The structure of the double‐stranded RNA pentamer 5′(CACAG) · 5′(CUGUG) determined by nuclear Overhauser enhancement measurements: Interproton distance determination and structure refinement on the basis of X‐ray coordinates

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Abstract
The structure in solution of the duplex RNA pentamer 5′(CACAG) · 5′(CUGUG), comprising the stem of the TΨC loop of yeast tRNAPhe, has been investigated by means of one‐ and two‐dimensional nuclear Overhauser enhancement measurements. All non‐exchangeable base and sugar proton resonances with the exception of the H5′/H5” sugar resonances are assigned in a sequential manner. From the relative intensities of the cross‐peaks obtained in the pure‐phase absorption two‐dimensional nuclear Overhauser enhancement spectra at several mixing times, it is deduced that the RNA pentamer adopts an A‐type conformation in solution. Cross‐relaxation rates and interproton distances are determined from the time dependence of the nuclear Overhauser effets, principally by one‐dimensional measurements. The structure of the RNA pentamer is then refined by restrained least‐squares minimization on the basis of both distance and planarity restraints using fibre diffraction data as an initial model. The refined structure of the RNA pentamer is of the A type but exhibits local structural variations in glycosidic bond and backbone torsion angles as well as in propellor twist, base roll and base tilt angles.