Ne-22 Ion-Beam Radiation Damage to DNA: From Initial Free Radical Formation to Resulting DNA-Base Damage

Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system

DNA data storage is a potential alternative to magnetic tape for archival storage purposes, promising substantial gains in information density. Critical to the success of DNA as a storage media is an understanding of the role of environmental factors on the longevity of the stored information. In this paper, we evaluate the effect of exposure to ionizing particle radiation, a cause of data loss in traditional magnetic media, on the longevity of data in DNA data storage pools. We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. Finally, we experimentally validate our model by exposing dried DNA samples to different levels of neutron irradiation and analyzing the resulting error profile. Our results show that particle radiation is not a significant contributor to data loss in DNA data storage pools under typical storage conditions.

8-OxodG: A Potential Biomarker for Chronic Oxidative Stress Induced by High-LET Radiation

Oxidative stress-mediated biomolecular damage is a characteristic feature of ionizing radiation (IR) injury, leading to genomic instability and chronic health implications. Specifically, a dose- and linear energy transfer (LET)-dependent persistent increase in oxidative DNA damage has been reported in many tissues and biofluids months after IR exposure. Contrary to low-LET photon radiation, high-LET IR exposure is known to cause significantly higher accumulations of DNA damage, even at sublethal doses, compared to low-LET IR. High-LET IR is prevalent in the deep space environment (i.e., beyond Earth's magnetosphere), and its exposure could potentially impair astronauts' health. Therefore, the development of biomarkers to assess and monitor the levels of oxidative DNA damage can aid in the early detection of health risks and would also allow timely intervention. Among the recognized biomarkers of oxidative DNA damage, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OxodG) has emerged as a promising candidate, indicative of chronic oxidative stress. It has been reported to exhibit differing levels following equivalent doses of low- and high-LET IR. This review discusses 8-OxodG as a potential biomarker of high-LET radiation-induced chronic stress, with special emphasis on its potential sources, formation, repair mechanisms, and detection methods. Furthermore, this review addresses the pathobiological implications of high-LET IR exposure and its association with 8-OxodG. Understanding the association between high-LET IR exposure-induced chronic oxidative stress, systemic levels of 8-OxodG, and their potential health risks can provide a framework for developing a comprehensive health monitoring biomarker system to safeguard the well-being of astronauts during space missions and optimize long-term health outcomes.

Radiation Chemistry and Radiation Research: A History from the Beginning to the Platinum Edition

At the dawn of the 20th Century, the underlying chemistry that produced the observed effects of ionizing radiation, e.g., X rays and Radium salts, on aqueous solutions was either unknown or restricted to products found postirradiation. For example, the Curies noted that sealed aqueous solutions of Radium inexplicably decomposed over time, even when kept in the dark. By 1928 there were numerous papers describing the phenomenological effects of ionizing radiation on a wide variety of materials, including the irradiated hands of early radiologists. One scientist who became intensely interested in these radiation effects was Hugo Fricke (Fricke Dosimetry) who established a laboratory in 1928 dedicated to studies on chemical effects of radiation, the results of which he believed were necessary to understand observed radiobiological effects. In this Platinum Issue of Radiation Research (70 years of continuous publication), we present the early history of the development of radiation chemistry and its contributions to all levels of mechanistic radiobiology. We summarize its development as one of the four disciplinary pillars of the Radiation Research Society and its Journal, Radiation Research, founded during the period 1952-1954. In addition, the work of scientists who contributed substantially to the discipline of Radiation Chemistry and to the birth, life and culture of the Society and its journal is presented. In the years following 1954, the increasing knowledge about the underlying temporal and spatial properties of the species produced by various types of radiation is summarized and related to its radiobiology and to modern technologies (e.g., pulsed radiolysis, electron paramagnetic resonance) which became available as the discipline of radiation chemistry developed. A summary of important results from these studies on Radiation Chemistry/Biochemistry in the 20th and 21st Century up to the present time is presented. Finally, we look into the future to see what possible directions radiation chemistry studies might take, based upon promising current research. We find at least two possible directions that will need radiation chemistry expertise to ensure proper experimental design and interpretation of data. These are FLASH radiotherapy, and mechanisms underlying the effects of low doses of radiation delivered at low dose rates. Examples of how radiation chemists could provide beneficial input to these studies are provided.

The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage

Motivation

Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5-250 keV/μm.

Methods

Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, e aq - , and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation.

Results

The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/μm. Minimum LETs of 9.4 and 11.5 keV/μm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites.

Conclusions

The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.

Spin-orbit charge transfer from guanine and 9-methylguanine radical cations to nitric oxide radicals and the induced triplet-to-singlet intersystem crossing

Nitric oxide (●NO) participates in many biological activities, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. To help understand the radiosensitization of ●NO, we report reaction dynamics between ●NO and the radical cations of guanine (a 9HG●+ conformer) and 9-methylguanine (9MG●+). On the basis of the formation of 9HG●+ and 9MG●+ in the gas phase and the collisions of the radical cations with ●NO in a guided-ion beam mass spectrometer, the charge transfer reactions of 9HG●+ and 9MG●+ with ●NO were examined. For both reactions, the kinetic energy-dependent product ion cross sections revealed a threshold energy that is 0.24 (or 0.37) eV above the 0 K product 9HG (or 9MG) + NO+ asymptote. To interrogate this abnormal threshold behavior, the reaction potential energy surface for [9MG + NO]+ was mapped out at closed-shell singlet, open-shell singlet, and triplet states using density functional and coupled cluster theories. The results showed that the charge transfer reaction requires the interaction of a triplet-state surface originating from a reactant-like precursor complex 3[9MG●+(↑)⋅(↑)●NO] with a closed-shell singlet-state surface evolving from a charge-transferred complex 1[9MG⋅NO+]. During the reaction, an electron is transferred from π∗(NO) to perpendicular π∗(9MG), which introduces a change in orbital angular momentum. The latter offsets the change in electron spin angular momentum and facilitates intersystem crossing. The reaction threshold in excess of the 0 K thermochemistry and the low charge-transfer efficiency are rationalized by the vibrational excitation in the product ion NO+ and the kinetic shift arising from a long-lived triplet intermediate.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study

Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found to be important therapeutic targets and material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton-transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6-31++G**) and considered single layer of Gq [G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)] to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron-oxidized G4 and its various proton-transfer states: G^•+, G(N₁-H)^•, G(N₂-H')^•, G(N₂-H″)^•, G(N₁-H)^•-(H⁺O₆)G, and G(N₂-H)^•-(H⁺N₇)G. The present calculation predicts the formation of G(N₂-H)^•-(H⁺N₇)G, which is only ca. 0.8 kcal/mol higher in energy than the initially formed G^•+. The formation of G(N₂-H)^•-(H⁺N₇)G plays a key role in explaining the formation of 8-OG along with G(N₁-H)^• formation via tautomerization from G(N₂-H)^•, as proposed recently.

Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group

This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O^-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O^-)═S)). ESR investigations show that DMTP(O^-)═S reacts with Cl₂^•- to form the σ²σ*¹ adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O^-)═S to produce [-P-S[Formula: see text]S-P-]^-. -P-S[Formula: see text]Cl in G-P(O^-)═S undergoes hole transfer to Gua, forming the cation radical (G^•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O^-)═S forms the thiyl radical (-P-S^•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]^-. Gua in G-P(O^-)═S is oxidized unimolecularly by the -P-S^• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.