How do you choose primers for PCR? A good length for PCR primers is generally around 18-30 bases. Specificity usually is dependent on length and annealing temperature. The shorter the primers are, the more efficiently they will bind or anneal to the target.
Do primer pairs have to be the same length? You can use primer set having different lengths. No problem.
How many base pairs should a primer be? For ideal amplification, the best primers are 17 to 24 bases long. The shorter the primers, the more efficiently they can anneal to target DNA. Primers that are longer—say 28 to 35 bases—work better when troubleshooting closely related species, for instance.
How do I choose a genotype primer? Select the best primer position on the wild-type or mutant(s) allele(s). Ideally, primer position is optimized so that the primer can be used as one primer pair for different PCR assays. With this strategy, combining common primers with different, unique primers allows all possible alleles to be detected.