NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine
- 398 Downloads
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.
KeywordsRNA Aptamer NMR assignment Tetramethylrhodamine Site-specific isotope labeling Fluorescent RNA aptamers 5-TAMRA
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).
- Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J (2016) What a difference an OH makes: conformational dynamics as the basis for the ligand specificity of the neomycin-sensing riboswitch. Angew Chem Int Ed Engl 55:1527–1530CrossRefGoogle Scholar
- Marino JP, Schwalbe H, Anklin C, Bermel W, Crothers DM, Griesinger C (1994) A 3-dimensional triple-resonance H-1, C-13, P-31 experiment—sequential through-bond correlation of ribose protons and intervening phosphorus along the RNA oligonucleotide backbone. J Am Chem Soc 116:6472–6473CrossRefGoogle Scholar
- Sklenar V, Peterson RD, Rejante MR, Feigon J (1994) Correlation of nucleotide base and sugar protons in a 15 N-labeled HIV-1 RNA oligonucleotide by 1H-15N HSQC experiments. J Biomol NMR 4:117–122Google Scholar