Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding

Yusuke Takashima, Asako Murata, Kei Iida, Ayako Sugai, Masatoshi Hagiwara, Kazuhiko Nakatani

Research output: Contribution to journalArticlepeer-review


Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer cleavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated cleavage was significantly altered by the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method.

Original languageEnglish
Pages (from-to)2817-2827
Number of pages11
JournalACS Chemical Biology
Issue number10
Publication statusPublished - Oct 21 2022
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Medicine


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