Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
Anna Wacker, Julia E. Weigand, Sabine R. Akabayov, Nadide Altincekic, Jasleen Kaur Bains, Seyedeh Elnaz Banijamali, Oliver Binas, Jesús Castillo-Martínez, Erhan Can Çetiner, Betül Ceylan, Liang-Yuan Chiu, Jesse Davila‐Calderon, Karthikeyan Dhamotharan, Elke Duchardt‐Ferner, Jan Ferner, Lucio Frydman, Boris Fürtig, José Gallego, J. Tassilo Grün, Carolin Hacker, Christina Haddad, Martin Hähnke, Martin Hengesbach, Fabian Hiller, Katharina F. Hohmann, Daniel Hymon, Vanessa de Jesus, H.R.A. Jonker, Heiko Keller, Božana Knezic, Tom Landgraf, Frank Löhr, Le Luo, Klara R. Mertinkus, Christina Muhs, Mihajlo Novakovic, Andreas Oxenfarth, Martina Palomino‐Schätzlein, Katja Petzold, Stephen A. Peter, Dennis J. Pyper, Nusrat S. Qureshi, Magdalena Riad, Christian Richter, Krishna Saxena, Tatjana Schamber, Tali Scherf, Judith Schlagnitweit, Andreas Schlundt, Robbin Schnieders, Harald Schwalbe, Álvaro Simba-Lahuasi, Sridhar Sreeramulu, Elke Stirnal, Alexey Sudakov, Jan‐Niklas Tants, Blanton S. Tolbert, Jennifer Vögele, Lena Weiß, Julia Wirmer‐Bartoschek, Maria A. Wirtz Martin, Jens Wöhnert, Heidi Zetzsche
Abstract
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.