Ribocomputing devices for sophisticated in vivo logic computation
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 rema...
| Main Authors: | , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Association for Computing Machinery (ACM)
2017
|
| Online Access: | http://hdl.handle.net/1721.1/109202 https://orcid.org/0000-0002-5560-8246 |
| _version_ | 1826194527105318912 |
|---|---|
| author | Green, Alexander A. Kim, Jongmin Ma, Duo Silver, Pamela A. Yin, Peng Collins, James J. |
| author2 | Massachusetts Institute of Technology. Institute for Medical Engineering & Science |
| author_facet | Massachusetts Institute of Technology. Institute for Medical Engineering & Science Green, Alexander A. Kim, Jongmin Ma, Duo Silver, Pamela A. Yin, Peng Collins, James J. |
| author_sort | Green, Alexander A. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T09:57:27Z |
| format | Article |
| id | mit-1721.1/109202 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:57:27Z |
| publishDate | 2017 |
| publisher | Association for Computing Machinery (ACM) |
| record_format | dspace |
| spelling | mit-1721.1/1092022024-03-20T19:40:44Z Ribocomputing devices for sophisticated in vivo logic computation Green, Alexander A. Kim, Jongmin Ma, Duo Silver, Pamela A. Yin, Peng Collins, James J. Massachusetts Institute of Technology. Institute for Medical Engineering & Science Collins, James Collins, James J. 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. 2017-05-19T13:47:04Z 2017-05-19T13:47:04Z 2016-09 2016-09 Article http://purl.org/eprint/type/ConferencePaper 978-1-4503-4061-8 http://hdl.handle.net/1721.1/109202 Green, Alexander A.; Kim, Jongmin; Ma, Duo; Silver, Pamela A.; Collins, James J. and Yin, Peng. “Ribocomputing Devices for Sophisticated in Vivo Logic Computation.” NANOCOM’16, Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, September 28-30 2016, New York, New York, Association for Computing Machinery (ACM), September 2016 https://orcid.org/0000-0002-5560-8246 en_US http://dx.doi.org/10.1145/2967446.2970373 NANOCOM '16, Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Association for Computing Machinery (ACM) Prof. Collins via Howard Silver |
| spellingShingle | Green, Alexander A. Kim, Jongmin Ma, Duo Silver, Pamela A. Yin, Peng Collins, James J. Ribocomputing devices for sophisticated in vivo logic computation |
| title | Ribocomputing devices for sophisticated in vivo logic computation |
| title_full | Ribocomputing devices for sophisticated in vivo logic computation |
| title_fullStr | Ribocomputing devices for sophisticated in vivo logic computation |
| title_full_unstemmed | Ribocomputing devices for sophisticated in vivo logic computation |
| title_short | Ribocomputing devices for sophisticated in vivo logic computation |
| title_sort | ribocomputing devices for sophisticated in vivo logic computation |
| url | http://hdl.handle.net/1721.1/109202 https://orcid.org/0000-0002-5560-8246 |
| work_keys_str_mv | AT greenalexandera ribocomputingdevicesforsophisticatedinvivologiccomputation AT kimjongmin ribocomputingdevicesforsophisticatedinvivologiccomputation AT maduo ribocomputingdevicesforsophisticatedinvivologiccomputation AT silverpamelaa ribocomputingdevicesforsophisticatedinvivologiccomputation AT yinpeng ribocomputingdevicesforsophisticatedinvivologiccomputation AT collinsjamesj ribocomputingdevicesforsophisticatedinvivologiccomputation |