Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

Nuno M.G. Paulino; Mathias Foo; Tom F.A. de Greef; Jongmin Kim; Declan G. Bates

doi:10.1016/j.ifacol.2020.12.1135

Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

Nuno M.G. Paulino, Mathias Foo, Tom F.A. de Greef, Jongmin Kim, Declan G. Bates

Research output: Contribution to journal › Conference article › peer-review

1 Citation (Scopus)

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Abstract

Chemical reaction networks based on catalysis, degradation, and annihilation may be used as building blocks to construct a variety of dynamical and feedback control systems in Synthetic Biology. DNA strand-displacement, which is based on DNA hybridisation programmed using Watson-Crick base pairing, is an effective primitive to implement such reactions experimentally. However, experimental construction, validation and scale-up of nucleic acid control systems is still significantly lagging theoretical developments, due to several technical challenges, such as leakage, crosstalk, and toehold sequence design. To help the progress towards experimental implementation, we provide here designs representing two fundamental classes of reference tracking control circuits (integral and state-feedback control), for which the complexity of the chemical reactions required for implementation has been minimised. The supplied 'minimally complex' control circuits should be ideal candidates for first experimental validations of nucleic acid controllers.

Original language	English
Pages (from-to)	16745-16752
Number of pages	8
Journal	IFAC-PapersOnLine
Volume	53
Issue number	2
DOIs	https://doi.org/10.1016/j.ifacol.2020.12.1135
Publication status	Published - 2020
Event	21st World Congress of the International Federation of Aufomatic Control (IFAC 2020 World Congress) - Berlin, Germany Duration: 12 Jul 2020 → 17 Jul 2020 Conference number: 21 https://www.ifac2020.org/

Funding

Biotechnology and Biological Sciences Research Council Acronym: BBSRC Funding numbers: BB/M017982/1

Keywords

Chemical reaction networks
Feedback control
Nucleic acids
Strand Displacement Circuits
Synthetic Biology

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10.1016/j.ifacol.2020.12.1135

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title = "Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations",

abstract = "Chemical reaction networks based on catalysis, degradation, and annihilation may be used as building blocks to construct a variety of dynamical and feedback control systems in Synthetic Biology. DNA strand-displacement, which is based on DNA hybridisation programmed using Watson-Crick base pairing, is an effective primitive to implement such reactions experimentally. However, experimental construction, validation and scale-up of nucleic acid control systems is still significantly lagging theoretical developments, due to several technical challenges, such as leakage, crosstalk, and toehold sequence design. To help the progress towards experimental implementation, we provide here designs representing two fundamental classes of reference tracking control circuits (integral and state-feedback control), for which the complexity of the chemical reactions required for implementation has been minimised. The supplied 'minimally complex' control circuits should be ideal candidates for first experimental validations of nucleic acid controllers.",

keywords = "Chemical reaction networks, Feedback control, Nucleic acids, Strand Displacement Circuits, Synthetic Biology",

author = "Paulino, {Nuno M.G.} and Mathias Foo and {de Greef}, {Tom F.A.} and Jongmin Kim and Bates, {Declan G.}",

note = "Publisher Copyright: {\textcopyright} 2020 Elsevier B.V.. All rights reserved.; 21st World Congress of the International Federation of Aufomatic Control (IFAC 2020 World Congress), IFAC 2020 ; Conference date: 12-07-2020 Through 17-07-2020",

year = "2020",

doi = "10.1016/j.ifacol.2020.12.1135",

language = "English",

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T1 - Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

AU - Paulino, Nuno M.G.

AU - Foo, Mathias

AU - de Greef, Tom F.A.

AU - Kim, Jongmin

AU - Bates, Declan G.

N1 - Conference code: 21

PY - 2020

Y1 - 2020

N2 - Chemical reaction networks based on catalysis, degradation, and annihilation may be used as building blocks to construct a variety of dynamical and feedback control systems in Synthetic Biology. DNA strand-displacement, which is based on DNA hybridisation programmed using Watson-Crick base pairing, is an effective primitive to implement such reactions experimentally. However, experimental construction, validation and scale-up of nucleic acid control systems is still significantly lagging theoretical developments, due to several technical challenges, such as leakage, crosstalk, and toehold sequence design. To help the progress towards experimental implementation, we provide here designs representing two fundamental classes of reference tracking control circuits (integral and state-feedback control), for which the complexity of the chemical reactions required for implementation has been minimised. The supplied 'minimally complex' control circuits should be ideal candidates for first experimental validations of nucleic acid controllers.

AB - Chemical reaction networks based on catalysis, degradation, and annihilation may be used as building blocks to construct a variety of dynamical and feedback control systems in Synthetic Biology. DNA strand-displacement, which is based on DNA hybridisation programmed using Watson-Crick base pairing, is an effective primitive to implement such reactions experimentally. However, experimental construction, validation and scale-up of nucleic acid control systems is still significantly lagging theoretical developments, due to several technical challenges, such as leakage, crosstalk, and toehold sequence design. To help the progress towards experimental implementation, we provide here designs representing two fundamental classes of reference tracking control circuits (integral and state-feedback control), for which the complexity of the chemical reactions required for implementation has been minimised. The supplied 'minimally complex' control circuits should be ideal candidates for first experimental validations of nucleic acid controllers.

KW - Chemical reaction networks

KW - Feedback control

KW - Nucleic acids

KW - Strand Displacement Circuits

KW - Synthetic Biology

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U2 - 10.1016/j.ifacol.2020.12.1135

DO - 10.1016/j.ifacol.2020.12.1135

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SN - 2405-8963

VL - 53

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JO - IFAC-PapersOnLine

JF - IFAC-PapersOnLine

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T2 - 21st World Congress of the International Federation of Aufomatic Control (IFAC 2020 World Congress)

Y2 - 12 July 2020 through 17 July 2020

ER -

Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

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