Double-strand break induction and repair in V79-4 hamster cells: the role of core ionisations, as probed by ultrasoft X-rays

Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment

Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.

Superoxide Production under Soft X-ray Irradiation of Liquid Water

Soft X-rays behave like particles with high linear energy transfer, as they deposit a large amount of their energy in the nanometric range, triggered by inner-shell ionization. In water, this can lead to the formation of a doubly ionized water molecule (H₂O²⁺) and the emission of two secondary electrons (photoelectron and Auger electron). Our focus lies on detecting and quantifying the superoxide (HO₂°) production via the direct pathway, i.e., from the reaction between the dissociation product of H₂O²⁺, i.e., the oxygen atom (∼4 fs), and the °OH radicals present in the secondary electron tracks. The HO₂° yield for 1620 eV photons, via this reaction pathway, was found to be 0.005 (±0.0007) μmol/J (formed within the ∼ps range). Experiments were also performed to determine the yield of HO₂° production via another (indirect) pathway, involving solvated electrons. The indirect HO₂° yield, measured experimentally as a function of photon energy (from 1700 to 350 eV), resulted in a steep decrease at around 1280 eV and a minimum close to zero at 800 eV. This behavior in contradiction with the theoretical prediction reveals the complexity hidden in the intratrack reactions.

A double-strand-break model for the relative biological effectiveness of electrons based on ionization clustering

BACKGROUND

The effectiveness of ionizing radiation regarding DNA damage induction depends on its spatial energy deposition pattern. For electrons an increased effectiveness is observed at low kinetic energies due to the enhanced density of energy deposition events at electron track ends.

PURPOSE

A model is presented, which enables the calculation of the double-strand-break (DSB) yield and the relative biological effectiveness (RBE) for DSB induction of electrons.

METHODS

The model applies the mean free path between two ionizations and the assumption that two ionizations within a certain threshold distance are necessary to potentially lead to a DSB. Next to an expression for the electron RBE according to its common definition, a local RBE is determined, which describes the electrons' local effectiveness at a defined point on their track.

RESULTS

This local RBE allows a better understanding of microscopic processes resulting from radiation and can be used, for instance, to describe the mean effectiveness of the mixed electron radiation field as a function of the radial distance to the center of an ion track.

CONCLUSIONS

The presented model reflects the experimentally observed increased effectiveness of low-energetic electrons. It will be used in a future work to improve RBE predictions for ions performed with the local effect model.

Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs

Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.

A microfluidic dosimetry cell to irradiate solutions with poorly penetrating radiations: a step towards online dosimetry for synchrotron beamlines

Synchrotron radiation can induce sample damage, whether intended or not. In the case of sensitive samples, such as biological ones, modifications can be significant. To understand and predict the effects due to exposure, it is necessary to know the ionizing radiation dose deposited in the sample. In the case of aqueous samples, deleterious effects are mostly induced by the production of reactive oxygen species via water radiolysis. These species are therefore good indicators of the dose. Here the application of a microfluidic cell specifically optimized for low penetrating soft X-ray radiation is reported. Sodium benzoate was used as a fluorescent dosimeter thanks to its specific detection of hydroxyl radicals, a radiolytic product of water. Measurements at 1.28 keV led to the determination of a hydroxyl production yield, G(HO.), of 0.025 ± 0.004 µmol J-1. This result is in agreement with the literature and confirms the high linear energy transfer behavior of soft X-rays. An analysis of the important parameters of the microfluidic dosimetry cell, as well as their influences over dosimetry, is also reported.

Soft X-ray Radiation and Monte Carlo Simulations: Good Tools to Describe the Radiation Chemistry of Sub-keV Electrons

The description of the biological effects of ionizing radiation requires a good knowledge of the dose deposition processes at both the cellular and molecular scales. However, experimental studies on the energy deposition specificity of sub-keV electrons, produced by most radiations, including high-energy photons and heavy ions, are scarce. Soft X-rays (0.2-2 keV) are here used to probe the physical and physico-chemical events occurring upon exposure of liquid water to sub-keV electrons. Liquid water samples were irradiated with a monochromatic photon beam at the SOLEIL synchrotron. Hydroxyl radical quantification was conducted through HO^• scavenging using benzoate to form fluorescent hydroxybenzoate. The yields of HO^• radicals exhibit a minimum around 1.5 keV, in good agreement with indirect observation. Moreover, they are relatively independent of the benzoate concentration in the range investigated, which corresponds to scavenging times of 170 ns to 170 ps. These results provide evidence that sub-keV electrons behave as high linear energy transfer particles, since they are able to deposit tens to hundreds of electronvolts in nanometric volumes.

