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.

We are grateful to Matthew Conley and Christophe Coperet from ETH Zurich for providing the mesoporous silica materials. We are grateful to Prof. P. Tordo, Dr. O. Ouari, and Dr. G. Casano (Aix-Marseille Universite, France) for providing the biradicals used in the DNP NMR experiments.International audienceWe show how dynamic nuclear polarization (DNP) NMR can be used in combination with models for polarization dynamics to determine the domain sizes in complex materials. By selectively doping a source component with radicals and leaving the target undoped, we Can measure experimental polarization buildup curves which can be compared with simulations based on heterogeneous distributions of polarization-within the sample. The variation of the integrated DNP enhancement as a function of the polarization time is found to be characteristic of the geometry. We demonstrate the method experimentally on four different systems where we successfully determine domain sizes between 200 and 20 000 nm, specifically in powdered histidine hydrochloride monohydrate) pore lengths of mesoporous silica materials, and two domain sizes in two component polymer film coatings. Additionally, we find that even in the apparently homogeneous frozen solutions used as polarization sources in most DNP experiments, polarization is relayed from protons near the radicals to the bulk of the solution by spin diffusion, which explains the experimentally observed buildup times in these samples