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Beacon Designer™

SYBR® Green PCR Assays

Beacon Designer™ designs SYBR® Green PCR primer pairs that are specific to our target gene and efficiently amplify the target region. The SYBR® Green primers are designed after avoiding significant cross homologies that your sequence of interest shows with the database sequences.For verifying the specificity of the design SYBR® Green PCR assays designed, you can BLAST search the primers against the nr database which comprises of all the genomic databases available at NCBI.

The other unique feature of this tool is the automatic avoidance of the secondary structures that can prevent the SYBR® Green primer extension. The template forms a loop in the region of the secondary structures and this loop prevents the PCR product formation.

You can use pre-designed or published or well proven forward or reverse primers and Beacon Designer™ will evaluate them for you. For example, for a given forward primer, Beacon Designer™ would design the reverse primer for SYBR® Green assays (and would design both the reverse primer and the TaqMan® probe for TaqMan® assays). All these primers are rated according to a ranking algorithm which determines how closely the specified primer pair and primer search parameters match the target values.

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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