Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published August 2014 | Supplemental Material + Published
Journal Article Open

Computational Design of Nucleic Acid Feedback Control Circuits

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.

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.

Attached Files

Published - sb400169s.pdf

Supplemental Material - sb400169s_si_001.pdf

Files

sb400169s_si_001.pdf
Files (6.6 MB)
Name Size Download all
md5:01688de383d4006954eacd035becce92
1.7 MB Preview Download
md5:f7d02ab4baaf052ac1c3fa2fa379ad34
5.0 MB Preview Download

Additional details

Created:
August 22, 2023
Modified:
October 17, 2023