| TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK and Radovan FIALA. NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop. Journal of Biomolecular Structure and Dynamics. GUILDERLAND: Adenine Press, 2007, vol. 25, No 3, p. 307-326, 19 pp. ISSN 0739-1102. |
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@article{728047,
author = {Trantírek, Lukáš and Caha, Erik and Kadeřávek, Pavel and Fiala, Radovan},
article_location = {GUILDERLAND},
article_number = {3},
keywords = {RNA; nucleic acid; dynamics; internal motion; NMR; C-13},
language = {eng},
issn = {0739-1102},
journal = {Journal of Biomolecular Structure and Dynamics},
title = {NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop},
url = {http://www.jbsdonline.com/},
volume = {25},
year = {2007}
}
TY - JOUR
ID - 728047
AU - Trantírek, Lukáš - Caha, Erik - Kadeřávek, Pavel - Fiala, Radovan
PY - 2007
TI - NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop
JF - Journal of Biomolecular Structure and Dynamics
VL - 25
IS - 3
SP - 307-326
EP - 307-326
PB - Adenine Press
SN - 07391102
KW - RNA
KW - nucleic acid
KW - dynamics
KW - internal motion
KW - NMR
KW - C-13
UR - http://www.jbsdonline.com/
N2 - 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.
ER -
TRANTÍREK, Lukáš, Erik CAHA, Pavel KADEŘÁVEK and Radovan FIALA. NMR 13C-relaxation Study of Base and Sugar Dynamics in GCAA RNA Hairpin Tetraloop. \textit{Journal of Biomolecular Structure and Dynamics}. GUILDERLAND: Adenine Press, 2007, vol.~25, No~3, p.~307-326, 19 pp. ISSN~0739-1102.
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