Why is primer and probe modeling necessary?
Poor primer design is the one major cause of all failures in single and multiplex PCR. Similarly, poor probe design is the major cause of failure in many diagnostic assays such as those involving molecular beacons or scorpions. Primers and probes may fail for many different reasons, among them: mishybridization, significant internal secondary structure or homodimerization. Since these causes may lead to failure and/or false positives, proper primer or probe design becomes a necessary first step to many simple and most complex assays.
