Probing RNA–Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation

Somdeb Mitra, Borries Demeler

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

3 Scopus citations


Recent advances in multi-wavelength analytical ultracentrifugation (MWL-AUC) combine the power of an exquisitely sensitive hydrodynamic-based separation technique with the added dimension of spectral separation. This added dimension has opened up new doors to much improved characterization of multiple, interacting species in solution. When applied to structural investigations of RNA, MWL-AUC can precisely report on the hydrodynamic radius and the overall shape of an RNA molecule by enabling precise measurements of its sedimentation and diffusion coefficients and identify the stoichiometry of interacting components based on spectral decomposition. Information provided in this chapter will allow an investigator to design experiments for probing ion and/or protein-induced global conformational changes of an RNA molecule and exploit spectral differences between proteins and RNA to characterize their interactions in a physiological solution environment.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages37
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Counterion
  • Hydrodynamic measurements
  • Multi-wavelength analytical ultracentrifugation
  • RNA folding
  • Sedimentation velocity


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