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Proofreading tile sets: Error correction for algorithmic self-assembly

Winfree, Erik and Bekbolatov, Renat (2004) Proofreading tile sets: Error correction for algorithmic self-assembly. In: DNA Computing. Lecture Notes in Computer Science. No.2943. Springer , Berlin, pp. 126-144. ISBN 3-540-20930-1

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For robust molecular implementation of tile-based algorithmic self-assembly, methods for reducing errors must be developed. Previous studies suggested that by control of physical conditions, such as temperature and the concentration of tiles, errors (ε) can be reduced to an arbitrarily low rate - but at the cost of reduced speed (r) for the self-assembly process. For tile sets directly implementing blocked cellular automata, it was shown that r ≈ βε^2 was optimal. Here, we show that an improved construction, which we refer to as proofreading tile sets, can in principle exploit the cooperativity of tile assembly reactions to dramatically improve the scaling behavior to r ≈ βε and better. This suggests that existing DNA-based molecular tile approaches may be improved to produce macroscopic algorithmic crystals with few errors. Generalizations and limitations of the proofreading tile set construction are discussed.

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Winfree, Erik0000-0002-5899-7523
Additional Information:© 2004 Springer-Verlag Berlin Heidelberg. This work benefited from discussions with Leonard Adleman, Matthew Cook, Ashish Gael, Paul Rothemund, Rebecca Schulman, Georg Seelig, David Soloveichik, and Chris Umans. Thanks to John Reif for encouraging me to write this up and for sharing his unpublished manuscript. EW and RB were supported by NSF CAREER Grant No. 0093486, DARPA BioComputation Contract F30602-01-2-0561, NASA NRA2-37143, and GenTel. Simulation code and tile sets used in this paper, as well as MATLAB scripts for evaluating the kinetic trapping models, may be obtained from http://www
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Defense Advanced Research Projects Agency (DARPA) BioComputation Contract F30602-01-2-0561
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ID Code:22768
Deposited By: Lucinda Acosta
Deposited On:25 Oct 2011 22:44
Last Modified:07 Mar 2015 00:29

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