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One dimensional boundaries for DNA tile self-assembly

Schulman, Rebecca and Lee, Shaun and Papadakis, Nick and Winfree, Erik (2004) One dimensional boundaries for DNA tile self-assembly. In: DNA Computing. Lecture Notes in Computer Science. No.2943. Springer , Berlin, pp. 108-125. ISBN 3-540-20930-1

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In this paper we report the design and synthesis of DNA molecules (referred to as DNA tiles) with specific binding interactions that guide self-assembly to make one-dimensional assemblies shaped as lines, V's and X's. These DNA tile assemblies have been visualized by atomic force microscopy. The highly-variable distribution of shapes - e.g., the length of the arms of X-shaped assemblies - gives us insight into how the assembly process is occurring. Using stochastic models that simulate addition and dissociation of each type of DNA tile, as well as simplified models that more cleanly examine the generic phenomena, we dissect the contribution of accretion vs aggregation, reversible vs irreversible and seeded vs unseeded assumptions for describing the growth processes. The results suggest strategies for controlling self-assembly to make more uniformly-shaped assemblies.

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Winfree, Erik0000-0002-5899-7523
Additional Information:© 2004 Springer-Verlag Berlin Heidelberg. We would like to thank Bernie Yurke for pointing out the effects of slight differences in stoichiometry, and for his very descriptive term "stoichiometry poisoning". Paul Rnthemund, Rizal Hariadi, and other members of the DNA Lab provided helpful hints and stimulating conversation. This work was supported by NSF CAREER Grant No. 0093486, DARPA BioComputation Contract F30602-01-2-0561, NASA NRA2-37143, and GenTel.
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Defense Advanced Research Projects Agency (DARPA) BioComputation ContractF30602-01-2-0561
Record Number:CaltechAUTHORS:20110309-104202835
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22767
Deposited By: Lucinda Acosta
Deposited On:25 Oct 2011 22:54
Last Modified:07 Mar 2015 00:29

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