Nanoscale structure determination of Murray Valley encephalitis and Powassan virus non-coding RNAs

Tyler Mrozowich, Amy Henrickson, Borries Demeler, Trushar R. Patel

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


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. Information on their structural features is essential to gain detailed insights into their functions and interactions with host proteins. In this study, the 5’ and 3’ terminal regions of Murray Valley encephalitis virus and Powassan virus were examined using biophysical and computational modeling methods. First, we used size exclusion chromatography and analytical ultracentrifuge methods to investigate the purity of in-vitro transcribed RNAs. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs, which suggest that the 3’ terminal regions are highly extended as 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 reinforce that the 5’ terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3’ terminal regions.

Original languageEnglish
Article number190
Issue number2
StatePublished - 2020


  • Analytical ultracentrifugation
  • Computational RNA structure modeling
  • Flavivirus
  • Murray Valley encephalitis virus
  • Non-coding RNA
  • Powassan virus
  • Small-angle X-ray scattering


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