A Theoretical Framework for Implementable Nucleic Acids Feedback Systems

• Published in: Bioengineering (Basel) Vol. 10; no. 4; p. 466
• Main Authors: Paulino, Nuno M. G., Foo, Mathias, de Greef, Tom F. A., Kim, Jongmin, Bates, Declan G.
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.04.2023; MDPI
• Subjects: Bioengineering; Catalysis; chemical reaction networks; Chemical reactions; Circuit design; Circuits; Control systems design; Control theory; Controllers; Design; Feedback; Feedback control; Feedback control systems; Hybridization; Localization; Networks; Nucleic acids; Physiological aspects; Stability analysis; State feedback; strand displacement circuits; synthetic biology; United States; synthetic biology; nucleic acids; chemical reaction networks; feedback control; strand displacement circuits
• ISSN: 2306-5354; 2306-5354
• DOI: 10.3390/bioengineering10040466

Chemical reaction networks can be utilised as basic components for nucleic acid feedback control systems’ design for Synthetic Biology application. DNA hybridisation and programmed strand-displacement reactions are effective primitives for implementation. However, the experimental validation and scale-up of nucleic acid control systems are still considerably falling behind their theoretical designs. To aid with the progress heading into experimental implementations, we provide here chemical reaction networks that represent two fundamental classes of linear controllers: integral and static negative state feedback. We reduced the complexity of the networks by finding designs with fewer reactions and chemical species, to take account of the limits of current experimental capabilities and mitigate issues pertaining to crosstalk and leakage, along with toehold sequence design. The supplied control circuits are quintessential candidates for the first experimental validations of nucleic acid controllers, since they have a number of parameters, species, and reactions small enough for viable experimentation with current technical capabilities, but still represent challenging feedback control systems. They are also well suited to further theoretical analysis to verify results on the stability, performance, and robustness of this important new class of control systems.