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 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:
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.
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.
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.
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 Assay Design
Designing optimal multiplex primer probe sets that work well and accurately quantitate can be a challenging task. Beacon Designer™ uses innovative proprietary algorithms to design optimal primer-probe sets for single tube multiplex assays using TaqMan® for up to 5 targets. All sets are analyzed for cross compatibility and cross homology to other targets to ensure specific and efficient amplification. If you want to incorporate well-proven sets for some of the templates, or include reference or housekeeping genes for normalization purposes in the assay, Beacon Designer™ is equipped to fully support your needs.