Oxidation of deoxyribose in DNA leads to the formation of a spectrum of electrophilic products unique to each position in the sugar. For example, chemical reactions following abstraction of the C5‘-hydrogen atom partition to form either a nucleoside 5‘-aldehyde residue attached to the 5‘-end of the DNA strand or a 5‘-formyl phosphate residue attached to the 3‘-end of the DNA strand that is accompanied by a four-carbon fragment on the 5‘-end. We now present two approaches that both identify the latter fragment as 5‘-(2-phosphoryl-1,4-dioxobutane) and provide a means to quantify the formation of this residue by different oxidizing agents. The first approach involves oxidation of DNA followed by reaction with O-benzylhydroxylamine to form stable dioxime derivatives of the putative 5‘-(2-phosphoryl-1,4-dioxobutane) residues. The β-elimination product of this dioxime proved to be the expected trans-1,4-dioxo-2-butene, as judged by gas chromatographic and mass spectrometric (GC/MS) comparison to authentic dioximes of cis- and trans-1,4-dioxo-2-butene, which revealed a unique pattern of three signals for each isomer, and by X-ray crystallography. Using a benzylhydroxylamine dioxime derivative of [2H4]-labeled cis-1,4-dioxo-2-butene as an internal standard, the dose−response for the formation of 5‘-(2-phosphoryl-1,4-dioxobutane) was determined to be linear for γ-radiation, with ∼6 lesions per 106 nt per Gy, and nonlinear for Fe2+-EDTA. A comparison of 5‘-(2-phosphoryl-1,4-dioxobutane) formation to total deoxyribose oxidation suggests that γ-radiation produces ∼0.04 lesions per deoxyribose oxidation event. As a positive control for 5‘-oxidation of deoxyribose, the enediyne calicheamicin was observed to produce 5‘-(2-phosphoryl-1,4-dioxobutane) at the rate of ∼9 lesions per 106 nt per μM. A second approach to identifying and quantifying the sugar residue involved derivatization with hydrazine and β-elimination to form pyridazine followed by quantification of the pyridazine by GC/MS. Using this approach, it was observed that the enediyne, neocarzinostatin, produced a linear dose−response for pyridazine formation, as expected given the ability of this oxidant to cause 1‘-, 4‘-, and 5‘-oxidation of deoxyribose in DNA. The antitumor antibiotic, bleomycin, on the other hand, produced pyridazine at a 10-fold lower rate, which is consistent with 4‘-chemistry as the predominant mode of deoxyribose oxidation by this agent. These results provide novel insights into the chemistry of deoxyribose oxidation in DNA and two approaches to quantifying the 5‘-(2-phosphoryl-1,4-dioxobutane) precursor of trans-1,4-dioxo-2-butene, an electrophile known to react with nucleobases to form novel DNA adducts.

The oxidation of 2-deoxyribose in DNA has emerged as a critical determinant of the cellular toxicity of oxidative damage to DNA, with oxidation of each carbon producing a unique spectrum of electrophilic products. We have developed and validated an isotope-dilution gas chromatography-coupled mass spectrometry (GC-MS) method for the rigorous quantification of two major 2-deoxyribose oxidation products: the 2-deoxyribonolactone abasic site of 1’-oxidation and the nucleoside 5’-aldehyde of 5’-oxidation chemistry. The method entails elimination of these products as 5-methylene-2(5H)-furanone (5MF) and furfural, respectively, followed by derivatization with pentafluorophenylhydrazine (PFPH), addition of isotopically labeled PFPH derivatives as internal standards, extraction of the derivatives, and quantification by GC-MS analysis. The precision and accuracy of the method were validated with oligodeoxynucleotides containing the 2-deoxyribonolactone and nucleoside 5’-aldehyde lesions. Further, the well defined 2-deoxyribose oxidation chemistry of the enediyne antibiotics, neocarzinostatin and calicheamicin γ1I, was exploited in control studies, with neocarzinostatin producing 10 2-deoxyribonolactone and 300 nucleoside 5’-aldehyde per 106 nt per µM in accord