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Model-guided design of ligand-regulated RNAi for programmable control of gene expression

Beisel, Chase L. and Bayer, Travis S. and Hoff, Kevin G. and Smolke, Christina D. (2008) Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Molecular Systems Biology, 4 . Art. No. 224. ISSN 1744-4292. http://resolver.caltech.edu/CaltechAUTHORS:BEImsb08

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Abstract

Progress in constructing biological networks will rely on the development of more advanced components that can be predictably modified to yield optimal system performance. We have engineered an RNA-based platform, which we call an shRNA switch, that provides for integrated ligand control of RNA interference (RNAi) by modular coupling of an aptamer, competing strand, and small hairpin (sh) RNA stem into a single component that links ligand concentration and target gene expression levels. A combined experimental and mathematical modelling approach identified multiple tuning strategies and moves towards a predictable framework for the forward design of shRNA switches. The utility of our platform is highlighted by the demonstration of fine-tuning, multi-input control, and model-guided design of shRNA switches with an optimized dynamic range. Thus, shRNA switches can serve as an advanced component for the construction of complex biological systems and offer a controlled means of activating RNAi in disease therapeutics.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://www.nature.com/msb/journal/v4/n1/full/msb200862.htmlPublisherArticle
http://dx.doi.org/10.1038/msb.2008.62DOIArticle
ORCID:
AuthorORCID
Smolke, Christina D.0000-0002-5449-8495
Additional Information:© 2008 EMBO and Macmillan Publishers Limited. This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission. Received 9 April 2008; Accepted 15 September 2008; Published online 28 October 2008. We thank G Soukup and D Endy for critical reading and comments on this manuscript, P Aebischer for providing the HEK293T tTA-d2EGFP cells, and S Culler for providing assistance with qRT–PCR. This work was supported by the Caltech Joseph Jacobs Institute for Molecular Engineering for Medicine (grant to CDS), the Defense Advanced Research Projects Agency (grant to CDS), the National Institutes of Health (training grant to TSB; fellowship to KGH), and the Department of Defense (fellowship to CLB). Conflict of interest: The authors declare competing financial interests in the form of a pending patent application.
Funders:
Funding AgencyGrant Number
Caltech Joseph Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
NIHUNSPECIFIED
Department of DefenseUNSPECIFIED
Subject Keywords:aptamer; mathematical modelling; RNA; shRNA; synthetic biology
Record Number:CaltechAUTHORS:BEImsb08
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:BEImsb08
Usage Policy:This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission.
ID Code:13255
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:05 Feb 2009 21:40
Last Modified:25 Jul 2017 20:00

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