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Updated: Jul 10, 2026
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
DMS footprinting of structured RNAs and RNA-protein complexes
Pilar Tijerina1, Sabine Mohr, Rick Russell
1Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
Abstract:
We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (< or = 500 nt). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as 'control' conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a 'footprint'), it is possible to detect local changes in the secondary and tertiary structure of RNA, as well as the formation of RNA-protein contacts. This protocol takes 1.5-3 d to complete, depending on the type of analysis used.
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