title: Mechanisms of strand break formation in DNA due to the direct effect of ionizing radiation: the dependency of free base release on the length of alternating CG oligodeoxynucleotides.
abstract: The question of how NA base sequence influences the yield of DNA strand breaks produced by the direct effect of ionizing radiation was investigated in a series of oligodeoxynucleotides of the form (d(CG)(n))(2) and (d(GC)(n))(2). The yields of free base release from X-irradiated DNA films containing 2.5 waters/nucleotide were measured by HPLC as a function of oligomer length. For (d(CG)(n))(2), the ratio of the Gua yield to Cyt yield, R, was relatively constant at 2.4-2.5 for n = 2-4 and it decreased to 1.2 as n increased from 5 to 10. When Gua was moved to the 5' end, for example going from d(CG)(5) to d(GC)(5), R dropped from 1.9 +/- 0.1 to 1.1 +/- 0.1. These effects are poorly described if the chemistry at the oligomer ends is assumed to be independent of the remainder of the oligomer. A mathematical model incorporating charge transfer through the base stack was derived to explain these effects. In addition, EPR was used to measure the yield of trapped-deoxyribose radicals at 4 K following X-irradiation at 4 K. The yield of free base release was substantially greater, by 50-100 nmol/J, than the yield of trapped-deoxyribose radicals. Therefore, a large fraction of free base release stems from a nonradical intermediate. For this intermediate, a deoxyribose carbocation formed by two one-electron oxidations is proposed. This reaction pathway requires that the hole (electron loss site) transfers through the base stack and, upon encountering a deoxyribose hole, oxidizes that site to form a deoxyribose carbocation. This reaction mechanism provides a consistent way of explaining both the absence of trapped radical intermediates and the unusual dependence of free base release on oligomer length.
authors.affiliation: Department of Biochemistry, University of Rochester Medical Center, Rochester, New York 14642, USA.
authors.forename: Kiran K
authors.initials: KK
authors.lastname: Sharma
authors.forename: Yuriy
authors.initials: Y
authors.lastname: Razskazovskiy
authors.forename: Shubhadeep
authors.initials: S
authors.lastname: Purkayastha
authors.forename: William A
authors.initials: WA
authors.lastname: Bernhard
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004249:DNA Damage; D004578:Electron Spin Resonance Spectroscopy; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011839:Radiation, Ionizing
chemical_list: D009838:Oligodeoxyribonucleotides