Computing with living hardware

Our multi-institutional team of eleven undergraduates, one high school student, one postdoctoral fellow, and four faculty members explored the emerging field of synthetic biology and presented our results at the 2006 international Genetically Engineered Machine (iGEM) competition. Having had little or no previous research experience, biology, chemistry and mathematics students from four different institutions collaborated during the summer and fall semester of 2006. We identified the burnt pancake problem (sorting by reversals) as a mathematical puzzle ideal for solving with 'living computer hardware': Escherichia coli cells programmed to sort tandem fragments of DNA by reversals (DNA inversions or 'flipping'). Flipping is driven by a Salmonella typhimurium Hin/hix recombinase system that we reconstituted as a collection of BioBrick-compatible interchangeable parts. We tested functionality of these synthesised genetic parts and mathematically modeled the behaviour of pancake flipping. The living hardware system allowed us to consider future research applications such as regulating genetic element rearrangements in vivo and DNA computing. We found the field of synthetic biology to be ideal for learning, teaching, sharing, collaborating, and conducting integrative and original research with undergraduates.