As we know, real-time PCR is an easy and straight forward method which can be used in many applications in basic research, molecular medicine and genetic engineering. Beacon Designer designs oligos for SYBR® Green, TaqMan®, LNA spiked TaqMan®, MethyLight, molecular beacon, NASBA®, Scorpions® and FRET assays. Primers and probes designed by Beacon Designer worked well in my experiments. This software helps me in designing multiplex, SNP genotyping and differential gene expression assays. The primers and probe it designed produced excellent results. I came across Beacon Designer when I first came to Morehouse School of Medicine and since then it has become part of all my projects which involve real-time PCR experiments. It is so popular in my lab that my colleagues have stopped using other programs and come to me for primer designs using Beacon Designer.
Algorithmically, it does an incredible job. It looks at every position on the entire sequence, rates every possible oligo within the specified length range and design parameters, and ranks them. It screens each oligonucleotide for secondary structures and outputs the best primer pair. I especially liked its ability to design alternative assays and choose the one which fits my needs the best. The output is automatically loaded into a spreadsheet containing the sequence, oligo and design information. I can also a generate report of my assays (very useful for my lab notebook) as well as order oligos online.
In addition to all these functionalities, Beacon Designer allows me to evaluate my pre-designed or published primers and probes. I can use the SYBR® Green primers I have already tested and design compatible probes for any supported chemistry.
The best part of Beacon Designer is that it uses an innovative algorithm to avoid significant homologies and template secondary structures. The program automatically processes BLAST submissions against either a local custom database or a public database by connecting directly to NCBI. It then avoids the regions of significant homology to design highly specific primers. I am also able to perform a template secondary structures search to avoid designing primers in the regions which form stable secondary structures at the PCR extension temperature.
With Beacon Designer, I can easily design a multiplex assay. Beacon Designer uses a fast and efficient algorithm to design optimal primer-probe sets for single tube multiplex reactions. You can choose the set best suited for your experimental needs from a list of alternates. It is possible to incorporate well-proven sets for some of the templates, or include reference or housekeeping genes for normalization purposes. It can check the suitability of pre-designed oligo sets for multiplex reactions and design oligos for additional sequences in the multiplex reaction that would be compatible with the pre-designed sets.
The program is backed by a strong technical support team; help is freely available by email, live chat, skype and telephone. A tutorial is available to help you get started quickly. I own a Windows version of Beacon Designer which I can run on Windows 98, ME, NT 4.0, 2000 and XP Professional; it is also available for Apple's Mac OS X 10.4.
I would recommend Beacon Designer to any group performing real-time PCR, whether in academic institutions, industry, or core facilities. It can also be used in expression profiling studies where the level of expression and the up- or down-regulation of the target genes are studied in a quantitative way.
Associate Professor
Department of Microbiology, Biochemistry, and Immunology
Morehouse School of Medicine