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Updated: Dec 29, 2025

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Keth-seq for transcriptome-wide RNA structure mapping.

Xiaocheng Weng1,2, Jing Gong3, Yi Chen2

  • 1Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.

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Summary

Researchers developed a new N3-kethoxal reagent for fast, reversible labeling of single-stranded guanine bases in live cells. This method enables efficient RNA labeling and transcriptome-wide secondary structure mapping.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • RNA secondary structure plays a crucial role in regulating RNA function.
  • Understanding RNA structure in live cells is essential for deciphering biological processes.

Purpose of the Study:

  • To introduce a novel reagent for labeling single-stranded guanine bases in RNA within live cells.
  • To enable fast and reversible RNA labeling for secondary structure analysis.
  • To develop a method for transcriptome-wide RNA secondary structure mapping.

Main Methods:

  • Development and application of a new N3-kethoxal reagent.
  • Utilizing N3-kethoxal-based chemistry for RNA labeling under mild conditions.
  • Performing transcriptome-wide analysis of RNA secondary structure.

Main Results:

  • The N3-kethoxal reagent allows for rapid and reversible labeling of single-stranded guanine bases.
  • Efficient RNA labeling is achieved under mild experimental conditions.
  • The method facilitates comprehensive mapping of RNA secondary structures across the transcriptome.

Conclusions:

  • The N3-kethoxal reagent is a powerful tool for studying RNA secondary structure in live cells.
  • This chemistry provides a new avenue for investigating RNA regulation and function.
  • The developed method enables high-throughput RNA structure analysis at the transcriptome level.