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A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

Grun, Casey and Sarma, Karthik and Wolfe, Brian and Shin, Seung Woo and Winfree, Erik (2015) A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures. . (Unpublished)

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DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages by formalizing DNA strand displacement mechanisms and modeling interactions at the "domain" level - one level of abstraction above models that explicitly describe DNA strand sequences. Unfortunately, the most-developed models currently only treat pseudo-linear DNA structures, while many systems being experimentally and theoretically pursued exploit a much broader range of secondary structure configurations. Here, we describe a new domain-level reaction enumerator that can handle arbitrary non-pseudoknotted secondary structures and reaction mechanisms including association and dissociation, 3-way and 4-way branch migration, and direct as well as remote toehold activation. To avoid polymerization that is inherent when considering general structures, we employ a time-scale separation technique that holds in the limit of low concentrations. This also allows us to "condense" the detailed reactions by eliminating fast transients, with provable guarantees of correctness for the set of reactions and their kinetics. We hope that the new reaction enumerator will be used in new molecular programming languages, compilers, and tools for analysis and verification that treat a wider variety of mechanisms of interest to experimental and theoretical work. We have implemented this enumerator in Python, and it is included in the DyNAMiC Workbench Integrated Development Environment.

Item Type:Report or Paper (Discussion Paper)
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URLURL TypeDescription Paper
Winfree, Erik0000-0002-5899-7523
Additional Information:The authors thank Chris Thachuk, Niles Pierce, Peng Yin, and Justin Werfel for discussion and support. This work was supported by the National Science Foundation grants CCF-1317694 and CCF-0832824 (The Molecular Programming Project).
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Record Number:CaltechAUTHORS:20190621-092351430
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:96621
Deposited By: Tony Diaz
Deposited On:21 Jun 2019 17:53
Last Modified:03 Oct 2019 21:23

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