Enhanced Tile Design

While several results have successfully demonstrated several techniques for reducing errors that occur during DNA tile-based self-assembly, many of them have done so without allowing for the modification of the basic structures of the tiles themselves. However, the simple and static nature of DNA tiles lends itself to the possibility of extension.

In , Majumder, LaBean, and Reif proposed such an extension. Namely, the authors defined a model in which the "input" glues of tiles are "active" (that is, free to bind to complementary glue strands) when the tiles are freely floating in solution, but their "output" glues are "inactive" (this is, prevented from forming bonds). Only once a tile has associated to an assembly and bound with its input sides are its output sides activated. They presented a theoretical model of such systems and showed that they provide instances of compact (i.e. not requiring scaling factors over the original tile set), error-resilient, and self-healing assembly systems. Furthermore, they provided a possible physical implementation for such systems using DNA polymerase enzymes and strand displacement.

In , Fujibayashi, Zhang, Winfree, and Murata introduced a similar approach in order to provide for both error-resilience and fast speed of assembly. The Protected Tile Mechanism and the Layered Tile Mechanism, which utilize stand displacement, were presented. These mechanisms make use of additional DNA strands which "protect", or cover, glues either partially or fully. By balancing the length of the glue strands available for binding on input and output sides at various stages of tile binding, they were able to demonstrate - via simulation - that these mechanisms can in fact improve error rates while maintaining fast assembly.