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De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
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Rodrigo, Guillermo, Landrain, T. E. and Jaramillo, Alfonso (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences of the United States of America, 109 (38). pp. 15271-15276. doi:10.1073/pnas.1203831109 ISSN 0027-8424.
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Official URL: http://dx.doi.org/10.1073/pnas.1203831109
Abstract
A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. The computational algorithm, based on a physicochemical model, produces novel RNA sequences by exploring the space of possible sequences compatible with predefined structures. We tested our methodology in Escherichia coli by designing several positive riboregulators with diverse structures and interaction models, suggesting that only the energy of formation and the activation energy (free energy barrier to overcome for initiating the hybridization reaction) are sufficient criteria to engineer RNA interaction and regulation in bacteria. The designed sequences exhibit nonsignificant similarity to any known noncoding RNA sequence. Our riboregulatory devices work independently and in combination with transcription regulation to create complex logic circuits. Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells.
Item Type: | Journal Article | ||||||
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Subjects: | Q Science > QH Natural history Q Science > QP Physiology T Technology > TA Engineering (General). Civil engineering (General) T Technology > TP Chemical technology |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Library of Congress Subject Headings (LCSH): | RNA, Synthetic biology, Post-translational modification, Evolutionary computation | ||||||
Journal or Publication Title: | Proceedings of the National Academy of Sciences of the United States of America | ||||||
Publisher: | National Academy of Sciences | ||||||
ISSN: | 0027-8424 | ||||||
Official Date: | 20 March 2012 | ||||||
Dates: |
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Volume: | 109 | ||||||
Number: | 38 | ||||||
Page Range: | pp. 15271-15276 | ||||||
DOI: | 10.1073/pnas.1203831109 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||
Funder: | Actions Thématiques Incitatives de Genopole, Fondation pour la Recherche Medicale | ||||||
RIOXX Funder/Project Grant: |
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