5‐Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson–Crick like cmo⁵U‐G Base Pairs

Abstract

Watson–Crick like G‐U mismatches with tautomeric Genol or Uenol bases can evade fidelity checkpoints and thereby contribute to translational errors. The 5‐oxyacetic acid uridine (cmo5U) modification is a base modification at the wobble position on tRNAs and is presumed to expand the decoding capability of tRNA at this position by forming Watson–Crick like cmo5Uenol‐G mismatches. A detailed investigation on the influence of the cmo5U modification on structural and dynamic features of RNA was carried out by using solution NMR spectroscopy and UV melting curve analysis. The introduction of a stable isotope labeled variant of the cmo5U modifier allowed the application of relaxation dispersion NMR to probe the potentially formed Watson–Crick like cmo5Uenol‐G base pair. Surprisingly, we find that at neutral pH, the modification promotes transient formation of anionic Watson–Crick like cmo5U−‐G, and not enolic base pairs. Our results suggest that recoding is mediated by an anionic Watson–Crick like species, as well as bring an interesting aspect of naturally occurring RNA modifications into focus—the fine tuning of nucleobase properties leading to modulation of the RNA structural landscape by adoption of alternative base pairing patterns.

The multiple flavors of GoU pairs in RNA

“…A similar model for the U34*oG(+3) pair had put been forward by Takai and Yokoyama . More recently, NMR experiments support an anionic state of the modified 5‐oxyacetic acid‐uracil base . It was therefore suggested that, like mnm 5 s 2 U34, cmo 5 U34 forms a minor groove–displaced UoG pair and not a Watson‐Crick–like tautomeric UoG pair .…”

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

“…The WC-like sugar-backbone conformation further supports a mutagenic role for these fleeting WC-like states as this is likely to align functional groups for phosphodiester bond formation during catalysis by DNA polymerases. Based on these results, it is very likely that base modifications that stabilize ionization and promote miscoding such as 5-Bromo and Fluoro uridine (Yu et al 1993 ), and Uridine 5-oxyacetic acid (Strebitzer et al 2018 ) do so in part via formation of a WC-like ES conformation.…”

“…This anionic WC-like species could explain the increase in G·T misincorporation probability with increasing pH. Yu et al ( 1993 ) Together, the tautomeric and anionic WC-like G·T mismatches could rationalize why chemical modifications that stabilize or mimic either tautomeric (Harris et al 2003 ; Budowsky 1976 ; Woodside and Guengerich 2002 ; Cantara et al 2013 ; Vendeix et al 2012 ; Kurata et al 2008 ; Ikeuchi et al 2010 ) or ionic (Yu et al 1993 ; Strebitzer et al 2018 ; Weixlbaumer et al 2007 ) forms of the bases increase the probability of errors during replication and translation.…”

Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function

“…To suppress efficiently this artifact, a phase-modulated CLEAN chemical exchange spectroscopy (CLEANEX-PM) was applied to the mixing period of a water-selective pulse sequence [53]. The hydrogen exchange data for various nucleic acids using CLEANEX-PM have been reported [[53], [54], [55], [56]].…”