Download MendeleyRNA-binding landscape of amiloride: large-scale profiling and structural basis of U-U mismatch recognition.
Tsuzuki, K., Onizuka, K., Okada, M., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Kondo, J., Nagatsugi, F.(2026) RSC Chem Biol
- PubMed: 42100640 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1039/d6cb00055j
- Primary Citation Related Structures:
23JY, 23JZ, 23KA - PubMed Abstract:
Amiloride possesses a characteristic chemical scaffold capable of recognizing uracil (U) through three complementary hydrogen bonds; however, its binding selectivity toward naturally occurring RNA structural motifs has remained uncharacterized. In this study, we present a large-scale analysis of amiloride's RNA binding properties and structural characterization of the amiloride-RNA complex. Using folded RNA element profiling with structure library (FOREST), we evaluated the RNA-binding selectivity of amiloride across 3000 structured RNA motifs and uncovered pronounced binding preferences for G-quadruplexes and, notably, for a specific internal loop motif containing a U-U mismatch ( K Dapp = 0.31 µM). Furthermore, a motif extraction strategy was used to enable detailed structural investigation. The X-ray crystal structure of the amiloride-RNA complex provides the first structural evidence that amiloride recognizes a U residue within a naturally occurring RNA context via its signature complementary hydrogen bonding interactions.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Miyagi 980-8577 Japan onizuka@tohoku.ac.jp nagatugi@tohoku.ac.jp.
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