Review Time-Resolved NMR Studies of RNA Folding Boris Fu ¨rtig, 1 Janina Buck, 1 Vijayalaxmi Manoharan, 1 Wolfgang Bermel, 2 Andres Ja ¨schke, 3 Philipp Wenter, 4 Stefan Pitsch, 4 Harald Schwalbe 1 1 Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany 2 Bruker Biospin GmbH, Silberstreifen 4, D-76287 Rheinstetten, Germany 3 Department of Chemistry, Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany 4 Laboratory of Nucleic Acid Chemistry, E ´ cole Polytechnique Fe´de´ralede Lausanne, EPFL-BCH, CH-1015 Lausanne, Switzerland Received 3 April 2007; revised 8 May 2007; accepted 9 May 2007 Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/bip.20761 This article was originally published online as an accepted preprint. The ‘‘Published Online’’date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com INTRODUCTION RNA Structural Transitions R NA structural transitions are implied in a number of cellular events: Large amplitude structural transi- tions occur during RNA folding itself, i.e. the transi- tion from an unstructured polynucleotide chain to its functional three-dimensional structure. Similarly, structural transitions are observed for the refolding of RNA structures involving a so-called conformational switch of one particular RNA conformation into another different one Review Time-Resolved NMR Studies of RNA Folding Correspondence to: Harald Schwalbe; e-mail: schwalbe@nmr.uni-frankfurt.de ABSTRACT: The application of real-time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time-resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long-range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time-resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non-coding RNAs in cells. # 2007 Wiley Periodicals, Inc. Biopolymers 86: 360–383, 2007. Keywords: NMR spectroscopy; RNA folding; time-resolved NMR; photolabile caged compounds Contract grant sponsor: DFG (SFB 579: ‘‘RNA-Ligand-Interaction’’), Studienstif- tung des Deutschen Volkes, EU (Joint Research Activity within Integrated Infra- structure Initiative: EU-NMR), state Hesse (Center for Biomolecular Magnetic Resonance (BMRZ)) V V C 2007 Wiley Periodicals, Inc. 360 Biopolymers Volume 86 / Number 5-6