Residue specific ribose and nucleobase dynamics of the cUUCGg RNA tetraloop motif by NMR 13C relaxation

The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with C-13 and N-15 were studied by C-13 spin relaxation experiments. R-1, R-1 rho and the (13/) C-{H-1} steady-state NOE of C-6 and C-1' in pyrimidine and C-8 and C-1' in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time tau(c) of 2.31 +/- 0.13 ns and an axial ratio of 1.35 +/- 0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported C-13 chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539 - 10551; Fiala et al., 2000 J. Biomol. NMR 16, 291 - 302; Sitko., D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165 - 190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82< S-2 < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution ( S-2 = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of C-13 relaxation rates were found to be in agreement with N-15 relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702 - 709).