Nano: Error-Resilient DNA Tiling Assemblies

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The self-assembly process for bottom-up construction of nanostructures is offundamental importance to the emerging discipline of Nanoscience. For example,the self-assembly of DNA tile nanostructures into 2D lattices can be used tomanufacture patterned nanostructures from smaller unit nanostructurescomponents known as DNA tiles on which other molecules such as metallicparticles and proteins can be affixed, and DNA tiling lattices can be used toperform parallel universal computation. However, self-assemblies at themolecular scale are prone to a quite high rate of error, ranging fromapproximately between 0.5% to 5%, and the key barrier to large-scaleexperimental implementation of DNA tiling is this significant error rate in the self-assemblyprocess. The problem of tiling errors is particularly critical for DNAlattices that use computational tilings to produce complex patterns, The limitationand/or elimination of these errors in self-assembly is perhaps the single mostimportant major challenge to nanostructure self-assembly. The goals of theproposed research are to develop methods for error-resilient self-assembly; toanalyze these by probabilistic, kinetic analysis and computer simulation; and todemonstrate these error-resilient self-assembly methods by a series of laboratoryexperiments. Research will be done in the context of DNA tiling assemblies. Priorwork by Winfree provided a method to decrease tiling self-assembly errorswithout decreasing the intrinsic error rate of assembling a single tile, however, histechnique resulted in a final assembled structure that is four times the size of theoriginal one. This research team at Duke University has developed compacterror-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 redundancysuch that a single pad mismatch between a tile and its immediate neighbor forcesone or more further pad mismatches between adjacent tiles in the neighborhoodof this tile. The research will use a combination of theoretical and experimentalmethods. Theoretical probabilistic kinetic analysis and empirical studies of thecomputer simulation of tilings will first be used to validate these error-resilientoverlay redundancy tiling methods; the analysis will allow prediction of thereduced error rate and verify the speed of the assembly is not reduced. Followingthis, actual experimental demonstrations will be made using DNA tiles, Theoverall goal is to demonstrate the feasibility of error-free assemblies of thousandsof tiles.