David Becker

Radiation-induced DNA damage as a function of hydration. I: Release of unaltered bases

The release of unaltered bases from irradiated DNA, hydrated between 2.5 and 32.7 mol of water per mole of nucleotide (gamma), was investigated using HPLC. The objective of this study was to elucidate the yield of the four DNA bases as a function of dose, extent of hydration, and the presence or absence of oxygen. The increase in the yield of radiation-induced free bases was linear with dose up to 90 kGy, except for the DNA with gamma = 2.5, for which the increase was linear only to 10 kGy. The yield of free bases as a function of gamma was not constant in either the absence or the presence of oxygen over the range of hydration examined. For DNA with gamma between 2.5 and 15, the yield of free bases was nearly constant under nitrogen, but decreased under oxygen. However, for DNA with gamma greater than 15, the yield increased rapidly under both nitrogen and oxygen. The yield of free bases was described by a model that depended on two factors: 1) a change in the DNA conformation from a mixture of the A and C conformers in vacuum-dried DNA to predominantly the B conformer in the fully hydrated DNA, and 2) the proximity of the water molecules to the DNA. Irradiation of the inner water molecules (gamma less than 15) was less efficient than irradiation of the outer water molecules (gamma greater than 15), by a factor of approximately 3.3, in forming DNA lesions that resulted in the release of an unaltered base. This factor is similar to the previously published relative efficiency of 2.8 with which hydroxyl radicals and base cations induce DNA strand breaks. Our irradiation results are consistent with the hypothesis that the G value for the first 12-15 water molecules of the DNA hydration layer is the same as the G value for the form of DNA to which it is bound (i.e., the pseudo-C or the B form). Thus we suggest that the release of bases originating from irradiation of the hydration water is obtained predominantly: (1) by charge transfer from the direct ionization of the first 12-15 water molecules of the primary hydration layer and (2) by the attack of hydroxyl radicals generated in the outer, more loosely bound water molecules.

The Chemical Consequences of Radiation Damage to DNA

Publisher Summary This chapter discusses the chemical consequences of radiation damage to DNA. Irradiation of DNA causes ionizations in all parts of the DNA molecule, namely, the bases, the sugar-phosphate moiety, and any closely bound water; in addition, bound proteins are also ionized. Even though ionizations occur throughout the DNA molecules, initial radicals have been observed only on the DNA bases in low-temperature ESR studies of moist DNA. Radiation damage to DNA occurs in a number of ways, which, are classified as either direct or indirect. The direct effect corresponds to direct ionization of the DNA resulting in the formation of radical cations and radical anions on the DNA itself. The indirect effect corresponds to energy deposition in the surrounding phase followed by attack by radicals from this phase. However, in complex systems such as the cell, damage may also be caused by irradiation of molecules bound to the DNA that transfer positive holes and/or electrons to the DNA strands or later react by cross-linking or hydrogen abstraction. The quasi-direct effect refers to a third process, where ionizations from irradiation result in holes and dry electrons in biomolecular species and hydration water very near the DNA. These then undergo fast transfer to the DNA to form ion radicals on the DNA itself. The indirect effect produces many of the same radicals and diamagnetic products as the direct and quasi-direct effects.

The Formation and Structure of the Sulfoxyl Radicals RSO·, RSOO·, RSO2·, and RSO2OO· from the Reaction of Cysteine, Glutathione and Penicillamine Thiyl Radicals with Molecular Oxygen

This work reports an electron spin resonance study of the reactions of cysteine, glutathione and penicillamine thiyl radicals with molecular oxygen in frozen aqueous solutions at low temperatures. For all three thiols, the thiyl radical, RS., is found to react with oxygen to form the thiol peroxyl radical, RSOO(.). On the absorption of visible light, RSOO(.) photoisomerizes to the sulfonyl radical, RSO2(.), which subsequently reacts with molecular oxygen to form RSO2OO(.), the sulfonyl peroxyl radical. The identities of the sulfonyl and sulfonyl peroxyl radicals were confirmed by their production by a different route, from sulfinic acid. Sulfinyl radicals, RSO(.), are found as the final radical species in the reactions of thiyl radicals and oxygen. Parallel 17O hyperfine couplings (A parallel) are reported for each sulfoxyl radical and a correlation between the spin density on oxygen and the reactivity of the radical is suggested. As a result of this correlation sulfonyl peroxyl radicals are predicted to be far more reactive than thiol peroxyl radicals. We also report molecular orbital calculations on the nature of the spin density distribution and the molecular geometry of the model radicals CH3SO2(.) and CH3SO2OO(.).

