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Updated: Jan 21, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
RNA imaging by chemical probes
Fumiaki Tomoike1, Hiroshi Abe2
1Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
Abstract:
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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