Characterization and Modeling of Conserved RNA Elements Within the Human Coronavirus OC43 5’ UTR

Abstract

Recent global events have highlighted the need for the rapid characterization of viral components used for replication which may serve as potential drug interaction sites. Structural RNA elements serve as a scaffold for various cellular and viral proteins to assemble, providing opportunities for small molecules to act as potential drug targets. Here, we report the rapid identification and characterization of four conserved RNA elements of the 5’‐untranslated region (5’‐UTR) of human coronavirus OC43 (HCoV‐OC43) genome using a combination of experimental and computational methods. Evolutionary trace analysis (ETA) was used to determine highly conserved regions within the 5’‐UTR. The hydrogen‐bonding patterns were studied using chemical probing with dimethyl sulfate (DMS) and NMR‐based experimentation. In order to refine the de novo structures generated using AMBER force fields, semi‐empirical models were generated using small‐angle X‐ray scattering (SAXS) data, as well as experimental data collected with NMR and chemical probing. These models were then used to visualize the evolutionary trace and DMS reactivity data in a site‐specific manner throughout the 5’‐UTR of OC43. Analysis of these results provides insight and a structural basis for the evolutionary importance of cis‐acting RNA elements within the HCoV‐OC43 5’‐UTR. The data presented herein provide a foundation for further biophysical characterization of small molecule interactions with effects on viral processes.