title: Rapid NMR screening of RNA secondary structure and binding.
abstract: Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3' end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Helmling
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
authors.forename: Sara
authors.initials: S
authors.lastname: Keyhani
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Sochor
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
authors.forename: Boris
authors.initials: B
authors.lastname: Fürtig
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hengesbach
authors.affiliation: Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, 60438, Frankfurt am Main, Germany. schwalbe@nmr.uni-frankfurt.de.
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry; D001483:Base Sequence; D002021:Buffers; D008024:Ligands; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D058928:Riboswitch; D014158:Transcription, Genetic
chemical_list: D052157:Aptamers, Nucleotide; D002021:Buffers; D008024:Ligands; D058928:Riboswitch; D012313:RNA
keywords: High throughput method; In vitro transcription; NMR spectroscopy; RNA secondary structure; Riboswitch RNA