with its established minor 1’- and major 5’-oxidation chemistry. Calicheamicin unexpectedly caused 1’-oxidation at a low level of 10 2-deoxyribonolactone per 106 nt per µM in addition to the expected predominance of 5’-oxidation at 560 nucleoside 5’-aldehyde per 106 nt per µM. The two hydroxyl radical-mediated DNA oxidants, γ-radiation and Fe2+-EDTA, produced nucleoside 5’-aldehyde at a frequency of 57 per 106 nt per Gy (G-value 74 nmol/J) and 3.5 per 106 nt per µM, respectively, which amounted to 40% and 35%, respectively, of total 2-deoxyribose oxidation as measured by a plasmid nicking assay. However, γ-radiation and Fe2+-EDTA produced different proportions of 2-deoxyribonolactone at 7% and 24% of total 2-deoxyribose oxidation, respectively, with frequencies of 10 lesions per 106 nt per Gy (G-value, 13 nmol/J) and 2.4 lesions per 106 nt per µM. Studies in TK6 human lymphoblastoid cells, in which the analytical data were corrected for losses sustained during DNA isolation, revealed background levels of 2-deoxyribonolactone and nucleoside 5’-aldehyde of 9.7 and 73 lesions per 106 nt, respectively. γ-Irradiation of the cells caused increases of 0.045 and 0.22 lesions per 106 nt per Gy, respectively, which represents a ~250-fold quenching effect of the cellular environment similar to that observed in previous studies. The proportions of the various 2-deoxyribose oxidation products generated by γ-radiation are similar for purified DNA and cells. These results are consistent with solvent exposure as a major determinant of hydroxyl radical reactivity with 2-deoxyribose in DNA, but the large differences between γ-radiation and Fe2+-EDTA suggest that factors other than hydroxyl radical reactivity govern DNA oxidation chemistry.

DNA oxidation plays a substantive role in the pathophysiology of human diseases such as cancer. While the chemistry of nucleobase lesions has dominated studies of DNA damage, there is growing evidence that oxidation of 2-deoxyribose in DNA plays a critical role in the genetic toxicology of oxidative stress. As part of an effort to define the spectrum of 2-deoxyribose oxidation products arising in vitro and in vivo, we now describe methods for quantifying products arising from 4′-oxidation of 2-deoxyribose in DNA. The chemistry of 4′-oxidation partitions between either of two pathways to form either a 2-deoxypentos-4-ulose abasic site (oxAB), or a strand break comprised of a 3′-phosphoglycolate (3PG) residue and a 5′-phosphate, with release of either malondialdehyde and free base or a base propenal. Highly sensitive gas chromatography-mass spectrometry (GC/MS) methods were developed to quantify both lesions. The abasic site was converted to a 3′-phosphoro-3-pyridazinylmethylate derivative by treatment of the damaged DNA with hydrazine, which was released from DNA as 3-hydroxymethylpyridazine (HMP) by enzymatic hydrolysis. Similarly, 3PG was released as 2-phosphoglycolic acid (PG) by enzymatic hydrolysis. Following HPLC prepurification, both PG and HMP were silylated and quantified by GC-MS with limits of detection of 100 and 200 fmol, and sensitivities of 2 and 4 lesions per 10 6 nucleotides (nt) in 250 μg of DNA, respectively. Following validation of the methods with oligodeoxynucleotides containing the two lesions, the methods were applied to DNA damage produced by bleomycin and γ-radiation. As expected for an agent known to produce only 4′-oxidation of DNA, the quantities of 3PG and oxAB accounted for all 2-deoxyribose oxidation events, as indicated by slopes of 0.8 and 0.3, respectively, in plots of lesion frequency against total 2-deoxyribose oxidation events, the latter determined by a plasmid nicking assay. 3PG residues and oxAB were produced at the rate of 32 and 12 lesions per 10 6 nt per μM, respectively. For γ-radiation, on the other hand, 4′-oxidation was found to comprise only 13% of 2-deoxyribose oxidation chemistry, with 3% oxAB (4 per 10 6 nt per Gy) and 10% 3PG (13 per 10 6 nt per Gy).