Modeling of Linker Stoichiometry for Optimization of DNA Nanostructure Self-Assembly

摘要

The Chemistry Department at Simpson College is constructing complex nanostructures by linking together many triangle shaped DNA nanostructures. The experiments conducted by the Chemistry Department have resulted in low yields of connected triangles, which led us to believe that the ratio of linkers to triangles is important. Our program simulates the assembly process using thermodynamics of DNA hybridization. The program outputs the final component counts, the most important of which is the number of good connections. Currently we know that the ratio is best at one linker for every triangle pair. Most importantly, we have determined that the curve is steeply dependent on the ratio, meaning the cause for inconsistencies in experiments is a result of a tiny margin for error in dispensing the components for the reaction.