Development of an interdisciplinary laboratory experiment for teaching molecular computation, Boolean logic gates, hybridization probes and cancer RNA markers

Quynh Vo, Andrea Bardales, and Dmitry M. Kolpashchikov

Chemistry Department, University of Central Florida

Computational circuits made of DNA may provide an innovative tool to solve complex problems by leveraging the unique properties of nucleic acids such as predictable complementary and nanometer-scale size. This technology requires the integration of computer engineering, biochemistry and molecular biology knowledge. An important part of nurturing multidisciplinary-cutting edge technologies is teaching their principles at early academic stages. Thus, our lab has developed a laboratory educational kit focusing on teaching undergraduate students the principles for constructing DNA computers. In the laboratory, students were asked to assemble DNA circuits to detect microRNAs (miRNAs) associated with liver cancer thus connecting the theoretical concepts of Boolean logic gates and DNA hybridization probes with biomedical applications. Positive and/or negative DNA four-way junction logic gates are connected as circuits to detect the overexpression or under expression of the miRNA markers. For the readout of the DNA circuits, a molecular beacon probe or split aptamer can be use and it can be done quantitatively using a fluorometer or qualitatively by visually observing the fluorescence intensity with a handheld lamp, with the latter method requiring less equipment and cost to be adopted for educational purposes.