Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes

Methods Mol Biol. 2020:2113:111-118. doi: 10.1007/978-1-0716-0278-2_9.


Native electrospray ionization mass spectrometry (native ESI-MS) is a powerful tool to investigate non-covalent biomolecular interactions. It has been widely used to study protein complexes, but only few examples are described for the analysis of complexes involving RNA-RNA interactions. Here, we provide a detailed protocol for native ESI-MS analysis of RNA complexes. As an example, we present the analysis of the HIV-1 genomic RNA dimerization initiation site (DIS) extended duplex dimer bound to the aminoglycoside antibiotic lividomycin.

Keywords: Native mass spectrometry; RNA.

MeSH terms

  • Dimerization
  • HIV-1 / genetics
  • HIV-1 / metabolism*
  • Ligands
  • Nucleic Acid Conformation
  • Paromomycin / analogs & derivatives*
  • Paromomycin / chemistry
  • Paromomycin / metabolism
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism*
  • Spectrometry, Mass, Electrospray Ionization


  • Ligands
  • RNA, Viral
  • Paromomycin
  • lividomycin