Strong Anion Exchange for Studying Protein–DNA Interactions by H/D Exchange Mass Spectrometry

The use of mass spectrometry to study protein–ligand interactions is expanding into more complex systems including protein–DNA interactions. The excess amount of a model DNA or, more typically, an oligodeoxynucleotide (ODN), needed to study such interactions in an amide hydrogen-deuterium (H/D) exchange experiment, for example, causes serious signal suppression in the protein analysis. We describe here a modification of the traditional H/D exchange protocol whereby we utilize a strong anion exchange column to rapidly remove the ODN from solution before MS analysis. We showed the successful incorporation of such a column in a study of two protein–ODN systems: (1) the DNA-binding domain of human telomeric repeat binding factor 2 with a telomeric oligodeoxynucleotide and (2) thrombin with the thrombin-binding aptamer. The approach gave no appreciable difference in back-exchange compared to a method in which no strong anion exchange (SAX) is used.