23JY

pre-miR-6074 internal loop

Summary for 23JY

• Entry DOI: 10.2210/pdb23jy/pdb
• Descriptor: RNA (5'-R(*UP*UP*GP*CP*GP*GP*AP*UP*AP*CP*CP*CP*GP*GP*GP*UP*UP*GP*CP*CP*GP*C)-3') (2 entities in total)
• Functional Keywords: pre-mir-6074, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 14084.40

Authors

Kondo, J.,Okada, M.,Tsuzuki, K.,Onizuka, K.,Nagasawa, R.,Miyashita, E.,Komatsu, K.R.,Saito, H.,Nagatsugi, F. (deposition date: 2026-02-09, release date: 2026-05-06, Last modification date: 2026-05-20)

Primary citation

Tsuzuki, K.,Onizuka, K.,Okada, M.,Nagasawa, R.,Miyashita, E.,Komatsu, K.R.,Saito, H.,Kondo, J.,Nagatsugi, F.
RNA-binding landscape of amiloride: large-scale profiling and structural basis of U-U mismatch recognition.
Rsc Chem Biol, 2026

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 ( = 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 its signature complementary hydrogen bonding interactions.

PubMed: 42100640
DOI: 10.1039/d6cb00055j

Experimental method

X-RAY DIFFRACTION (2.8 Å)