DNA to go: A do-it-yourself PCR thermocycler lab

Abstract

There is currently a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between physics, molecular biology, and the chemical sciences. These experiences also empower students by helping them recognize how this knowledge can be applied to develop new products and technologies that benefit society. This presentation describes our efforts to address this need by creating innovative hands-on lab activities that introduce chemical engineering students to molecular biology by challenging them to harness natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting the cylindrical PCR reactor between independently controlled thermal plates. Each station independently interfaces with a Windows-based PC via a USB connection, and is operated by a custom designed software package that enables temperature profiles to be easily input and monitored. A motion analysis microscope enables flow patterns inside the convective PCR reactors to be directly visualized. We have also developed course modules focused on modeling the problem of thermal convection in a fluid layer heated from below (the Rayleigh-Bénard problem) in the context of geometries that could be used to design lava lamps. After the fundamental problem is introduced and connected with the course material, the students are walked through a hands-on CFD exercise, then assigned a problem that gives them an opportunity to explore the effects of varying parameters in the model. Initial feedback has been very positive, as the computer simulations seem to excite student interest because they can actually "see" what they have been learning in the lecture. These capabilities uniquely enable us to connect the theoretical/computational, experimental, and biochemical reaction into a unified experience. © 2012 American Society for Engineering Education.