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.

One-Electron Oxidation of DNA by Ionizing Radiation: Competition between Base-to-Base Hole-Transfer and Hole-Trapping

“…Variations in the M factors display interesting properties, including the end effect reported on previously 14. A pronounced end effect occurs when Gua is at the 3' end of short oligomers, resulting in M(Gua) > M(Cyt).…”

“…The fraction of trapped radicals due to dRib(C n' -H) • is known to be ∼11% of the total: G dRib(fr) = ∼0.11 × G tot (fr). 13,14…”

Direct Damage to the Backbone of DNA Oligomers Is Influenced by the OH Moiety at Strand Ends, by the Type of Base, and by Context

“…It was changes in R G/C in our earlier work on d(GC) n that first drew our attention to an end effect; e.g., d(CG) 5 and d(CG) 10 gave R G/C =1.9 ± 0.1 and 1.1 ± 0.1, respectively 7. Similar changes were observed in the work reported here, as can be seen by comparing R G/C in rows 1 and 2 of Table 1.…”

“…Mathematical equations were derived to describe the yield of free base release as a function of CG-oligomer length 7. Two reaction pathways in the model were key.…”

Plant Extracts and Plant-Derived Compounds: Promising Players in Countermeasure Strategy Against Radiological Exposure: A Review

“…The interactions of these agents with cells has been shown to cause alterations in the gene expression pattern, mutations, weakening of repair mechanisms (Little, 2000;Sharma et al, 2009;Cramers et al, 2011;Mukherjee et al, 2012;Francois et al, 2013;Mikhailenko et al, 2013). Agents that can be radioprotective must counter some or all the damaging effects of radiological exposure in the cell including those mentioned above.…”