Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-coding RNAs

Abstract

Viral infections are responsible for numerous deaths worldwide. Flaviviruses, which contain RNA as their genetic material, are one of the most pathogenic families of viruses. There is an increasing amount of evidence suggesting that their 5 and 3 non-coding terminal regions are critical for their survival. In this study, the 5 and 3 terminal regions of Murray Valley Encephalitis and Powassan virus were examined using biophysical and computational modeling methods. First, the purity of in-vitro transcribed RNAs were investigated using size exclusion chromatography and analytical ultracentrifuge methods. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs, which suggested that the 3 terminal regions are highly extended, compared to the 5 terminal regions for both viruses. Using computational modeling tools, we reconstructed 3-dimensional structures of each RNA fragment and compared them with derived small-angle X-ray scattering low-resolution structures. This approach allowed us to further reinforce that the 5 terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3 terminal regions.