Studying Protein–DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry

  • Ruzena Filandrova
  • Daniel Kavan
  • Alan Kadek
  • Petr Novak
  • Petr ManEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2247)


Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein–DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.

Key words

DNA Hydrogen/deuterium exchange Protein–DNA binding Structural mass spectrometry Transcription factor 



Czech Science Foundation projects 16-24309S and 16-20860S are gratefully acknowledged. Additional support was obtained from EU/MEYS projects BioCeV (CZ.1.05/1.1.00/02.0109) and NPU II (LQ1604). R.F. also thanks Charles University Grant Agency (project 1618218) and SVV260427/2019.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  • Ruzena Filandrova
    • 1
    • 2
  • Daniel Kavan
    • 1
  • Alan Kadek
    • 1
    • 3
  • Petr Novak
    • 1
  • Petr Man
    • 1
    Email author
  1. 1.Institute of Microbiology of the Czech Academy of SciencesPragueCzech Republic
  2. 2.Faculty of Sciences, Charles UniversityPragueCzech Republic
  3. 3.Heinrich Pette InstituteLeibniz Institute for Experimental VirologyHamburgGermany

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