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Updated: Jan 17, 2026
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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
Published on: April 4, 2025
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Profiling RNA G-Quadruplexes In vivo
Bibo Yang1, Yiliang Ding1, Yueying Zhang1
1Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
Current Protocols
|September 19, 2025
Summary
SHALiPE-Seq quantifies RNA G-quadruplexes (RG4s) in living cells using chemical probing. This method compares in vivo RNA folding to in vitro benchmarks, revealing RG4 formation dynamics.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- RNA G-quadruplexes (RG4s) are complex tertiary structures formed in guanine-rich RNA regions.
- Detecting RG4s in vivo has been challenging, limiting understanding of their biological roles.
Purpose of the Study:
- To present SHALiPE-Seq, a transcriptome-wide method for assessing RG4 folding status in living cells.
- To enable quantitative analysis of RG4 formation and dynamics within cellular environments.
Main Methods:
- SHALiPE-Seq integrates chemical probing with high-throughput sequencing.
- It utilizes 2-methylnicotinic acid imidazolide (NAI) to selectively modify folded RG4s.
- In vitro NAI modification patterns under folding (K⁺) and unfolding (Li⁺) conditions serve as benchmarks.
Main Results:
- SHALiPE-Seq allows for the identification and evaluation of RG4 formation in vivo.
- The method provides quantitative profiles of RG4 folding status across the transcriptome.
- Successful application demonstrated in *Arabidopsis thaliana* and rice.
Conclusions:
- SHALiPE-Seq is a powerful tool for studying the in vivo dynamics of RG4s.
- This approach is broadly applicable to various biological systems.
- It facilitates investigation into the potential biological functions of RG4s.
