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Beacon Designer™

rt-PCR Primer Design

Beacon Designer™ is the only qPCR assay design software that supports design of qPCR primers (including rt-pcr primers) optimized for different probe chemistries. The design criteria for qpcr (and rt-pcr) primers varies slightly between different chemistries but can have a huge impact on the experimentation success rate. Beacon Designer™ designs primers for TaqMan®, molecular beacons, FRET, MethyLight, Scorpions®, LNA™ Substituted TaqMan® and NASBA® assays. Beacon Designer supports rt-pcr oligo design and analysis (evaluation) in following ways:

  • Primer Specificity: Highly specific primers are designed by avoiding significant cross homologies found by automatically interpreting BLAST search results.

  • Primer Efficiency: Template secondary structures may hinder the primers from annealing and extension and hence prevent the complete product formation by polymerases. The program avoids regions which may fold upon themselves at lower temperatures and hence increasing the efficiency of the rt-pcr primers.

  • Multiplex PCR Primer Design: Beacon Designer™ supports design of primers that can be used in multiplex PCR assays. It supports multiplexing of upto four sequences in the TaqMan® mode and five sequences in molecular beacon mode. In the TaqMan® design mode, the software allows you to lock assays corresponding to a reference gene and then design assays for other target sequences. More on multiplex Real Time PCR assays.

  • Use Pre-designed Primers: You can design primers for probes that you already have or vice-versa. You can also design a reverse primer for a forward one or vice-versa. The primer evaluation algorithm of Beacon Designer™ finds suitable priming partners for your primer of choice.

Real Time PCR primer design is also supported in our other product, AlleleID.

Automate Your Real Time PCR Primer and Probe Design

Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

Specific and Efficient Design: How Beacon Designer™ Makes it Possible?

You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.


  • SYBR® Green Primer Design
  • TaqMan® Probe Design
  • Multiplex Real Time PCR Assay Design
  • HRMA Primer Design
  • MethyLight TaqMan® Design
  • Molecular Beacon Design
  • NASBA® Assay Design
  • FRET Probe Design
  • Scorpions® Design
  • Avoiding Cross Homology- For Specific Oligo Design
  • Avoid Template Structures- Increase Primer Efficiency
  • Oligo Rating


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