Error Rate Reduction in DNA Self-Assembly by Non-Constant Monomer Concentrations and Profiling

Abstract

This paper proposes a novel technique based on profiling the monomers for reducing the error rate in DNA self-assembly. This technique utilizes the average concentration of the monomers (tiles) for a specific pattern as found by profiling its growth. The validity of profiling and the large difference in the concentrations of the monomers are shown to be applicable to different tile sets. To evaluate the error rate new Markov based models are proposed to account for the different types of bonding (i.e. single, double and triple) in the monomers as modification to the commonly assumed kinetic trap model. A significant error rates reduction is accomplished compared to a scheme with constant concentration as commonly utilized under the kinetic trap model. Simulation results are provided