Publication details

Limits of Accuracy of RNA Dynamics Studied by Model Free Analysis of C-13 Relaxation



Year of publication 2007
Type Article in Proceedings
Conference 22nd NMR Valtice
MU Faculty or unit

Faculty of Science

Field Biochemistry
Keywords dynamics; NMR spectroscopy; nucleic acid; relaxation; chemical shift anisotropy
Description The model free analysis of the relaxation data is one of the possible approaches to the investigation of the internal dynamics via NMR. However, the validity of the model-free approach for C-13 relaxation of nucleic acids has not been tested sufficiently. Especially, the properties of the chemical shielding tensor may not always meet the assumptions on which the model-free approach is based. The goal of this work was to find the conditions under which the model free analysis of the C-13 relaxation rates in nucleic acid bases is applicable with an acceptable accuracy. We have studied the effect for axially symmetric molecules with the ratio of the diffusion coefficients parallel and perpendicular to the axis of the molecule ranging from 2.4 to 8.2, corresponding to DNA duplexes with 12 to 30 base pairs. The results show that the studies of the relaxation behavior at 800 MHz of carbon C6 in pyrimidines are inaccurate for all studied molecules. On the other hand, the relaxation rates at the lowest studied magnetic field corresponding to 400 MHz provide acceptably accurate order parameters for all studied cases except for carbons C6 in pyrimidines and the molecule 30 base pairs long.
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