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Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo

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Bacterial Regulatory RNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1737))

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.

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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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Author notes

  1. Abigail N. Leistra and Mia K. Mihailovic contributed equally to this work.

Authors and Affiliations

  1. McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA

    Abigail N. Leistra, Mia K. Mihailovic & Lydia M. Contreras

Authors
  1. Abigail N. Leistra
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  2. Mia K. Mihailovic
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  3. Lydia M. Contreras
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Corresponding author

Correspondence to Lydia M. Contreras .

Editor information

Editors and Affiliations

  1. Université Paris Diderot & LLB/CEA/CNRS, Gif-sur-Yvette, France

    Véronique Arluison

  2. Laboratorio de Bioquímica, Microbiología e Interacciones, Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Bernal, Argentina

    Claudio Valverde

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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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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7633-1

  • Online ISBN: 978-1-4939-7634-8

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