Radiation-induced DNA damage as a function of hydration. II. Base damage from electron-loss centers

The induction of base damage products in gamma-irradiated DNA, hydrated between 2.5 and 32.8 moles of water per mole of nucleotide (tau), was investigated using the gas chromatography/mass spectrometry-selected ion monitoring technique. In general, the yields of the measured base damage products were found to be dependent on the extent of the hydration when the DNA was irradiated under nitrogen. At low hydrations (tau < or = 13), the highest yields of the measured products were found for 7,8-dihydro-8-oxo-guanine, 5,6-dihydrothymine and, to a lesser extent, 2,6-diamino-4-oxo-5-formamidopyrimidine, products which are consistent with the base radicals found in low-temperature ESR studies. At higher hydrations (tau < or = 13), changes in DNA conformation and an increase in the attack of bulk water radicals on DNA play a significant role in the formation of radiation-induced DNA base damage products. Additional findings in our study include: (1) the sum of the yields of the products formed from electron-loss centers is greater than the sum of the yields of the products formed from electron-gain centers, indicating that there might be other electron-gain products which have not been identified; (2) the combined yield for the base damage products and the release of unaltered bases at tau < or = 13 is constant, implying that radiation damage in the tightly bound water molecules of the primary hydration layer causes DNA damage (quasi-direct effect) that is similar to the damage caused by direct ionization of the DNA (direct effect); and (3) the yields of the individual base damage products that were formed from electron-loss centers can be modeled on the basis of both the known reactions that lead to the formation of the initial charged base radicals in irradiated DNA, and the known reactions that involve the conversion of these initial DNA radicals into their respective nonradical end products.

An ESR Investigation of the Reactions of Glutathione, Cysteine and Penicillamine Thiyl Radicals: Competitive Formation of RSO·, R·, RSSR, and RSS·

The reactions of the cysteine, glutathione and penicillamine thiyl radicals with oxygen and their parent thiols in frozen aqueous solutions have been elucidated through electron spin resonance spectroscopy. The major sulfur radicals observed are: (1) thiyl radicals, RS.; (2) disulfide radical anions. RSSR-.; (3) perthiyl radicals, RSS. and upon introduction of oxygen; (4) sulfinyl radicals, RSO., where R represents the remainder of the cysteine, glutathione or penicillamine moiety. The radical product observed depends on the pH, concentration of thiol, and presence or absence of molecular oxygen. We find that the sulfinyl radical is a ubiquitous intermediate in the free radical chemistry of these important biological compounds, and also show that peroxyl radical attack on thiols may lead to sulfinyl radicals. We elaborate the observed reaction sequences that lead to sulfinyl radicals, and, using 17O isotopic substitution studies, demonstrate that the oxygen atom in sulfinyl radicals originates from dissolved molecular oxygen. In addition, the glutathione thiyl radical is found to abstract hydrogen from the alpha-carbon position on the cysteine residue of glutathione to form a carbon-centered radical.

Electron spin resonance of DNA irradiated with a heavy-ion beam ([16]O[8+]): evidence for damage to the deoxyribose phosphate backbone.

The free radicals produced from the irradiation of hydrated DNA with a heavy-ion beam have been investigated by ESR spectroscopy. The dominant free radical species formed after 60 MeV/nucleon (16)O(8+) ion-beam irradiations at low temperatures (77 K) are the same as those previously identified from studies using low-LET radiation, pyrimidine electron-gain radicals and purine electron-loss radicals; however, greater relative amounts of neutral carbon-centered radicals are found with the higher-LET radiation, and a new phosphorus-centered radical is identified. The fraction of neutral carbon radicals is also found to increase along the ion-beam track with the highest amounts found in the Bragg peak. The neutral carbon-centered radicals likely arise in part from the sugar moiety. The G values found for total trapped radicals at 77 K are significantly smaller for the (16)O(8+) ion beam than those found for low-LET radiation. The new phosphorus-centered radical species is identified by its large 31P parallel hyperfine coupling of about 780 G as a phosphoryl radical. This species is produced linearly with dose and is not found in significant amounts in DNA irradiated with low-LET radiation. The phosphoryl radical must be produced by the fragmentation of a P-O bond and suggests the possibility of a direct strand break. The yield of phosphoryl species is small (about 0.1% of all radicals); however, it clearly indicates that new mechanisms of damage which are not significant for low-LET radiation must be considered for high-LET radiation.

