B. Schierwater et al., THE EFFECTS OF NESTED PRIMER BINDING-SITES ON THE REPRODUCIBILITY OF PCR - MATHEMATICAL-MODELING AND COMPUTER-SIMULATION STUDIES, Journal of computational biology, 3(2), 1996, pp. 235-251
Citations number
35
Categorie Soggetti
Biology,"Biochemical Research Methods",Mathematics
The polymerase chain reaction (PCR) has become an indispensable tool i
n modern biological research, Although the application of PCR is a sta
ndard routine, we widely lack a theoretical understanding of the dynam
ic processes involved, especially with respect to the amplification of
nonreproducible and/or unexpected amplification products, For one pot
ential source of uncertainty, the presence of nested primer binding si
tes within an amplifyable DNA locus, we consider a simple stochastic m
odel for the dynamics of PCR amplification of competing products, For
commonly used thermostable DNA polymerases lacking a 5'-3'-exonuclease
activity, we predict the relative amplification frequencies of compet
ing PCR products dependent on the primer binding probability, the numb
er of PCR cycles, and the number of initial DNA template molecules, At
low primer binding probabilities and low numbers of initial DNA templ
ate molecules and PCR cycles, we expect the amplification of two produ
cts, At high primer binding probabilities and/or high copy numbers of
initial template molecules only one main amplification product is pred
icted at increasing cycle numbers, Furthermore, by means of computer s
imulation studies we quantify the stochastic variation for the amplifi
cation frequencies of competing products.