Integration of modern bioinformatics tools to teach primer design in a general introductory biology course

In many introductory biology courses, students are exposed to molecular biology techniques by performing experiments with preset materials. At Emory University, we teach our introductory majors biology course in a modular format, where students have 6 weeks to explore topics in‐depth. In the molecular biology module, we have incorporated a bioinformatics exercise that endeavors to teach students the basics of primer design using web‐based tools. In the wet lab, the students amplify the pMCT118 locus on chromosome 1 using standard PCR techniques and primers that were previously designed by Carolina Biological. To complete our bioinformatics exercise, students first use the NCBI database to locate the sequence for a particular number of repeat units contained within the pMCT118 locus. Students then obtain their sequence, they use the PrimerQuest online design tool to learn not only how primers are generated, but also how to choose an ideal primer pair. Finally, students locate their chosen primer pair within the original DNA sequence, and determine whether or not all the repeat units within the pMCT118 locus are actually the same. By performing this exercise, the students not only begin to understand primer design, but they also acquire a suite of tools that they will likely use either in future upper‐division biology courses or undergraduate laboratory research experiences.