The effects of nested primer binding sites on the reproducibility of PCR: mathematical modeling and computer simulation studies.

摘要: The polymerase chain reaction (PCR) has become an indispensable tool in modern biological research. Although the application of PCR is a standard routine, we widely lack theoretical understanding dynamic processes involved, especially with respect to amplification nonreproducible and/or unexpected products. For one potential source uncertainty, presence nested primer binding sites within amplifyable DNA locus, consider simple stochastic model for dynamics competing commonly used thermostable polymerases lacking 5'-3'-exonuclease activity, predict relative frequencies products dependent on probability, number cycles, and initial template molecules. At low probabilities numbers molecules expect two high copy only main product predicted at increasing cycle numbers. Furthermore, by means computer simulation studies quantify variation