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Updated: Apr 16, 2026
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes
Lee E Vandivier1, Fan Li, Brian D Gregory
1Department of Biology, University of Pennsylvania, 433 S. University Ave., Philadelphia, PA, 19104, USA.
Abstract:
Empirical measurement of RNA secondary structure is an invaluable tool that has provided a more complete understanding of the RNA life cycle and functionality of this extremely important molecule. In general, methods for probing structural information involve treating RNA with either a chemical or an enzyme that preferentially targets regions of the RNA in a single- or double-stranded conformation (ssRNA and dsRNA, respectively). Here, we describe an approach that utilizes a combination of ssRNA- and dsRNA-specific nuclease (ss- and dsRNase, respectively) treatments along with high-throughput sequencing technology to provide comprehensive and robust measurements of RNA secondary structure across entire plant transcriptomes.
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