Observation of cleavage in DNA and nucleotides following oxygen K-shell ionization by measuring X-ray absorption near edge structure

Abstract

Purpose: To investigate which type of bond is more likely to be cleaved in functional groups in DNA including the nucleobases by the K-shell ionization of oxygen of DNA, and to determine whether the production of propenal is specific to the oxygen resonant excitation. To investigate the degradation pattern which depends on the type of nucleobase in the DNA monomer.Materials and methods: Calf thymus DNA film and four nucleotides (dAMP, TMP, dGMP, and dCMP) films were used as samples. Soft X-rays with energy of 560 eV were used to irradiate the samples, and the changes in the X-ray absorption near edge structure (XANES) spectra during the irradiation were measured. The XANES measurements were performed by using a 0.02 eV scanning photon energy step.Results: The difference spectra for DNA and nucleotides were similar to those for pyridine deprotonation. The oxygen K-edge regions in the difference spectra were all similar apart from the spectrum obtained at the resonant excitation energy of oxygen in DNA. The spectral change did not depend on the type of nucleotide.Conclusion: (1) Deprotonation of the nucleobase -NH is usually induced by core ionization of carbon, nitrogen, and oxygen; (2) propenal production is specific to the oxygen K-shell resonant excitation; and (3) the pattern of XANES spectral changes does not significantly depend on the type of nucleobase.