Thiol peroxyl radical formation from the reaction of cysteine thiyl radical with molecular oxygen: an ESR investigation

Using Electron Spin Resonance (ESR) spectroscopy, we have identified the cysteine thiol peroxyl radical (CysSOO.) at low temperatures in two aqueous glasses. This radical shows a typical peroxyl radical ESR spectrum, but unlike carbon-based peroxyl radicals has a violet color (lambda max = 540 nm) and forms a new radical showing a singlet ESR spectrum when photobleached with visible light. The cysteine peroxyl radical reacts to form the cysteine sulfinyl radical (CysSO.) in the glass which allows warming to 165K. 17O isotopic substitution studies indicate dissolved molecular oxygen is the source of oxygen in CysSOO.. Anisotropic g-values and the parallel anisotropic 17O hyperfine couplings for this radical are reported.

Electron Spin Resonance Study of DNA Irradiated with an Argon-Ion Beam: Evidence for Formation of Sugar Phosphate Backbone Radicals

Abstract Becker, D., Bryant-Friedrich, A., Trzasko, C. and Sevilla, M. D. Electron Spin Resonance Study of DNA Irradiated with an Argon-Ion Beam: Evidence for Formation of Sugar Phosphate Backbone Radicals. Radiat. Res. 160, 174–185 (2003). In this study, the effects of high-LET radiation on DNA were investigated and compared with the effects of γ radiation. Hydrated DNA samples at 77 K were irradiated with argon-ion beams (36Ar or 40Ar beam at energies between 60 and 100 MeV/nucleon). The individual free radicals formed were identified and their yields were investigated by electron spin resonance spectroscopy. Argon-ion irradiation resulted in lower yields of base ion radicals and higher yields of neutral radicals than γ irradiation. A hitherto unknown species was assigned to the radical formed by C–O bond rupture at the deoxyribose C3′, resulting in a sugar carbon-centered radical. A previously characterized phosphorus-centered radical was also found. The formation of each of these species was accompanied by an immediate strand break. G values, k values, and analyses for the individual yields of neutral radicals and ion radical composition for argon-ion-irradiated hydrated DNA are reported and compared to those found previously for γ-irradiated DNA. The lower G values and k values for ion radicals and the higher fraction of neutral radicals found for argon-ion-irradiated DNA are attributed to differences in track structure inherent in the two radiations.

UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures

This work presents evidence that photo-excitation of guanine radical cations results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. In dsDNA at low temperatures, formation of C1′• is observed from photo-excitation of G•+ in the 310–480 nm range with no C1′• formation observed ≥520 nm. Illumination of guanine radical cations in 2′dG, 3′-dGMP and 5′-dGMP in aqueous LiCl glasses at 143 K is found to result in remarkably high yields (∼85–95%) of sugar radicals, namely C1′•, C3′• and C5′•. The amount of each of the sugar radicals formed varies dramatically with compound structure and temperature of illumination. Radical assignments were confirmed using selective deuteration at C5′ or C3′ in 2′-dG and at C8 in all the guanine nucleosides/tides. Studies of the effect of temperature, pH, and wavelength of excitation provide important information about the mechanism of formation of these sugar radicals. Time-dependent density functional theory calculations verify that specific excited states in G•+ show considerable hole delocalization into the sugar structure, in accord with our proposed mechanism of action, namely deprotonation from the sugar moiety of the excited molecular radical cation.

Sulfinyl radical formation from the reaction of cysteine and glutathione thiyl radicals with molecular oxygen

Using Electron Spin Resonance spectroscopy at low temperatures, we find that thiyl radicals resulting from irradiation of frozen aqueous solutions of a variety of thiols, including cysteine, glutathione, and penicillamine react with oxygen to form sulfinyl (RSO.) radicals. The identity of the cysteine sulfinyl radical has been confirmed by the use of molecular oxygen isotopically labeled with 17O. Previous workers have suggested the reaction of thiyl radicals and molecular oxygen resulted in the formation of the potentially damaging thiol peroxyl radical, RSOO.; our work shows no evidence for this species. The sulfinyl radicals are suggested to result from a direct reaction between thiyl radicals and molecular oxygen. This reaction results in the cleavage of the dioxygen bond.