Native Hydrogen/Deuterium Exchange Ion Mobility Mass Spectrometry of Structured DNA Oligonucleotides

Hydrogen/deuterium exchange coupled to mass spectrometry (HDX/MS) is a powerful technique to probe nucleic acid secondary structures and dynamics, but its ability to resolve conformers with identical masses remains limited. To overcome this challenge, we integrated ion mobility spectrometry (IMS) into our native HDX/MS workflow, and tested the approach on a variety of model DNA G-quadruplex structures. We show several examples of human telomeric sequence oligonucleotides where complexes of the same mass differ in their collision cross section, and each gas-phase conformational ensembles corresponds to unique solution exchange behaviors, allowing kinetic analysis beyond what is possible with HDX/native MS alone. But we also found examples where several gas-phase populations separated in ion mobility have exactly the same solution exchange behavior, suggesting that conformational rearrangements occur either during electrospray or at later stages in the gas phase. Finally, we show how IMS filtering can be leveraged to distinguish groups of non-specific cation binding on a given conformational ensemble, as indicated by populations with different masses and same exchange rates. These findings establish IMS as an essential tool for complementing HDX/MS in the characterization of structural polymorphism and conformational ensembles in DNA oligonucleotides.