(369d) Kinetic Modeling and Optimal Control of the Polymerase Chain Reaction

Marimuthu, K., Purdue University
Chakrabarti, R., Purdue University

Kinetic modeling and control of the polymerase chain reaction (PCR) are important for improving the accuracy and efficiency of DNA diagnostics. Methods that exist so far assume global values for the rate constants of the various reaction steps involved. Biophysical studies suggest that PCR steps depend on many parameters such as temperature and the sequence of DNA - in particular, the number of GC base pairs. Hence, current studies give the same DNA amplification efficiency for any type of DNA sequence. Using equilibrium reaction modeling, we have shown that equilibrium conversion of this reaction is a strong function of the number of GC base pairs and hence, we have demonstrated the need for temperature and DNA sequence-dependent rate constants for the PCR reaction. We report a method for the estimation of such rate constants using relaxation kinetics and equilibrium reaction modeling. Since the reaction is conducted in batch, once these rate constants are available, we can solve the mole and energy balance equations for PCR. We present preliminary results on the application of optimal control theory to the computation of optimal reaction temperatures and times based on this model, and compare to standard three-step cycling conditions.