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Published 2004 | Submitted
Book Section - Chapter Open

One dimensional boundaries for DNA tile self-assembly

Abstract

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.

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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