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Computational design of nucleic acid feedback control circuits
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Yordanov, Boyan, Kim, Jongmin, Petersen, Rasmus, Shudy, Angelina, Kulkarni, Vishwesh V. and Phillips, Andrew (2014) Computational design of nucleic acid feedback control circuits. ACS Synthetic Biology, 3 (8). pp. 600-616. doi:10.1021/sb400169s ISSN 2161-5063.
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Official URL: http://dx.doi.org/10.1021/sb400169s
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: | Journal Article | ||||||||||
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Subjects: | Q Science > QP Physiology T Technology > TA Engineering (General). Civil engineering (General) T Technology > TP Chemical technology |
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Divisions: | Faculty of Science, Engineering and Medicine > Engineering > Engineering | ||||||||||
Library of Congress Subject Headings (LCSH): | Synthetic biology, Biotechnology, Nucleic acids | ||||||||||
Journal or Publication Title: | ACS Synthetic Biology | ||||||||||
Publisher: | American Chemical Society | ||||||||||
ISSN: | 2161-5063 | ||||||||||
Official Date: | 25 July 2014 | ||||||||||
Dates: |
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Volume: | 3 | ||||||||||
Number: | 8 | ||||||||||
Page Range: | pp. 600-616 | ||||||||||
DOI: | 10.1021/sb400169s | ||||||||||
Status: | Peer Reviewed | ||||||||||
Publication Status: | Published | ||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||
Copyright Holders: | American Chemical Society | ||||||||||
Date of first compliant deposit: | 29 November 2016 | ||||||||||
Date of first compliant Open Access: | 1 December 2016 | ||||||||||
Funder: | National Science Foundation (U.S.) (NSF), United States. Air Force. Office of Scientific Research (AFOSR) | ||||||||||
Grant number: | NSF CAREER Award 0845650, NSF CCF 0946601, NSF CCF 1117168, NSF Award 0832824 (NSF) |
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