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Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments

Winfree, Erik (2000) Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments. Journal of Biomolecular Structure and Dynamics, 11 (2). pp. 263-270. ISSN 0739-1102.

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Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang?s purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures.

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Winfree, Erik0000-0002-5899-7523
Additional Information: © 2000 Adenine Press. This work would have been impossible without the sage advise of my thesis advisor, John Hopfield. John Abelson welcomed me into his laboratory, where this work was done. Ned Seeman taught me experimental science and gave me generous technical and conceptual advice on this project from its inception. Thanks to Anca Segall, Ely Rabani, and Bob Moision for instruction and advice on AFM imaging, and to the Beckman Institute Molecular Materials resource center for assistance and use of their AFM facilities. I also thank Paul Rothemund, Hui Wang, Len Adleman, John Reif, and many others whose discussions have been invaluable and inspirational. Computer models of the DX molecules used in this study, shown in Figure 6, were generated using NAMOT2 (Carter and Tung 96).
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ID Code:22774
Deposited By: Lucinda Acosta
Deposited On:10 Mar 2011 16:38
Last Modified:03 Oct 2019 02:40

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