30SC

Hairpin Inosine GCAA tetraloop

Summary for 30SC

• Entry DOI: 10.2210/pdb30sc/pdb
• NMR Information: BMRB: 35053
• Descriptor: RNA (5'-R(*GP*AP*AP*IP*GP*GP*CP*AP*AP*CP*CP*UP*UP*CP*G)-3') (1 entity in total)
• Functional Keywords: inosine modified hairpin, gcaa tetraloop, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 4815.94

Authors

Mitteregger, C.,Micura, R.,Kreutz, C. (deposition date: 2026-05-11, release date: 2026-07-22, Last modification date: 2026-08-05)

Primary citation

Mitteregger, C.,Bereiter, R.,Schramm, A.,Ennifar, E.,Kreutz, C.,Micura, R.
1-Deazainosine-impact on RNA structure and role in exploring ribozyme catalysis.
Chem Sci, 17:13874-13883, 2026

PubMed Abstract: Synthetic RNAs bearing deazapurine nucleobases are powerful probes for dissecting RNA-catalyzed reactions by atomic mutagenesis. Here we systematically characterize RNA containing 1-deazainosine (cI) and compare it with inosine (I). We first report the synthesis of a suitably protected cI phosphoramidite and its incorporation into RNA by solid-phase synthesis. We then provide a comprehensive thermodynamic analysis of base-pair stability from UV-melting experiments, showing that cI-C pairs are less stable than the corresponding I-C pairs. Although a two-hydrogen-bond Hoogsteen interaction between cI and protonated C is conceivable, NMR spectroscopy indicates that cI-C predominantly adopts a Watson-Crick-like geometry with a single hydrogen bond. These pairs are accommodated within RNA duplexes without disrupting neighboring base pairing. We also use cI to probe poly(I:C) motifs that mimic viral double-stranded RNA, assessing how strand length governs duplex hairpin formation. Finally, atomic mutagenesis of the twister ribozyme with cI supports the hypothesis that an active-site guanine participates directly in phosphodiester-bond cleavage. Together, these results clarify how deazapurines modulate nucleic-acid properties and provide guidance for their use in atomic mutagenesis to interrogate RNA catalysis.

PubMed: 42266902
DOI: 10.1039/d6sc04009h

Experimental method

SOLUTION NMR