Charging of DNA Complexes\nin Positive-Mode Native\nElectrospray Ionization Mass Spectrometry

Native mass spectrometry (nMS) provides insights into\nthe structures\nand dynamics of biomacromolecules in their native-like states by preserving\nnoncovalent interactions through “soft” electrospray\nionization (ESI). For native proteins, the number of charges that\nare acquired scales with the surface area and mass. Here, we explore\nthe effect of highly negatively charged DNA on the ESI charge of protein\ncomplexes and find a reduction of the mass-to-charge ratio as well\nas a greater variation. The charge state distributions of pure DNA\nassemblies show a lower mass-to-charge ratio than proteins due to\ntheir greater density in the gas phase, whereas the charge of protein–DNA\ncomplexes can additionally be influenced by the distribution of the\nESI charges, ion pairing events, and collapse of the DNA components.\nOur findings suggest that structural features of protein–DNA\ncomplexes can result in lower charge states than expected for proteins.