Publication details

NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop



Year of publication 2007
Type Article in Periodical
Magazine / Source Journal of Biomolecular Structure and Dynamics
MU Faculty or unit

Faculty of Science

Field Biochemistry
Keywords RNA; nucleic acid; dynamics; internal motion; NMR; C-13
Description Intramolecular dynamics of a 14-mer RNA hairpin including GCAA tetraloop was investigated by 13C NMR relaxation. R1 and R1rho relaxation rates were measured for all protonated base carbons as well as for C1' carbons of ribose sugars at several magnetic field strengths. The data has been interpreted in the framework of modelfree analysis (G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4546-4559 (1982); G. Lipari and A. Szabo, J. Am. Chem. Soc. 104, 4559-4570 (1982)) characterizing the internal dynamics of the molecule by order parameters and correlation times for fast motions on picosecond to nanosecond time scale and by contributions of the chemical exchange. The fast dynamics reveals a rather rigid stem and a significantly more flexible loop. The cytosine and the last adenine bases in the loop as well as all the loop sugars exhibit a significant contribution of conformational equilibrium on microsecond to millisecond time scale. The high R1rho values detected on both base and sugar moieties of the loop indicate coordinated motions in this region. A semiquantitative analysis of the conformational equilibrium suggests the exchange rates on the order of 10000/s. The results are in general agreement with dynamics studies of GAAA loops by NMR relaxation and fluorescent spectroscopy and support the data on the GCAA loop dynamics obtained by MD simulations.
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