Due to the universal need to amplify DNA for biochemistry applications ranging from molecular cloning to DNA sequencing, the Polymerase Chain Reactions (PCR) is the workhorse of every molecular biology laboratory. Despite the apparent simplicity of the PCR, the method is often fraught with difficulties that can decrease the efficiency or result in competitive amplification of undesired products. To date, nearly all approaches to PCR optimization have been based on either heuristic experimental sampling of reaction conditions or calculation of the effects of changes in reaction mixture on thermodynamic parameters. By contrast, the discipline of control theory can derive prescriptions for the optimal temperature for a PCR, if a suitable kinetic model exists. We develop the first sequence-dependent kinetic model for PCR, validating this model through comparison to experimental data. Based on this model, we describe how to derive optimal operating conditions for a PCR using the optimal control theory.

Optimal control of the polymerase chain reaction

245th National Meeting (2013)

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