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RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis

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Abstract

We have analyzed the relaxation properties of all 31P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R 1 and R 2 relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample. In order to interpret the 31P relaxation data (R 1, R 2), we measured the 31P chemical shift anisotropy (CSA) by solid-state NMR spectroscopy under various salt and hydration conditions. A value of 178.5 ppm for the 31P CSA in the static state (S 2 = 1) could be determined. In order to obtain information about fast time scale dynamics we performed a modelfree analysis on the basis of our relaxation data. The results show that subnanosecond dynamics detected around the phosphodiester backbone are more pronounced than the dynamics detected for the ribofuranosyl and nucleobase moieties of the individual nucleotides (Duchardt and Schwalbe, J Biomol NMR 32:295–308, 2005; Ferner et al., Nucleic Acids Res 36:1928–1940, 2008). Furthermore, the dynamics of the individual phosphate groups seem to be correlated to the 5′ neighbouring nucleobases.

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Acknowledgments

The work has been supported by the state of Hesse (Center for Biomolecular Magnetic Resonance, BMRZ) and the DFG (Sonderforschungsbereich 579: RNA-ligand-interactions). H·S. and C.G. are members of the DFG Cluster of Excellence: Macromolecular Complexes (EXC 115).

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  1. Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany

    Jörg Rinnenthal, Christian Richter, Senada Nozinovic, Boris Fürtig & Harald Schwalbe

  2. Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany

    Jakob J. Lopez & Clemens Glaubitz

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  1. Jörg Rinnenthal
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Correspondence to Harald Schwalbe.

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Rinnenthal, J., Richter, C., Nozinovic, S. et al. RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis. J Biomol NMR 45, 143–155 (2009). https://doi.org/10.1007/s10858-009-9343-x

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