Chemical Dosimetry in the "Water Window": Ferric Ions and Hydroxyl Radicals Produced by Intense Soft X Rays

A standard Fricke dosimeter was used to measure the absorbed dose via the oxidation yields of Fe³⁺ ions in an aqueous environment induced by soft X rays within the "water window" spectral range. We also exploited the property of a neutral solution containing terephthalic acid as a tool for selective detection of OH radicals. Both dosimetric systems were irradiated using the experimental pulsed laser-plasma soft X-ray source as well as conventional 1.25-MeV gamma rays. Radiation chemical yields of Fe³⁺ ions and OH radicals were determined to be (5.13 ± 0.94) × 10^-1 µmol·J^-1 (4.95 ± 0.91 100eV^-1) and (2.33 ± 0.35) × 10^-2 µmol·J^-1 (0.23 ± 0.03 100eV^-1), respectively. Measurements were supported by Monte Carlo simulations to estimate the linear energy transfer of the water window radiation. The simulation results are in good agreement with expected linear energy transfer of ions inducing the same Fe³⁺ ion and OH radical radiation chemical yield.

Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

Radiation-induced clustered DNA lesions: Repair and mutagenesis

Clustered DNA lesions, also called Multiply Damaged Sites, is the hallmark of ionizing radiation. It is defined as the combination of two or more lesions, comprising strand breaks, oxidatively generated base damage, abasic sites within one or two DNA helix turns, created by the passage of a single radiation track. DSB clustered lesions associate DSB and several base damage and abasic sites in close vicinity, and are assimilated to complex DSB. Non-DSB clustered lesions comprise single strand break, base damage and abasic sites. At radiation with low Linear Energy Transfer (LET), such as X-rays or γ-rays clustered DNA lesions are 3-4 times more abundant than DSB. Their proportion and their complexity increase with increasing LET; they may represent a large part of the damage to DNA. Studies in vitro using engineered clustered DNA lesions of increasing complexity have greatly enhanced our understanding on how non-DSB clustered lesions are processed. Base excision repair is compromised, the observed hierarchy in the processing of the lesions within a cluster leads to the formation of SSB or DSB as repair intermediates and increases the lifetime of the lesions. As a consequence, the chances of mutation drastically increase. Complex DSB, either formed directly by irradiation or by the processing of non-DSB clustered lesions, are repaired by slow kinetics or left unrepaired and cause cell death or pass mitosis. In surviving cells, large deletions, translocations, and chromosomal aberrations are observed. This review details the most recent data on the processing of non-DSB clustered lesions and complex DSB and tends to demonstrate the high significance of these specific DNA damage in terms of genomic instability induction.

Fragmentation of pure and hydrated clusters of 5Br-uracil by low energy carbon ions: observation of hydrated fragments

The fragmentation of the isolated 5-bromouracil (5BrU) molecule and pure and nano-hydrated 5BrU clusters induced by low energy ¹²C⁴⁺ ions has been studied.

Investigation of the fragmentation of core-ionised deoxyribose: a study as a function of the tautomeric form

Fragmentation dynamics following the core ionisation of isolated 2-deoxy-d-ribose by DFT-MD simulations.

Conception and realization of a parallel-plate free-air ionization chamber for the absolute dosimetry of an ultrasoft X-ray beam

We report the design of a millimeter-sized parallel plate free-air ionization chamber (IC) aimed at determining the absolute air kerma rate of an ultra-soft X-ray beam (E = 1.5 keV). The size of the IC was determined so that the measurement volume satisfies the condition of charged-particle equilibrium. The correction factors necessary to properly measure the absolute kerma using the IC have been established. Particular attention was given to the determination of the effective mean energy for the 1.5 keV photons using the PENELOPE code. Other correction factors were determined by means of computer simulation (COMSOL™ and FLUKA). Measurements of air kerma rates under specific operating parameters of the lab-bench X-ray source have been performed at various distances from that source and compared to Monte Carlo calculations. We show that the developed ionization chamber makes it possible to determine accurate photon fluence rates in routine work and will constitute substantial time-savings for future radiobiological experiments based on the use of ultra-soft X-rays.