Activatable tiles: compact, robust programmable assembly and other applications

Authors:
Urmi Majumder;Thomas H. LaBean;John H. Reif
Affiliations:
Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC
Venue:
DNA13'07 Proceedings of the 13th international conference on DNA computing
Year:
2007

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Abstract

While algorithmic DNA self-assembly is, in theory, capable of forming complex patterns, its experimental demonstration has been limited by significant assembly errors. In this paper we describe a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Tiles are initially inactive, meaning that each tile's output pads are protected and cannot bind with other tiles. After other tiles bind to the tile's input pads, the tile transitions to an active state and its output pads are exposed, allowing further growth. We prove that an activatable tile set is an instance of a compact, error-resilient and self-healing tile-set. We also describe a DNA design for activatable tiles and a deprotection mechanism using DNA polymerase enzymes and strand displacement. We conclude with a discussion on some applications of activatable tiles beyond computational tiling.