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Beacon Designer™

MethyLight TaqMan® Assay Design

The MethyLight TaqMan® probe design involves the following two steps:

a) Prediction of CpG islands

Beacon Designer™ predicts CpG islands in accordance with Gardiner-Garden and Frommer guidelines. Just load the sequence in Beacon Designer™ and the program will automatically predict these regions. You can also specify the CpG regions manually in a sequence. The CpG islands are displayed in green in the Sequence view tab and the regions that are rich in GC are displayed in red.

b) Designing MethyLight assays

Beacon Designer™ designs TaqMan® probes & methyl sensitive PCR primers. The MethyLight assays involves treatment of genomic DNA with sodium bisulphite followed by an alkaline treatment. Beacon Designer™ displays the corresponding bisulphite treated strand when the genomic sequence is provided. The program designs primers and TaqMan® probes for the specified CpG islands. You can also design suitable control primers and probes by designing them for unmethylated and untreated DNA sequences. These primers and TaqMan® probes are highly specific as they are designed by avoiding regions of significant cross homology identified by automatically interpreting BLAST search results. Template structures are also avoided during the design.

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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