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Beacon Designerâ„¢ automates the design of real time primers and probes
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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. As one of our esteemed customers says:

"We love your program - it has saved time in that we don't have to use 3 or 4 different programs to determine how well the probes we have designed will bind to other sequences. And it has saved money because I don't have to purchase several expensive labeled probes to test which one will work the best." - Dr. Gale Newman, Dept. Micro, Biochem, Immuno Morehouse School of Medicine, Atlanta, GA

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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 Assay Design

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. You can even choose your own default design parameters for your specific research needs.

In addition to locating the primer anywhere on the gene of interest, Beacon Designer can design primers across exon-exon or exon-intron junctions. These primers designed across exon intron junctions help selective amplification of cDNA from gDNA.

HRMA Assay Design

Beacon Designer™ offers a comprehensive solution for mutation detection. High Resolution Melting Analysis (HRMA) is a more cost-effective method than probe-based genotyping analysis. The program employs proprietary algorithms that enables designing the best primers for detecting mutations.

High Resolution Melting Analysis primers are designed flanking a mutation of interest to generate the shortest possible amplicons with detectable melting temperature variation. The primers are designed avoiding template secondary structures, assuring efficient primer extension. The HRMA primers designed can be BLAST searched against nucleotide databases at NCBI to check their specificity. Pre-designed or published primers can also be analyzed.

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. Using Beacon Designer™, you can design suitable control primers and probes by designing oligos for the methylated and the unmethylated strands, and for the untreated DNA sequence. With any of these chemistries, you could evaluate a pre-designed/published primers or TaqMan® probes. 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 in the online help 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 for upto five sequences including reference gene selection. Read more

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