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Toward Reliable Algorithmic Self-Assembly of DNA Tiles: A Fixed-Width Cellular Automaton Pattern

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Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8502, Japan, and Department of Applied Physics, Center for the Physics of Information, Department of Computation and Neural Systems, Department of Computer Science, California Institute of Technology, Pasadena, California 91125
* To whom correspondence should be addressed. E-mail: [email protected]
†Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology.
‡Department of Applied Physics, California Institute of Technology.
§Center for the Physics of Information, California Institute of Technology.
∥Department of Computation and Neural Systems, California Institute of Technology.
⊥Department of Computer Science, California Institute of Technology.
Cite this: Nano Lett. 2008, 8, 7, 1791–1797
Publication Date (Web):December 28, 2007
https://doi.org/10.1021/nl0722830
Copyright © 2008 American Chemical Society
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    Abstract

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    Bottom-up fabrication of nanoscale structures relies on chemical processes to direct self-assembly. The complexity, precision, and yield achievable by a one-pot reaction are limited by our ability to encode assembly instructions into the molecules themselves. Nucleic acids provide a platform for investigating these issues, as molecular structure and intramolecular interactions can encode growth rules. Here, we use DNA tiles and DNA origami to grow crystals containing a cellular automaton pattern. In a one-pot annealing reaction, 250 DNA strands first assemble into a set of 10 free tile types and a seed structure, then the free tiles grow algorithmically from the seed according to the automaton rules. In our experiments, crystals grew to ∼300 nm long, containing ∼300 tiles with an initial assembly error rate of ∼1.4% per tile. This work provides evidence that programmable molecular self-assembly may be sufficient to create a wide range of complex objects in one-pot reactions.

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