1-Deazainosine-impact on RNA structure and role in exploring ribozyme catalysis

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 (c¹I) and compare it with inosine (I). We first report the synthesis of a suitably protected c¹I 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 c¹I–C pairs are less stable than the corresponding I–C pairs. Although a two-hydrogen-bond Hoogsteen interaction between c¹I and protonated C is conceivable, NMR spectroscopy indicates that c¹I–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 c¹I to probe poly(I:C) motifs that mimic viral double-stranded RNA, assessing how strand length governs duplex versus hairpin formation. Finally, atomic mutagenesis of the twister ribozyme with c¹I 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.