A kinetic model for equilibrium binding of intercalation dye with DNA during its amplification

Abstract

Recently, a number of models of polymerase chain reaction (PCR) have been proposed. In such models, the kinetics of a reaction product and a fluorescence reporter used are usually identified. An intercalation dye is one of the two ways for “real time” detection of reaction product accumulation. In this work a PCR model is proposed, with using of intercalation dye to obtain a PCR curve. The concentration of bound intercalation dye was calculated at the end of each PCR cycle. This calculation is based on an equilibrium equation for intercalation dye binding with DNA. An analysis of simulation results demonstrates a significant difference between the accumulation kinetics of the reaction product and the fluorescent signal of the bound intercalation dye.