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Updated: Jul 15, 2026

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

Published on: August 6, 2014

A protocol for preparing, characterizing and using three RNA-specific, live cell imaging probes: E36, E144 and F22.

Qian Li¹, Young-Tae Chang

¹Department of Chemistry, New York University, New York, NY 10003, USA.

Nature Protocols

|April 5, 2007

Summary

This study details the preparation and characterization of three novel RNA-specific fluorescent probes for live cell imaging. These probes enable efficient RNA visualization within cells, offering a valuable tool for biological research.

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Area of Science:

Molecular Biology
Cell Biology
Biochemistry

Background:

Accurate visualization of RNA in live cells is crucial for understanding gene expression and cellular processes.
Existing RNA imaging techniques may have limitations in specificity, brightness, or cellular toxicity.

Purpose of the Study:

To develop and validate a set of novel RNA-specific fluorescent probes (E36, E144, F22) for live cell imaging.
To establish a comprehensive protocol for the synthesis, characterization, and application of these probes.

Main Methods:

Chemical synthesis and purification of three distinct RNA-specific fluorescent probes.
Characterization including fluorescence properties, RNA specificity assays, and cellular toxicity assessments.
Live cell imaging experiments using counterstaining with Hoechst or DAPI.

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Main Results:

Successful preparation and purification of E36, E144, and F22 RNA imaging probes.
Demonstrated RNA specificity and favorable fluorescence properties in solution.
Effective live cell staining with minimal observed cellular toxicity.

Conclusions:

The developed protocol provides a reliable method for preparing and utilizing novel RNA-specific fluorescent probes.
These probes are suitable for live cell imaging, facilitating the study of RNA dynamics in biological systems.
The entire process from preparation to application can be completed within one week.