Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides

Although
solution hydrogen–deuterium exchange mass spectrometry (HDX/MS)
is well-established for the analysis of the structure and dynamics
of proteins, it is currently not exploited for nucleic acids. Here
we used DNA G-quadruplex structures as model systems to demonstrate
that DNA oligonucleotides are amenable to in-solution HDX/MS in native
conditions. In trimethylammonium acetate solutions and in soft source
conditions, the protonated phosphate groups are fully back-exchanged
in the source, while the exchanged nucleobases remain labeled without
detectable back-exchange. As a result, the exchange rates depend strongly
on the secondary structure (hydrogen bonding status) of the oligonucleotides,
but neither on their charge state nor on the presence of nonspecific
adducts. We show that native mass spectrometry methods can measure
these exchange rates on the second to the day time scale with high
precision. Such combination of HDX with native MS opens promising
avenues for the analysis of the structural and biophysical properties
of oligonucleotides and their complexes.