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Experimental Progress in Computation by Self-Assembly of DNA Tilings

LaBean, Thomas H. and Winfree, Erik and Reif, John H. (2000) Experimental Progress in Computation by Self-Assembly of DNA Tilings. In: DNA Based Computers V. American Mathematical Society , Providence, RI, pp. 123-40. ISBN 9780821820537 . http://resolver.caltech.edu/CaltechAUTHORS:20111101-150157119

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Abstract

Approaches to DNA-based computing by self-assembly require the use of D. T A nanostructures, called tiles, that have efficient chemistries, expressive computational power: and convenient input and output (I/O) mechanisms. We have designed two new classes of DNA tiles: TAO and TAE, both of which contain three double-helices linked by strand exchange. Structural analysis of a TAO molecule has shown that the molecule assembles efficiently from its four component strands. Here we demonstrate a novel method for I/O whereby multiple tiles assemble around a single-stranded (input) scaffold strand. Computation by tiling theoretically results in the formation of structures that contain single-stranded (output) reported strands, which can then be isolated for subsequent steps of computation if necessary. We illustrate the advantages of TAO and TAE designs by detailing two examples of massively parallel arithmetic: construction of complete XOR and addition tables by linear assemblies of DNA tiles. The three helix structures provide flexibility for topological routing of strands in the computation: allowing the implementation of string tile models.


Item Type:Book Section
ORCID:
AuthorORCID
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2000 American Mathematical Society. We wish to sincerely thank: Ned Seeman and Hao Yan for their considerable and invaluable roles in construction and analysis of the TAO tile; Tony Eng and Grzegorz Rosenberg for development and enlightening discussion of string tile concepts; and Wolfgang Frey and Ashutosh Chilkoti for assistance with atomic force microscopy. This work was supported in part by Grants NSF/DARPA CCR-9725021, CCR-96-33567, NSF IRI-9619647, ARO contract DAAH-04-96-1-0448, and ONR contract N00014-99-1-0406.
Funders:
Funding AgencyGrant Number
NSF/Defense Advanced Research Projects Agency (DARPA)CCR-9725021
NSF/Defense Advanced Research Projects Agency (DARPA)CCR-96-33567
NSFIRI-9619647
Army Research Office (ARO)DAAH-04-96-1-0448
Office of Naval Research (ONR)N00014-99-1-0406
Classification Code:2000 Mathematics Subject Classification: Primary 68Q05.
Record Number:CaltechAUTHORS:20111101-150157119
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20111101-150157119
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27564
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:01 Nov 2011 22:32
Last Modified:07 Mar 2015 00:28

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