Issue 36, 2025

Identification and structural insights into RNA motifs targeted by a CAG repeat DNA-binding small molecule

Abstract

RNA-targeting small molecules have the potential to modulate RNA function and offer possible applications in drug development. However, their molecular recognition mechanisms remain poorly understood due to limited structural insights. To advance our understanding of how these small molecules interact with their target RNAs, it is essential to identify and analyze RNA–small molecule complexes that can serve as models for structural studies. In this study, we identified novel RNA motifs that bind selectively to the small molecule naphthyridine–azaquinolone (NA), previously known to interact with CAG/CAG motif in DNA. Using different methods, including surface plasmon resonance (SPR), thermal melting, and cold-spray ionization mass spectrometry, we investigated the interaction between NA and the RNA motifs. Furthermore, we determined the solution structure of the NA–RNA complex, revealing a distinct binding mode from its DNA interaction. The findings in this study provide molecular-level insight into RNA–small molecule recognition and highlight the potential of NA as a scaffold for developing RNA-targeting small molecules.

Graphical abstract: Identification and structural insights into RNA motifs targeted by a CAG repeat DNA-binding small molecule

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Article information

Article type
Edge Article
Submitted
15 Jul 2025
Accepted
11 Aug 2025
First published
21 Aug 2025
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2025,16, 16819-16828

Identification and structural insights into RNA motifs targeted by a CAG repeat DNA-binding small molecule

Q. Chen, A. Fujiwara, K. Nakatani, G. Kawai and A. Murata, Chem. Sci., 2025, 16, 16819 DOI: 10.1039/D5SC05255F

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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