Abstract
The neomycin-sensing riboswitch is an engineered riboswitch developed to regulate gene expression in vivo in the lower eukaryote Saccharomyces cerevisiae upon binding to neomycin B. With a size of only 27nt it is the smallest functional riboswitch element identified so far. It binds not only neomycin B but also related aminoglycosides of the 2′-deoxystreptamine class with high affinity. The regulatory activity, however, strongly depends on the identity of the aminoglycoside. As a prerequisite for the structure determination of riboswitch-ligand complexes we report here the 1H, 15N, 13C and partial 31P chemical shift assignments for the minimal functional 27nt neomycin sensing riboswitch RNA in complex with the 4,5-linked neomycin analog ribostamycin and the 4,6-linked aminoglycoside tobramycin.
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References
Keller R (2004) The computer aided resonance assignment tutorial. CANTINA Verlag, Goldau
Legault P, Farmer BT, Mueller L, Pardi A (1994) Through-bond correlation of adenine protons in a 13C-labeled ribozyme. J Am Chem Soc 116:2203–2204
Marino JP, Schwalbe H, Anklin C, Bermel W, Crothers DM, Griesinger C (1995) Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotide by a 1H, 13C, 31P triple resonance experiment: HCP-CCH-TOCSY. J Biomol NMR 5:87–92
Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78:305–334
Scott LG, Hennig M (2008) RNA structure determination by NMR. Methods Mol Biol 452:29–61
Sklenar V, Dieckmann T, Butcher SE, Feigon J (1998) Optimization of triple-resonance HCN experiments for application to larger RNA oligonucleotides. J Mag Res 130:119–124
Wallis MG, Ahsen U, Schroeder R, Famulok M (1995) A novel RNA motif for neomycin recognition. Chem Biol 2:543–552
Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B (2008) Screening for engineered neomycin riboswitches that control translation initiation. RNA 14(1):89–97
Wöhnert J, Ramachandran R, Görlach M, Brown LR (1999) Triple resonance experiments for correlation of H5 and exchangeable pyrimidine base hydrogens in 13C, 15N labeled RNA. J Mag Res 139:430–433
Wöhnert J, Görlach M, Schwalbe H (2003) Triple resonance experiments for the simultaneous correlation of H5/H6 and exchangeable protons of pyrimidine nucleotides in 13C, 15N labeled RNA applicable to larger RNA molecules. J Biomol NMR 26:79–83
Acknowledgments
We thank Sabine Häfner and Matthias Görlach for a generous gift of T7-RNA-polymerase and Christian Richter for excellent technical support. We are grateful to the Center of Biomolecular Magnetic Resonance (BMRZ) of the Johann-Wolfgang-Goethe-University Frankfurt and the Deutsche Forschungsgemeinschaft (DFG) (grants WO 901/1-2 to J. W. and SU 402/4-1 to B.S.) for financial support. J. W. and B. S. are recipients of Aventis Foundation endowed professorships in Chemical Biology.
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Schmidtke, S.R., Duchardt-Ferner, E., Weigand, J.E. et al. NMR resonance assignments of an engineered neomycin-sensing riboswitch RNA bound to ribostamycin and tobramycin. Biomol NMR Assign 4, 115–118 (2010). https://doi.org/10.1007/s12104-010-9223-z
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DOI: https://doi.org/10.1007/s12104-010-9223-z