Abstract
RNA aptamers are used in a wide range of biotechnological or biomedical applications. In many cases the high resolution structures of these aptamers in their ligand-complexes have revealed fundamental aspects of RNA folding and RNA small molecule interactions. Fluorescent RNA-ligand complexes in particular find applications as optical sensors or as endogenous fluorescent tags for RNA tracking in vivo. Structures of RNA aptamers and aptamer ligand complexes constitute the starting point for rational function directed optimization approaches. Here, we present the NMR resonance assignment of an RNA aptamer binding to the fluorescent ligand tetramethylrhodamine (TMR) in complex with the ligand 5-carboxy-tetramethylrhodamine (5-TAMRA) as a starting point for a high-resolution structure determination using NMR spectroscopy in solution.
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Acknowledgments
This work was supported by the Adolf-Messer Foundation, the Center for Biomagnetic Resonance (BMRZ) of the Goethe-University Frankfurt and the Deutsche Forschungsgemeinschaft (DFG) (SFB 902 “Molecular principles of RNA-based regulation” B10) and the Austrian Science Fund (FWF, projects P28725 and P 26550).
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Duchardt-Ferner, E., Juen, M., Kreutz, C. et al. NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine. Biomol NMR Assign 11, 29–34 (2017). https://doi.org/10.1007/s12104-016-9715-6
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DOI: https://doi.org/10.1007/s12104-016-9715-6