Ribocomputing devices for sophisticated in vivo logic computation

Alexander Green, Jongmin Kim, Duo Ma, Pamela A. Silver, James J. Collins, Peng Yin

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Synthetic biology aims to create functional devices, systems, and organisms with novel and useful functions taking advantage of engineering principles applied to biology. Despite great progress over the last decade, an underlying problem in synthetic biology remains the limited number of high-performance, modular, composable parts. A potential route to solve parts bottleneck problem in synthetic biology utilizes the programmability of nucleic acids inspired by molecular programming approaches that have demonstrated complex biomolecular circuits evaluating logic expressions in test tubes. Using a library of de-novo-designed toehold switches with orthogonality and modular composability, we demonstrate how toehold switches can be incorporated into decision-making RNA networks termed ribocomputing devices to rapidly evaluate complex logic in living cells. We have successfully demonstrated a 4-input AND gate, a 6-input OR gate, and a 12-input expression in disjunctive normal form in E. coli. The compact encoding of ribocomputing system using a library of modular parts is amenable to aggressive scale-up towards complex control of in vivo circuitry towards autonomous behaviors and biomedical applications.

Original languageEnglish (US)
Title of host publicationProceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016
PublisherAssociation for Computing Machinery, Inc
ISBN (Electronic)9781450340618
DOIs
StatePublished - Sep 28 2016
Event3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016 - New York, United States
Duration: Sep 28 2016Sep 30 2016

Other

Other3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016
CountryUnited States
CityNew York
Period9/28/169/30/16

Fingerprint

biology
Switches
autonomous behavior
Logic circuits
Nucleic acids
RNA
Escherichia coli
logic
Decision making
Cells
programming
engineering
decision making
Synthetic Biology
performance

Keywords

  • RNA network
  • Synthetic biology
  • Toehold switch

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Communication
  • Computer Networks and Communications

Cite this

Green, A., Kim, J., Ma, D., Silver, P. A., Collins, J. J., & Yin, P. (2016). Ribocomputing devices for sophisticated in vivo logic computation. In Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016 [a11] Association for Computing Machinery, Inc. https://doi.org/10.1145/2967446.2970373

Ribocomputing devices for sophisticated in vivo logic computation. / Green, Alexander; Kim, Jongmin; Ma, Duo; Silver, Pamela A.; Collins, James J.; Yin, Peng.

Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016. Association for Computing Machinery, Inc, 2016. a11.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Green, A, Kim, J, Ma, D, Silver, PA, Collins, JJ & Yin, P 2016, Ribocomputing devices for sophisticated in vivo logic computation. in Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016., a11, Association for Computing Machinery, Inc, 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016, New York, United States, 9/28/16. https://doi.org/10.1145/2967446.2970373
Green A, Kim J, Ma D, Silver PA, Collins JJ, Yin P. Ribocomputing devices for sophisticated in vivo logic computation. In Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016. Association for Computing Machinery, Inc. 2016. a11 https://doi.org/10.1145/2967446.2970373
Green, Alexander ; Kim, Jongmin ; Ma, Duo ; Silver, Pamela A. ; Collins, James J. ; Yin, Peng. / Ribocomputing devices for sophisticated in vivo logic computation. Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016. Association for Computing Machinery, Inc, 2016.
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