Thermodynamic Simulations of DNA Tile Self-Assembly

Self-assembling DNA complexes have been intensively studied in recent years aiming to achieve bottom-up construction of nanoscale objects. Among them, a DNA complex called DNA tile is known for its high programmability. By using a set of DNA tiles, we are able to self-assemble two-dimensional crystals with programmable patterns. This is called algorithmic self-assembly. In order to create a wide range of complex objects by this self-assembly process, we need a methodology to predict its behavior. Especially, the relationship between the error rates and growth speed is of our interest. To estimate these properties, we use thermodynamic simulations based on the Monte Carlo method. However, conventional simulation models assume some much simplified conditions, therefore cannot explain the results of crystal growth experiments. Here, we propose Realistic Tile Assembly Model (R-TAM), in which we model the detailed conditions of the experimental protocol. We will show that the simulation can explain growth process of DNA tile crystals in experiment.