Development of a Primer Design Program for Multiplex PCR

Multiplex PCR method is a powerful technology as a potent tool to amplify specific DNA fragments from genomic DNA using Taq DNA polymerase and primer sets. Since multiple reactions occur in single tube, multiplex PCR has the potential to produce considerable savings of time and effort. Its applications are widely ranged from in vitro cloning of specific regions of DNA to diagnosis of disease [1]. Many amplification factors may interact and produce non-specific amplification. These nonspecific products may be amplified more efficiently than the desired target, consuming reaction components and producing impaired rates of annealing and extension. Thus, the optimization of multiplex PCR should aim to minimize or reduce such nonspecific interactions. To solve this problem, several bioinformatics tools are developed such as PRIMER3 [2] etc. However existing programs are not fully support for designing primer sets for multiplex PCR. We have developed the program which can design a primer set for multiplex PCR and scan a whole genome for validation. The need for higher speed has led to the development of other software tools such as SSAHA (Sequence Search and Alignment by Hashing Algorithm) [3]. We indexed the whole genomic sequence in binary data form for searching genomic positions of designed primers and present a new search algorithm which is 3’annealing method based on experiment data.