Rule-Based Design of Synthetic Transcription Factors in Eukaryotes
To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constrai...
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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American Chemical Society (ACS)
2016
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| Online Access: | http://hdl.handle.net/1721.1/100836 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-2031-8871 |
| _version_ | 1826194975028674560 |
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| author | Purcell, Oliver Peccoud, Jean Lu, Timothy K. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Purcell, Oliver Peccoud, Jean Lu, Timothy K. |
| author_sort | Purcell, Oliver |
| collection | MIT |
| description | To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger functional units. Here, we develop a grammar for the design of synthetic transcription factors (sTFs) in eukaryotic cells and implement it within GenoCAD, a Computer-Aided Design (CAD) software for synthetic biology. Knowledge derived from experimental evidence was captured in this grammar to guide the user to create designer transcription factors that should operate as intended. The grammar can be easily updated and refined as our experience with using sTFs in different contexts increases. In combination with grammars that define other synthetic systems, we anticipate that this work will enable the more reliable, efficient, and automated design of synthetic cells with rich functionalities. |
| first_indexed | 2024-09-23T10:05:06Z |
| format | Article |
| id | mit-1721.1/100836 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:05:06Z |
| publishDate | 2016 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/1008362022-09-30T18:50:11Z Rule-Based Design of Synthetic Transcription Factors in Eukaryotes Purcell, Oliver Peccoud, Jean Lu, Timothy K. Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Research Laboratory of Electronics Massachusetts Institute of Technology. Synthetic Biology Center Purcell, Oliver Lu, Timothy K. To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger functional units. Here, we develop a grammar for the design of synthetic transcription factors (sTFs) in eukaryotic cells and implement it within GenoCAD, a Computer-Aided Design (CAD) software for synthetic biology. Knowledge derived from experimental evidence was captured in this grammar to guide the user to create designer transcription factors that should operate as intended. The grammar can be easily updated and refined as our experience with using sTFs in different contexts increases. In combination with grammars that define other synthetic systems, we anticipate that this work will enable the more reliable, efficient, and automated design of synthetic cells with rich functionalities. United States. Defense Advanced Research Projects Agency National Institutes of Health (U.S.) (New Innovator Award 1DP2OD008435) National Science Foundation (U.S.) (1124247) United States. Office of Naval Research (N00014-13-1-0424) 2016-01-14T17:40:53Z 2016-01-14T17:40:53Z 2013-12 2013-09 Article http://purl.org/eprint/type/JournalArticle 2161-5063 http://hdl.handle.net/1721.1/100836 Purcell, Oliver, Jean Peccoud, and Timothy K. Lu. “Rule-Based Design of Synthetic Transcription Factors in Eukaryotes.” ACS Synthetic Biology 3, no. 10 (October 17, 2014): 737–744. https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-2031-8871 en_US http://dx.doi.org/10.1021/sb400134k ACS Synthetic Biology Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Chemical Society (ACS) PMC |
| spellingShingle | Purcell, Oliver Peccoud, Jean Lu, Timothy K. Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title | Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title_full | Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title_fullStr | Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title_full_unstemmed | Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title_short | Rule-Based Design of Synthetic Transcription Factors in Eukaryotes |
| title_sort | rule based design of synthetic transcription factors in eukaryotes |
| url | http://hdl.handle.net/1721.1/100836 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0002-2031-8871 |
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