Quantitative analysis of protein-RNA interactions by gel mobility shift

Methods Mol Biol. 2008;488:99-115. doi: 10.1007/978-1-60327-475-3_7.


The gel mobility shift assay is routinely used to visualize protein-RNA interactions. Its power resides in the ability to resolve free from bound RNA with high resolution in a gel matrix. We review the quantitative application of this approach to elucidate thermodynamic properties of protein-RNA complexes. Assay designs for titration, competition, and stoichiometry experiments are presented for two unrelated model complexes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Electrophoretic Mobility Shift Assay / methods*
  • Protein Binding
  • Proteins / chemistry*
  • Proteins / metabolism
  • RNA / chemistry*
  • RNA / metabolism


  • Proteins
  • RNA