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Updated: Feb 11, 2026
13:06
Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization FISH
Published on: October 7, 2012
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Single-Cell in Situ RNA Analysis With Switchable Fluorescent Oligonucleotides.
1Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ, United States.
Frontiers in Cell and Developmental Biology
|April 27, 2018
Summary
This study introduces a novel single-cell RNA analysis method using switchable fluorescent oligonucleotides (SFO) for spatial transcriptomics. This technique enables repeated imaging of RNA targets, advancing systems biology and molecular diagnostics.
Area of Science:
- Molecular Biology
- Genomics
- Cell Biology
Background:
- Understanding cellular function and disease requires analyzing RNA within its native spatial context.
- Existing single-cell RNA analysis methods face limitations in spatial resolution and multiplexing capabilities.
Purpose of the Study:
- To develop a novel single-cell in situ RNA analysis approach.
- To enable high-resolution spatial transcriptomics through cyclic multiplexed imaging.
Main Methods:
- Developed a method utilizing switchable fluorescent oligonucleotides (SFO) for RNA target staining.
- Employed pre-decoding oligonucleotides for initial RNA hybridization.
- Utilized DNA strand displacement reactions for simultaneous SFO removal, enabling cyclic imaging.
Main Results:
- Demonstrated efficient SFO stripping within 30 minutes via strand displacement.
- Confirmed that SFO removal preserves RNA target and oligonucleotide integrity for subsequent hybridizations.
- Achieved high-accuracy transcript restaining across at least eight hybridization cycles.
Conclusions:
- The switchable fluorescent oligonucleotide (SFO) approach enables robust, cyclic in situ RNA analysis.
- This technology theoretically allows whole transcriptome quantification at single-molecule sensitivity in individual cells.
- Potential applications include systems biology, molecular diagnostics, and targeted therapies.
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