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Related Experiment Video

Updated: Jan 17, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

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

This summary is machine-generated.

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.

Keywords:

G‐quadruplex RNA structure profiling SHALiPE‐Seq

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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.