title: NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine.
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.
authors.affiliation: Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany. duchardt@bio.uni-frankfurt.de.|Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany. duchardt@bio.uni-frankfurt.de.
authors.forename: Elke
authors.identifier: 0000-0001-7521-8264
authors.initials: E
authors.lastname: Duchardt-Ferner
authors.affiliation: Centre for Molecular Biosciences (CMBI), Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Juen
authors.affiliation: Centre for Molecular Biosciences (CMBI), Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Kreutz
authors.affiliation: Institute for Molecular Biosciences, Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.|Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Wöhnert
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D008024:Ligands; D019906:Nuclear Magnetic Resonance, Biomolecular; D012235:Rhodamines / Q000378:metabolism*
chemical_list: C437523:5-carboxytetramethylrhodamine; D052157:Aptamers, Nucleotide; D008024:Ligands; D012235:Rhodamines
keywords: 5-TAMRA; Aptamer; Fluorescent RNA aptamers; NMR assignment; RNA; Site-specific isotope labeling; Tetramethylrhodamine