Activatable tiles: Compact, robust programmable assembly and other applications

Abstract: Algorithmic DNA self-assembly is capable of forming complex patterns and shapes, that have been shown theoretically, and experimentally. Its experimental demonstrations, although improving over recent years, have been limited by signifi-cant assembly errors. Since 2003 there have been several designs of error-resilient tile sets but all of these existing error-resilient tile systems assumed directional growth of the tiling assembly. This is a very strong assumption because experiments show that tile self-assembly does not necessarily behave in such a fashion, since they may also grow in the reverse of the intended direction. The assumption of directional growth of the tiling assembly also underlies the growth model in theoretical assembly models such as the TAM. What is needed is a means for enforce this directionality constraint, which will allow us to reduce assembly errors. In this paper we describe a protection/deprotection strategy to strictly enforce the direction of tiling assembly growth so that the assembly process is robust against errors. Initially, we start with (i) a single “activated ” tile with output pads that can bind with other tiles, along with (ii) a set of “deactivated ” tiles, meaning that the tile’s output pads are protected and cannot bind with other tiles. After other tiles bind to a “deactivated ” tile’s input pads, the tile transitions to an active state and its output pads are exposed, allowing further growth