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Quantitative Γ-HCNCH: determination of the glycosidic torsion angle χ in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy

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Abstract

A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle χ in 13C,15N-labeled oligonucleotides. The quantitative Γ-HCNCH measures the dipolar cross-correlated relaxation rates \(\Gamma_{{\rm C6H6,C1}^{\prime}{\rm H1}^{\prime}}^{\rm DD,DD}\) (pyrimidines) and \(\Gamma_{{\rm C8H8,C1}^{\prime}{\rm H1}^{\prime}}^{\rm DD,DD}\) (purines). Cross-correlated relaxation rates of a 13C,15N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded χ-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the χ-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.

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Acknowledgements

The paper is dedicated to Christian Griesinger. The work has been supported by the state of Hesse (Center for Biomolecular Magnetic Resonance) and the DFG (Sonderforschungsbereich: RNA-Ligand-Interactions). We wish to thank Oliver Ohlenschläger, Jens Wöhnert and Matthias Görlach for providing us with the 30mer RNA sample.

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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, Jan Ferner, Elke Duchardt & Harald Schwalbe

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  1. Jörg Rinnenthal
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Correspondence to Harald Schwalbe.

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Rinnenthal, J., Richter, C., Ferner, J. et al. Quantitative Γ-HCNCH: determination of the glycosidic torsion angle χ in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy. J Biomol NMR 39, 17–29 (2007). https://doi.org/10.1007/s10858-007-9167-5

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