multiplex Compatibility | Multi-target assays require more than dye selection; they also need coordinated assay balance | Cross-reactivity risk, panel architecture, primer balance, and channel spacing | Panel feasibility summary and redesign priorities | Development |
| Purification & Analytical Plan | Complex labeled constructs often require tighter control than standard primers | Purification approach, expected purity target, mass confirmation, and reporting needs | QC package matched to project use requirements | Synthesis / release |
| Troubleshooting & Redesign | Underperforming assays may fail because of geometry, labels, or structural bias rather than target biology | Existing Ct behavior, signal curves, background trends, and design history | Root-cause summary and next-round redesign plan | Optimization |
Our workflow is designed for customers who need technical visibility from early assay discussion through construct delivery and follow-up optimization. Each stage is structured to reduce redesign risk and support confident adoption in research and qPCR development programs.
We collect the target sequence, intended application, instrument platform, preferred fluorophore channels, and any existing assay history. This step helps determine whether Scorpion chemistry is appropriate and what sequence constraints must be managed from the start.
Our team reviews amplicon logic, probe-target relationship, stem-loop behavior, blocker strategy, and multiplex needs. Customers receive a fit-for-purpose development plan that clarifies feasible construct options and key design risks before synthesis is approved.
We finalize the Scorpion architecture, including primer region, loop sequence, stem composition, fluorophore, quencher, and spacer or blocker elements. Where several designs are plausible, we can prepare comparative candidate sets for more efficient screening.
The approved construct moves into custom oligonucleotide synthesis with purification selected according to label complexity and assay sensitivity requirements. In-process review helps maintain alignment between the designed construct and the released material.
Released material is accompanied by the agreed analytical package, and optional support can be provided for assay setup review, signal interpretation, mismatch testing strategy, or multiplex planning. This stage helps teams move from delivered oligo to usable assay component more efficiently.
Final deliverables may include sequence records, modification details, QC documentation, and design commentary for future reordering or redesign. If the first-round construct needs tuning, we support next-step optimization rather than leaving customers to restart the project from scratch.
Scorpion probes are not routine fluorescent oligos. They require coordinated control of primer design, probe thermodynamics, label compatibility, and manufacturing detail. Our service is built around that complexity so customers can make technically informed decisions instead of relying on generic probe ordering workflows.
Scorpion probe chemistry is most valuable in amplification workflows where signal speed, sequence specificity, and probe-primer coordination directly influence data quality. Our service supports a range of research and assay development applications across genomics, molecular analysis, and platform optimization.
Whether you are building a new SNP assay, optimizing an allele discrimination workflow, expanding a multiplex qPCR panel, or replacing an underperforming fluorescent probe format, our team can support the full path from sequence review to custom Scorpion probe delivery. We work with biotech companies, research laboratories, assay development groups, and procurement teams that need practical design guidance, reliable synthesis support, and documentation that helps move projects forward efficiently. Contact us to discuss your target sequence, preferred channels, assay goals, and project timeline.
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.
