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Programmable Control of Nucleation for Algorithmic Self-assembly

Schulman, Rebecca and Winfree, Erik (2005) Programmable Control of Nucleation for Algorithmic Self-assembly. In: DNA Computing. Lecture Notes in Computer Science. No.3384. Springer , Berlin, pp. 319-328. ISBN 978-3-540-26174-2. https://resolver.caltech.edu/CaltechAUTHORS:20200221-152848969

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Abstract

Algorithmic self-assembly has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanodevices. Whereas much previous work has investigated self-assembly programs using an abstract model of irreversible, errorless assembly, experimental studies as well as more sophisticated reversible kinetic models indicate that algorithmic self-assembly is subject to several kinds of errors. Previously, it was shown that proofreading tile sets can reduce the occurrence of mismatch and facet errors. Here, we introduce the zig-zag tile set, which can reduce the occurrence of spurious nucleation errors. The zig-zag tile set takes advantage of the fact that assemblies must reach a critical size before their growth becomes favorable. By using a zig-zag tile set of greater width, we can increase the critical size of spurious assemblies without increasing the critical size of correctly seeded assemblies, exponentially reducing the spurious nucleation rate. In combination with proofreading results, this result indicates that algorithmic self-assembly can be performed with low error rates without a significant reduction in assembly speed. Furthermore, our zig-zag boundaries suggest methods for exquisite detection of DNA strands and for the replication of inheritable information without the use of enzymes.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1007/11493785_28DOIArticle
https://resolver.caltech.edu/CaltechAUTHORS:20100615-083346817Related ItemJournal Article
https://rdcu.be/b17pCPublisherFree ReadCube access
ORCID:
AuthorORCID
Schulman, Rebecca0000-0003-4555-3162
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2005 Springer-Verlag Berlin Heidelberg. The authors are grateful to Ho-Lin Chen, Ashish Goel, Rizal Hariadi, Paul Rothemund, Bernie Yurke, and Dave Zhang for helpful advice and discussions. This work was supported by NSF CAREER Grant No. 0093486 to EW and an NSF Graduate Fellowship to RS.
Funders:
Funding AgencyGrant Number
NSFCNS-0093486
NSF Graduate Research FellowshipUNSPECIFIED
Subject Keywords:Critical Nucleus; Mismatch Error; Target Strand; Facet Error; Tile Assembly Model
Series Name:Lecture Notes in Computer Science
Issue or Number:3384
Record Number:CaltechAUTHORS:20200221-152848969
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200221-152848969
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101473
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Feb 2020 17:09
Last Modified:24 Feb 2020 17:09

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