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Self-replication and evolution of DNA crystals

Schulman, Rebecca and Winfree, Erik (2005) Self-replication and evolution of DNA crystals. In: Advances in Artificial Life. Lecture Notes in Computer Science. No.3630. Springer , Berlin, pp. 734-743. ISBN 3-540-28848-1

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Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required.

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Winfree, Erik0000-0002-5899-7523
Additional Information:© 2005 Springer-Verlag Berlin Heidelberg. We would like to thank Bernie Yurke, Gerald Joyce, Andy Ellington, Graham Cairns-Smith, Paul Rothemund, Dave Zhang and David Soloveichik for helpful discussion on sequence amplification and evolution. The AFM image in the inset of Figure 1c was taken by Ho-Lin Chen. This research was partially supported by NSF awards #0093486 and #0432193.
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Record Number:CaltechAUTHORS:20110309-104201367
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:22758
Deposited By: Lucinda Acosta
Deposited On:24 Oct 2011 14:52
Last Modified:07 Mar 2015 00:30

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