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The Design Space of Strand Displacement Cascades with Toehold-Size Clamps

Wang, Boya and Thachuk, Chris and Ellington, Andrew D. and Soloveichik, David (2017) The Design Space of Strand Displacement Cascades with Toehold-Size Clamps. In: DNA Computing and Molecular Programming. Lecture Notes in Computer Science. No.10467. Springer , Cham, Switzerland, pp. 64-81. ISBN 978-3-319-66798-0. http://resolver.caltech.edu/CaltechAUTHORS:20181126-091057014

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Abstract

DNA strand displacement cascades have proven to be a uniquely flexible and programmable primitive for constructing molecular logic circuits, smart structures and devices, and for systems with complex autonomously generated dynamics. Limiting their utility, however, strand displacement systems are susceptible to the spurious release of output even in the absence of the proper combination of inputs—so-called leak. A common mechanism for reducing leak involves clamping the ends of helices to prevent fraying, and thereby kinetically blocking the initiation of undesired displacement. Since a clamp must act as the incumbent toehold for toehold exchange, clamps cannot be stronger than a toehold. In this paper we systematize the properties of the simplest of strand displacement cascades (a translator) with toehold-size clamps. Surprisingly, depending on a few basic parameters, we find a rich and diverse landscape for desired and undesired properties and trade-offs between them. Initial experiments demonstrate a significant reduction of leak.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1007/978-3-319-66799-7_5DOIArticle
Additional Information:© Springer International Publishing AG 2017. First Online: 24 August 2017. B. Wang—Supported by NSF grants CCF-1618895 and CCF-1652824. C. Thachuk—Supported by NSF grant CCF-1317694. A.D. Ellington—Supported by NSF grant DBI-0939454, international funding agency ERASynBio 1541244, and by the Welch Foundation F-1654. D. Soloveichik—Supported by NSF grants CCF-1618895 and CCF-1652824.
Funders:
Funding AgencyGrant Number
NSFCCF-1618895
NSFCCF-1652824
NSFCCF-1317694
NSFDBI-0939454
ERASynBio1541244
Robert A. Welch FoundationF-1654
Record Number:CaltechAUTHORS:20181126-091057014
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181126-091057014
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91154
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:26 Nov 2018 17:36
Last Modified:26 Nov 2018 17:36

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