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Probe Design Service for PCR and qPCR Applications

Custom qPCR and dPCR Probes

 
 
Effective probe design is critical for successful PCR-based assays—especially in in vitro diagnostics (IVD). Microsynth supports your project with self-service design tools for standard assays and expert design services for complex applications.

With over 20 years of experience in probe design and assay development, we help you achieve reliable, specific, and reproducible results.

Applications

  • qPCR and RT-qPCR assays
  • dPCR assays
  • Molecular diagnostics and IVD
  • Gene expression analysis
  • Pathogen detection

Design Approach

Low-complexity design (self-service)

For routine applications such as singleplex or standard multiplex qPCR/ddPCR assays, you can design primers and probes yourself using established tools and guidelines.

Typical use cases:

  • Singleplex assays
  • Standard dual-labeled probes (TaqMan / hydrolysis probes)
  • Lab-developed tests (LDT)

Benefits:

  • Fast and cost-efficient
  • Minimal optimization required
  • Easy data interpretation

Recommended tools:

Key design guidelines: For routine assays, please also refer to our key design guidelines to support efficient primer and probe design and reduce optimization effort.

High-complexity design (expert service)

For advanced or regulated applications, Microsynth offers dedicated design support as a paid service.

Typical use cases:

  • Multiplex assays
  • Splice-specific targets
  • SNP and CNV detection
  • Complex assay panels
  • Specialized chemistries (LNA, MGB, Propynyl)
  • Commercial or regulatory (IVD) applications

What we provide:

  • Custom primer and probe design
  • Assay optimization for specificity and sensitivity
  • In-depth sequence analysis
  • Troubleshooting and redesign of existing assays

Why Choose Microsynth?

  • 20+ years of probe design experience
  • Proven expertise in qPCR, dPCR and IVD applications
  • Seamless transition from design to oligo production
  • Support for both standard and complex assay requirements

How to Get Started

For standard assays: Use recommended design tools and order your oligonucleotides directly.

For complex projects: Contact our experts for a tailored design solution.

To help us support your project efficiently, please provide:

  • Experimental goal (e.g. gene expression, pathogen detection)
  • Target sequences or accession numbers
  • Desired scale and probe labeling (5’ / 3’)

Contact us: myproject@microsynth.ch

Frequently Asked Questions

When should I use expert design support?

For multiplex assays, SNP/CNV detection, or regulated diagnostic applications.

Can Microsynth improve existing assays?

Yes, we offer troubleshooting and redesign services.

Which tools can I use for standard designs?

Primer-BLAST and Primer3Plus are recommended for routine PCR/qPCR assay design.