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Published 2000 | Published
Book Section - Chapter Open

Experimental Progress in Computation by Self-Assembly of DNA Tilings

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.

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.

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