Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons

To experimentally investigate the role of hydration in the initial process of the decomposition of 2-deoxy-d-ribose (dR), which is a major component of the DNA backbone, we used mass spectrometry to monitor the ions desorbing from hydrated dR films exposed to monochromatic soft X rays (560 eV). The X-ray photons preferentially ionize the K-shell electrons of the oxygen atoms in DNA. Hydrated dR samples were prepared under vacuum by exposing a cooled (∼150 K) dR film deposited on a Si substrate to water vapor. Using a quadrupole mass spectrometer, we observed the desorption of ions such as H⁺, CH _x⁺, C₂H _x⁺, CH _xO⁺, C₃H _x⁺ and C₂H _xO⁺ ( x = 1, 2, 3 and 4). In addition, the desorption of H₂O⁺ or H₃O⁺ was observed in the mass spectra of hydrated dR films. Except for H⁺, the yields of these ions decreased when one layer of water molecules was deposited onto the film. These ions are produced by C-C or C-O bond scission. This result suggests that the water molecules act as a quencher, suppressing Coulomb repulsion and thus the extensive molecular decomposition of dR. Ab initio molecular dynamics simulations were performed to rationalize the fragments observed in the experiments. The results of the dynamical process of a hydrated dR molecule after oxygen K-ionization revealed elongation of a C-O bond of dR and the O-H bonds of both dR and water molecules prior to the Auger process, resulting in the ejection of H⁺ ions. These results strongly suggest that the very early process contributes to reducing the dR fragmentation, producing the H₃O⁺ and H⁺ detected from the hydrated dR films. These desorbed ions may be involved in the induction of other types of damage, such as oxidatively generated base lesions, concomitantly produced with a strand break when produced in DNA.