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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.

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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
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URLURL TypeDescription
Soloveichik, David0000-0002-2585-4120
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.
Funding AgencyGrant Number
Robert A. Welch FoundationF-1654
Series Name:Lecture Notes in Computer Science
Issue or Number:10467
Record Number:CaltechAUTHORS:20181126-091057014
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91154
Deposited By: Tony Diaz
Deposited On:26 Nov 2018 17:36
Last Modified:16 Nov 2021 03:38

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