Abstract
Fluorescence-based tools that measure RNA-RNA and RNA-protein interactions in vivo offer useful experimental approaches to probe the complex and dynamic physiological behavior of bacterial RNAs. Here we document the step-by-step design and application of two fluorescence-based methods for studying the regulatory interactions RNAs perform in vivo: (i) the in vivo RNA Structural Sensing System (iRS3) for measuring RNA accessibility and (ii) the trifluorescence complementation (TriFC) assay for measuring RNA-protein interactions.
Keywords
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Acknowledgments
This work is supported by the Welch Foundation (Grant F-1756 to L.M.C.), and the National Science Foundation (Grant MCB 1716777 to L.M.C., and DGE-1610403 to A.N.L. and M.K .M.).
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Leistra, A.N., Mihailovic, M.K., Contreras, L.M. (2018). Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo. In: Arluison, V., Valverde, C. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 1737. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7634-8_9
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DOI: https://doi.org/10.1007/978-1-4939-7634-8_9
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