Determination of the molecular conformation of uridine in aqueous solution by proton magnetic resonance spectroscopy. Comparison with β-pseudouridine

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Abstract
A complete analysis of the 220 MHz proton magnetic resonance spectrum of aqueous uridine is reported. From the data a model for the molecular conformation is presented and compared with that of β-pseudouridine. It is concluded that in both compounds the ribose rings are in rapid equilibrium between classical puckered structures. The temperature-independence of the ribose proton coupling constants and chemical shifts suggests that all the conformers involved in this equilibrium have very similar energies. Both compounds exhibit a preference for the gauche–gauche rotamer about the exocyclic 4′—5′ bond; this conclusion is shown to be independent of the parameters in the Karplus equation or the energy minima chosen for the rotamers. The anti conformation of the uracil base is shown to exist in both compounds. It is proposed that the special structural significance of β-pseudouridine in transfer RNA must be due to the potential hydrogen bond that may be formed by the nitrogen atom at position one in uracil.

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