An optimization-based approach for structural design of self-assembled DNA tiles



DNA tiles are self-assembled nanostructures, which offer exciting opportunities for synthesis of novel materials. A challenge for structural design of DNA tiles is to identify optimal locations for so-called crossovers, which are bridges between DNA double helices formed by pairs of single-stranded DNA. An optimization-based approach is presented to identify optimal locations for such crossovers. Minimization of a potential-energy model for a given structural design demonstrates the importance of local minima. Both deterministic global optimization of a reduced model and multistart optimization of the full model are applied successfully to identify the global minimum. MINLP optimization using a branch-and-bound algorithm (GAMS/SBB) identifies an optimal structural design of a DNA tile successfully with significant reduction in computational load compared to exhaustive enumeration, which demonstrates the potential of the proposed method to reduce trial-and-error efforts for structural design of DNA tiles. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1804–1817, 2017