NMR resonance assignments for the GTP-binding RNA aptamer 9-12 in complex with GTP

Abstract

Ligand binding RNAs such as artificially created RNA-aptamers are structurally highly diverse. Therefore, they represent important model systems for investigating RNA-folding, RNA-dynamics and the molecular recognition of chemically very different ligands, ranging from small molecules to whole cells. High-resolution structures of RNA-aptamers in complex with their cognate ligands often reveal unexpected tertiary structure elements. Recent studies on different classes of aptamers binding the nucleotide triphosphate GTP as a ligand showed that these systems not only differ widely in binding affinity but also in their ligand binding modes and structural complexity. We initiated the NMR-based structure determination of the high-affinity binding GTP-aptamer 9-12 in order to gain further insights into the diversity of ligand binding modes and structural variability of those aptamers. Here, we report 1H, 13C and 15N resonance assignments for the GTP 9-12-aptamer bound to GTP as the prerequisite for the structure determination by solution NMR.

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Acknowledgements

We are grateful to Christian Richter and Manfred Strupf for maintenance of the NMR facility and to Kerstin Yacoub for support in sample preparation. This work was supported by the Center for Biomolecular Magnetic Resonance (BMRZ) of the Goethe University Frankfurt, the Deutsche Forschungsgemeinschaft (DFG) (SFB 902 ‘‘Molecular principles of RNA-based regulation’’ B10) and the Austrian Science Fund (P28725 and P30370). Robbin Schnieders is recipient of a stipend of the Fonds der Chemischen Industrie.

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Correspondence to Antje C. Wolter or Jens Wöhnert.

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Wolter, A.C., Pianu, A., Kremser, J. et al. NMR resonance assignments for the GTP-binding RNA aptamer 9-12 in complex with GTP. Biomol NMR Assign 13, 281–286 (2019). https://doi.org/10.1007/s12104-019-09892-z

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Keywords

  • RNA
  • Aptamer
  • GTP
  • NMR assignment
  • Triple resonance experiments
  • Site-specific isotope labeling