A major challenge in practical DNA tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through abstract tile set design. In this paper, we instead investigate the effects of “sticky end” sequence choices in systems using the kinetic model along with the nearest-neighbor model of DNA interactions. We show that both the sticky end sequences present in a system and their positions in the system can significantly affect error rates, and propose algorithms for sequence design and assignment
