HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules

Sanjukta Mukherjee, Asako Murata, Ryoga Ishida, Ayako Sugai, Chikara Dohno, Michiaki Hamada, Sudhir Krishna, Kazuhiko Nakatani*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Selective targeting of biologically relevant RNAs with small molecules is a long-standing challenge due to the lack of clear understanding of the binding RNA motifs for small molecules. The standard SELEX procedure allows the identification of specific RNA binders (aptamers) for the target of interest. However, more effort is needed to identify and characterize the sequence-structure motifs in the aptamers important for binding to the target. Herein, we described a strategy integrating high-throughput (HT) sequencing with conventional SELEX followed by bioinformatic analysis to identify aptamers with high binding affinity and target specificity to unravel the sequence-structure motifs of pre-miRNA, which is essential for binding to the recently developed new water-soluble small-molecule CMBL3aL. To confirm the fidelity of this approach, we investigated the binding of CMBL3aL to the identified motifs by surface plasmon resonance (SPR) spectroscopy and its potential regulatory activity on dicer-mediated cleavage of the obtained aptamers and endogenous pre-miRNAs comprising the identified motif in its hairpin loop. This new approach would significantly accelerate the identification process of binding sequence-structure motifs of pre-miRNA for the compound of interest and would contribute to increase the spectrum of biomedical application.

Original languageEnglish
Pages (from-to)165-174
Number of pages10
JournalMolecular Therapy - Nucleic Acids
Volume27
DOIs
Publication statusPublished - 2022 Mar 8

Keywords

  • dicer cleavage
  • HT-SELEX
  • miRNA biogenesis
  • pre-miRNA
  • RaptRanker
  • RNA-small molecule interaction
  • sequence-structure motif identification

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery

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