PCR and cycle sequencing reactions: A new device and engineering model

Methods for analysis in biochemistry and molecular biology, particularly cycle sequencing and the polymerase chain reaction (PCR), have become extremely popular in recent years as part of the Human Genome Project. As larger projects are approached, there is a need for more sophisticated engineering of the automated equipment used in these reactions to lower cost and increase throughput while maintaining quality. This work illustrates a multi-disciplinary engineering approach to the design of such devices and presents an engineering model of these reactions useful for analysis of any device for these reactions. A novel device is presented which increases the per instrument throughput by roughly an order of magnitude while decreasing the per reaction cost by a similar factor compared to commercial devices. Device design, construction, and performance are discussed. This device is used for cycle sequencing reactions to generate data which both confirms the primary design advantages and supports an engineering model of DNA replication reactions. The model is developed from basic rate equations governing PCR and cycle sequencing which then gives a method to analytically compare the design of various thermal cyclers. The model shows excellent qualitative and acceptable quantitative agreement with the experimental data for cycle sequencing reactions.