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

Abstract

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