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Nucleic Acids Research Advance Access published online on November 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn924
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

A flow cytometry-based screen for synthetic riboswitches

Sean A. Lynch and Justin P. Gallivan*

Department of Chemistry and Center for Fundamental and Applied Molecular Evolution, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA

*To whom correspondence should be addressed. Tel: +1 404 712 2171; Fax: +1 404 727 6586; Email: justin.gallivan{at}emory.edu

Received June 24, 2008. Revised October 21, 2008. Accepted November 3, 2008.

Riboswitches regulate gene expression through direct, small molecule–mRNA interactions. The creation of new synthetic riboswitches from in vitro selected aptamers benefits from rapid, high-throughput methods for identifying switches capable of triggering dramatic changes in gene expression in the presence of a desired ligand. Here we present a flow cytometry-based screen for identifying synthetic riboswitches that induce robust increases in gene expression in the presence of theophylline. The performance characteristics of our newly identified riboswitches exceed those of previously described natural and synthetic riboswitches. Sequencing data and structure probing experiments reveal the ribosome binding site to be an important determinant of how well a switch performs and may provide insights into the design of new synthetic riboswitches.


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[Abstract] [Full Text] [PDF]


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