Primer Premier from Premier Biosoft International

In molecular biology, the polymerase chain reaction (PCR) is a technique to amplify a single or few copies of a DNA sequence across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. The method relies on the principle of thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA. Primers (short DNA fragments) containing sequences complementary to the target region along with a DNA polymerase (after which the method is named) are key components to enable selective and repeated amplification. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the DNA template is exponentially amplified. PCR can be extensively modified to perform a wide array of genetic manipulations.

Design of PCR primers requires a lot of time and potentially, a lot of money. There are many programs available which design primers for PCR assays, but the algorithms for many of them are not exhaustive. I have tried the PCR primer design software, Primer Premier 6.00 from Premier Biosoft International.

Using Primer Premier 6, I was successfully able to design PCR primers for Homo sapiens mitochondrion and for detection of influenza. The program automatically avoids homology and template structures and has a good Tm calculator. Primer Premier 6 saves a lot of experimentation time by designing highly efficient primers in a short period of time, leaving behind the traditional primer design methods. Designing a primer with Primer Premier takes from 3 to 6 hours. The primers designed are specific to the target. 99% of the primers that I have designed have performed well.

For a multiplex experiment, Primer Premier enables you to design multiplex primers by launching a primer search in batch mode and then checking the cross reactivity of the primers designed. Primer Premier checks for all the possible reactivity and displays the most stable structure formed by each oligo. This functionality reduces false priming and ensures a strong signal strength.

Primer Premier analyzes and evaluates the properties of pre-designed primers and ranks them for you to judge how far the primers are from their desired target values. This feature is especially useful if you are working with published or pre-designed and proven primers. For a particular primer, Primer Premier can even design a compatible set. For example, for a pre-designed or published forward primer, Primer Premier can find a compatible reverse primer that meets all the design criteria.

You can create presentation quality reports for lab notebooks and sharing with colleagues. Report options include a visualization of the positions of the primers on the sequence, a list of alternate primers, and a display of primers, amplicon and the design parameters used by the primer design program.

One downside, if you have not worked with AlleleID, then you may have some problems with the interface of Primer Premier because the application does not have a tutorial.

In conclusion, Primer Premier 6 is a very good program for PCR design and it is not a very expensive program. Other commercial programs are much more expensive as compared to Primer Premier 6.