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Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo

  • Abigail N. Leistra
  • Mia K. Mihailovic
  • Lydia M. Contreras
Protocol
Part of the Methods in Molecular Biology book series (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.

Keywords

RNA-RNA interaction RNA-protein interaction In vivo fluorescence assay Hybridization efficacy RNA accessibility Complementation assay RNA regulator Protein regulator Target network 

Notes

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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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Abigail N. Leistra
    • 1
  • Mia K. Mihailovic
    • 1
  • Lydia M. Contreras
    • 1
  1. 1.McKetta Department of Chemical EngineeringUniversity of Texas at AustinAustinUSA

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