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Updated: Jul 30, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Overview of Chemical Methods to Probe RNA Structure with Radionucleotides
Mrityunjay Gupta1, Chely M Garfio2, Robert C Spitale1,2,3
1Department of Chemistry, University of California, Irvine, California.
Abstract:
Structural features of RNA play an important role in its capability to perform various functions in biological systems. To probe structural features, chemical probes are used to conjugate or cleave RNA at solvent-accessible sites, differentiating between flexible and constrained regions. These conjugates or cleaved products are then detected using reverse transcription (RT), where enzymatic RNA-dependent DNA primer extension is abruptly halted at the conjugation site or cleavage site. Here, we provide an overview of methods to probe RNA structure in vitro using radioactively labeled DNA primers, which provide a highly sensitive method to visualize RT stop sites with gel electrophoresis. © 2023 Wiley Periodicals LLC.
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