TY  - JOUR
A1  - Ferner, Jan
A1  - Villa, Alessandra
A1  - Duchardt-Ferner, Elke
A1  - Widjajakusuma, Elisabeth
A1  - Wöhnert, Jens
A1  - Stock, Gerhard
A1  - Schwalbe, Harald
T1  - NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops
T2  - Nucleic acids research
N2  - In a combined NMR/MD study, the temperature-dependent changes in the conformation of two members of the RNA YNMG-tetraloop motif (cUUCGg and uCACGg) have been investigated at temperatures of 298, 317 and 325 K. The two members have considerable different thermal stability and biological functions. In order to address these differences, the combined NMR/MD study was performed. The large temperature range represents a challenge for both, NMR relaxation analysis (consistent choice of effective bond length and CSA parameter) and all-atom MD simulation with explicit solvent (necessity to rescale the temperature). A convincing agreement of experiment and theory is found. Employing a principle component analysis of the MD trajectories, the conformational distribution of both hairpins at various temperatures is investigated. The ground state conformation and dynamics of the two tetraloops are indeed found to be very similar. Furthermore, both systems are initially destabilized by a loss of the stacking interactions between the first and the third nucleobase in the loop region. While the global fold is still preserved, this initiation of unfolding is already observed at 317 K for the uCACGg hairpin but at a significantly higher temperature for the cUUCGg hairpin.
Y1  - 2008
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/5854
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30-57977
SN  - 1362-4962
SN  - 0305-1048
N1  - © 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
VL  - 36
IS  - 6
SP  - 1928
EP  - 1940
PB  - Oxford Univ. Press
CY  - Oxford
ER  -