A Close-Up Look at PCR

The Polymerase Chain Reaction (PCR) is a fundamental laboratory technique that allows for the amplification of many copies of a desired DNA target sequence. Despite its prevalence, undergraduate students often have poor comprehension about the underlying molecular mechanisms of PCR and the components necessary to carry out the reaction. We designed an interactive modeling activity to help students visualize the underlying molecular processes of denaturation, annealing, and extension, and to see how PCR parallels in vivo DNA replication. During the activity, students mimic denaturation, annealing, and extension by synthesizing DNA strands from individual nucleotides and primers in the 5' to 3' direction. Because they carry out three cycles, students construct and observe the intermediate products that lead to the exponential amplification of the target sequence. Instructors can easily assemble kits from relatively inexpensive foam nucleotide pieces, and the models can be reused indefinitely. Field testing with first and second year undergraduates suggested that students productively interacted with the models to improve their understanding of PCR.