Beacon Designer

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.

Design Options Available

SYBR Green® is perhaps the most commonly used real time PCR chemistry. Beacon Designer designs SYBR® Green PCR primers and helps you evaluate pre-designed SYBR® Green PCR primer sets. You have complete control over the design parameters or you can use the default values, chosen after considerable research and communication with experts.

Dual Labeled Probe Design

Beacon Designer currently supports four probe based chemistries:

• TaqMan® Probes

  Use Beacon Designer for optimal TaqMan® probes that help you study the differential gene expression or study SNP (single nucleotide polymorphisms) using TaqMan® SNP genotyping assays. You can also choose to design the increasingly popular Locked Nucleic Acid (LNA™) substituted TaqMan® probes, which are more stable than standard TaqMan® probes. To study DNA methylation, Beacon Designer helps design primers and TaqMan® probes for MethyLight assays. MethyLight is a high throughput assay used to discriminate between methylated and unmethylated DNA. With any of these chemistries, you could evaluate a pre-designed/published TaqMan® probe. The design results are reported in a ranked order, giving you a list of alternates to choose from. Depending on the oligo properties, a rating is assigned. Please read the Rating section for details.
  

• Molecular Beacons

  Design or evaluate standard molecular beacons or molecular beacons for NASBA® assays. NASBA® is a primer-dependent technology that can be used for the continuous amplification of nucleic acids in a single mixture at one temperature. You can now design molecular beacons for NASBA® assays for single template or multiplex reactions.
  
  

• Scorpions®

  Beacon Designer supports the design of Scorpions® primers and probes. Scorpions® assays are important in that they are independent of the enzymatic cleavage of the probe. The primer and probe element are physically coupled during the reaction. Read more about the Scorpions® technology.
  
  

• FRET Probes

  Beacon Designer supports design and evaluation of pre-designed FRET probes. FRET probes that are compatible with pre-designed SYBR® Green primers can be designed in Beacon Designer.
  

Multiplex Real Time PCR Assays

With Beacon Designer you can design TaqMan® based multiplex real time PCR assays.