RNA Detection pp 289-304 | Cite as

Visualizing RNA in Live Bacterial Cells Using Fluorophore- and Quencher-Binding Aptamers

  • Murat Sunbul
  • Ankita Arora
  • Andres JäschkeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1649)


To elucidate the roles, dynamics, and regulation of RNAs, it is vital to be able to visualize the RNA of interest (ROI) in living cells noninvasively. Here, we describe a novel live-cell RNA imaging method using fluorophore- and quencher-binding aptamers, which can be genetically fused to the ROI. In this method, new membrane permeable and nonfluorescent fluorophore–quencher conjugates were utilized, and we showed that their fluorescence increases dramatically upon binding to fluorophore- or quencher-binding aptamers. This phenomenon allowed for labeling the ROI with many different colored fluorophores and also dual-color imaging of two distinct RNAs in live bacteria. Our approach uses small RNA tags and small molecule fluorophores for labeling, thereby minimal perturbation on the function and dynamics of the RNA of interest is expected.

Key words

Aptamer Fluorophore RNA imaging RNA localization Contact quenching Live cell imaging Fluorescence microscopy RNA trafficking SRB-2 aptamer DNB aptamer 



This work is supported by Helmholtz Initiative on Synthetic Biology. Murat Sunbul thanks the Alexander von Humboldt Foundation for a postdoctoral fellowship. Ankita Arora thanks the DAAD for a doctoral fellowship.


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© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityHeidelbergGermany

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