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Load capacity improvements in nucleic acid based systems using partially open feedback control

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Kulkarni, Vishwesh V., Kharisov, Evgeny, Hovakimyan, Naira and Kim, Jongmin (2014) Load capacity improvements in nucleic acid based systems using partially open feedback control. ACS Synthetic Biology, 3 (8). pp. 617-626. doi:10.1021/sb5000675

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Official URL: http://dx.doi.org/10.1021/sb5000675

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Abstract

Synthetic biology is facilitating novel methods and components to build in vivo and in vitro circuits to better understand and re-engineer biological networks. Recently, Kim and Winfree have synthesized a remarkably elegant network of transcriptional oscillators in vitro using a modular architecture of synthetic gene analogues and a few enzymes that, in turn, could be used to drive a variety of downstream circuits and nanodevices. However, these oscillators are sensitive to initial conditions and downstream load processes. Furthermore, the oscillations are not sustained since the inherently closed design suffers from enzyme deactivation, NTP fuel exhaustion, and waste product build up. In this paper, we show that a partially open architecture in which an adaptive controller, implemented inside an in silico computer that resides outside the wet-lab apparatus, can ensure sustained tunable oscillations in two specific designs of the Kim–Winfree oscillator networks. We consider two broad cases of operation: (1) the oscillator network operating in isolation and (2) the oscillator network driving a DNA tweezer subject to a variable load. In both scenarios, our simulation results show a significant improvement in the tunability and robustness of these oscillator networks. Our approach can be easily adopted to improve the loading capacity of a wide range of synthetic biological devices.

Item Type: Journal Article
Subjects: Q Science > Q Science (General)
Q Science > QA Mathematics
Q Science > QC Physics
Q Science > QD Chemistry
T Technology > T Technology (General)
T Technology > TA Engineering (General). Civil engineering (General)
T Technology > TJ Mechanical engineering and machinery
T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions: Faculty of Science, Engineering and Medicine > Science > Chemistry
Faculty of Science, Engineering and Medicine > Research Centres > Centre for Complexity Science
Faculty of Science, Engineering and Medicine > Science > Computer Science
Faculty of Science, Engineering and Medicine > Engineering > Engineering
Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Faculty of Science, Engineering and Medicine > Science > Mathematics
Faculty of Science, Engineering and Medicine > Science > Physics
Faculty of Science, Engineering and Medicine > Science > Centre for Scientific Computing
Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre
Library of Congress Subject Headings (LCSH): Nucleic acids , DNA--Synthesis, Adaptive control systems, Synthetic biology
Journal or Publication Title: ACS Synthetic Biology
Publisher: American Chemical Society
Official Date: 1 May 2014
Dates:
DateEvent
1 May 2014Published
Volume: 3
Number: 8
Page Range: pp. 617-626
DOI: 10.1021/sb5000675
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Funder: National Science Foundation (U.S.) (NSF), United States. Air Force. Office of Scientific Research (AFOSR)
Embodied As: 1

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