The self-assembly process for bottom-up construction of nanostructures is of fundamental importance to the emerging discipline of Nanoscience. For example, the self-assembly of DNA tile nanostructures into 2D lattices can be used to manufacture patterned nanostructures from smaller unit nanostructures components known as DNA tiles on which other molecules such as metallic particles and proteins can be affixed, and DNA tiling lattices can be used to perform parallel universal computation. However, self-assemblies at the molecular scale are prone to a quite high rate of error, ranging from approximately between 0.5% to 5%, and the key barrier to large-scale experimental implementation of DNA tiling is this significant error rate in the self-assembly process. The problem of tiling errors is particularly critical for DNA lattices that use computational tilings to produce complex patterns, The limitation and/or elimination of these errors in self-assembly is perhaps the single most important major challenge to nanostructure self-assembly. The goals of the proposed research are to develop methods for error-resilient self-assembly; to analyze these by probabilistic, kinetic analysis and computer simulation; and to demonstrate these error-resilient self-assembly methods by a series of laboratory experiments. Research will be done in the context of DNA tiling assemblies. Prior work by Winfree provided a method to decrease tiling self-assembly errors without decreasing the intrinsic error rate of assembling a single tile, however, his technique resulted in a final assembled structure that is four times the size of the original one. This research team at Duke University has developed compact error-resilient tiling methods that do not increase the size of the tiling assembly. They will test their new error-resilient tiling methods that use overlay redundancy such that a single pad mismatch between a tile and its immediate neighbor forces one or more further pad mismatches between adjacent tiles in the neighborhood of this tile. The research will use a combination of theoretical and experimental methods. Theoretical probabilistic kinetic analysis and empirical studies of the computer simulation of tilings will first be used to validate these error-resilient overlay redundancy tiling methods; the analysis will allow prediction of the reduced error rate and verify the speed of the assembly is not reduced. Following this, actual experimental demonstrations will be made using DNA tiles, The overall goal is to demonstrate the feasibility of error-free assemblies of thousands of tiles.
