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Computational Design of Nucleic Acid Feedback Control Circuits

Yordanov, Boyan and Kim, Jongmin and Petersen, Rasmus L. and Shudy, Angelina and Kulkarny, Vishwesh V. and Phillips, Andrew (2014) Computational Design of Nucleic Acid Feedback Control Circuits. ACS Synthetic Biology, 3 (8). pp. 600-616. ISSN 2161-5063. https://resolver.caltech.edu/CaltechAUTHORS:20140911-153311409

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Abstract

The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed using just two classes of reactions: catalysis and annihilation. We then propose implementations of these reactions in three distinct classes of nucleic acid circuits, which rely on DNA strand displacement, DNA enzyme and RNA enzyme mechanisms, respectively. We use these implementations to design a Proportional Integral controller, capable of regulating the output of a system according to a given reference signal, and discuss the trade-offs between the different approaches. As a proof of principle, we implement our methodology as an extension to a DNA strand displacement software tool, thus allowing a broad range of nucleic acid circuits to be designed and analyzed within a common modeling framework.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://pubs.acs.org/doi/abs/10.1021/sb400169sPublisherArticle
http://pubs.acs.org/doi/suppl/10.1021/sb400169sPublisherSupporting Information
ORCID:
AuthorORCID
Kim, Jongmin0000-0002-2713-1006
Additional Information:© 2014 American Chemical Society. ACS AuthorChoice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Received: October 22, 2013. Published: July 25, 2014. Publication Date (Web): July 25, 2014. V.V.K. and A.S. were supported, in part, by the National Science Foundation (NSF CAREER Award 0845650, NSF CCF 0946601, NSF CCF 1117168) and AFOSR. J.K. was supported by NSF Award 0832824 (The Molecular Programming Project). The authors thank Yannick Rondelez for his helpful suggestions and the anonymous reviewers for their feedback.
Funders:
Funding AgencyGrant Number
NSFCCF-0845650
NSFCCF-0946601
NSFCCF-1117168
Air Force Office of Scientific Research (AFOSR)UNSPECIFIED
NSFCCF-0832824
Subject Keywords:feedback control; molecular programming; nucleic acid circuits; DNA strand displacement; genelet; DNA toolbox
Issue or Number:8
Record Number:CaltechAUTHORS:20140911-153311409
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20140911-153311409
Official Citation:Computational Design of Nucleic Acid Feedback Control Circuits Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, and Andrew Phillips ACS Synthetic Biology 2014 3 (8), 600-616
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:49628
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:12 Sep 2014 17:07
Last Modified:11 Nov 2020 20:56

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