Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge


  • Interactions between proteins and nucleic acids underpin many vital cellular processes. A significant proportion of cell proteins bind with RNA, and nuclear DNA interfaces with various proteins.
  • Studying these interactions is essential, but existing techniques have limitations. X-ray crystallography and NMR offer detailed views but are resource-intensive and require specific conditions.
  • Other methods can analyze interaction thermodynamics but are limited by factors such as resolution or non-physiological testing conditions.


  • The researchers introduced an approach that uses analytical ultracentrifugation (AUC) and sedimentation velocity (SV), combined with a novel multiwavelength analytical ultracentrifugation (MWL-AUC) detector and high-performance computing to analyze data.
  • It is recognized as a premier method for analyzing macromolecular assemblies in solution and can closely mimic physiological conditions. During AUC experiments, solutes are distinguished based on their hydrodynamic properties, which offers insights into their concentration and other attributes.
  • In traditional AUC devices, data collection has limitations. In contrast, the new method focuses on a multiwavelength approach, which can capture a broader range of data, allowing for the differentiation of solutes based not just on hydrodynamics but also on their UV-Vis absorbance spectra.
  • This method can identify and quantify mixtures by deconvoluting overlapping spectra.


  • The advancement in methodology was applied to the interaction between human T cell-restricted intracellular antigen-1-related protein (hTIAR) and a West Nile virus RNA structure.
  • This specific interaction is of interest because of its implications in human health and the absence of effective antiviral treatments for West Nile virus.
  • By studying the hTIAR and RNA binding processes using the MWL-AUC method, researchers aim to understand the mechanisms that regulate RNA synthesis, laying a foundation for future therapeutic designs against flaviviruses.
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