A new algorithm for primer design

The Polymerase Chain Reaction (PCR) technology is widely used to create DNA copies. It has impacted many diverse fields including genetics, forensics, molecular paleontology, medical applications and environmental microbiology. The main object in PCR is a primer, a short single strand of DNA, about 18-25 bases long, that serves as the starting point of DNA synthesis. Primers are essential for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The PCR starts at the 3’-end of the primer and copies the opposite strand.Designing good primers is essential for a successful PCR process. Primer3 is one of the main available programs that produce primers for a variety of applications. Other programs, such as PrimerBLAST, QuantPrime and PRIMEGENS, depend on Primer3 for generating candidate primers and then subject them to specificity checking. The primers produced must not have high similarity with sequences other than their targets, as this would enable unwanted cross-hybridization. We will discuss these techniques, focusing on the parameters required for designing good primers and the pros and cons of some of the above mentioned programs. We introduce a new program, bestPrimer, that produces better primers as shown by extensive comparison with Primer3