DNA strand breaks induced by low keV energy heavy ions

H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage

Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.

Charge-Exchange-Driven Low-Energy Electron Splash Induced by Heavy Ion Impact on Condensed Matter

Low-energy electrons (LEEs) are of great relevance for ion-induced radiation damage in cells and genes. We show that charge exchange of ions leads to LEE emission upon impact on condensed matter. By using a graphene monolayer as a simple model system for condensed organic matter and utilizing slow highly charged ions (HCIs) as projectiles, we highlight the importance of charge exchange alone for LEE emission. We find a large number of ejected electrons resulting from individual ion impacts (up to 80 electrons/ion for Xe⁴⁰⁺). More than 90% of emitted electrons have energies well below 15 eV. This "splash" of low-energy electrons is interpreted as the consequence of ion deexcitation via an interatomic Coulombic decay (ICD) process.

Low-Energy Ion-Species-Dependent Induction of DNA Double-Strand Breaks: Ion Energy and Fluence Thresholds

The goal of this study was to determine the critical ion-radiation conditions under which heavy ion beams can induce DNA double-strand breaks. Helium, nitrogen and argon-ion beams in the energy range of 20 eV to 2 keV were used to irradiate naked DNA plasmid pGFP to fluences of 1, 2 and 4 × 10¹⁵ ions/cm². The topological forms of DNA were subsequently analyzed using gel electrophoresis. The DNA forms were changed from the original supercoiled to damaged relaxed and linear forms, depending on the ion mass, energy, fluence and inertia. We found ion energy and fluence thresholds above which direct double-strand breaks can occur. The threshold is discussed in terms of the areal ion-energy density and the cross-section.

Absolute measurements of radiation damage in nanometer-thick films

The problem of absolute measurements of radiation damage in films of nanometer thicknesses is addressed. Thin films of DNA (∼2-160 nm) are deposited onto glass substrates and irradiated with varying doses of 1.5-keV X-rays under dry N(2) at atmospheric pressure and room temperature. For each different thickness, the damage is assessed by measuring the loss of the supercoiled configuration as a function of incident photon fluence. From the exposure curves, the G-values are deduced, assuming that X-ray photons interacting with DNA deposit all of their energy in the film. The results show that the G-value (i.e. damage per unit of deposited energy) increases with film thickness and reaches a plateau at 30±5 nm. This thickness dependence provides a correction factor to estimate the actual G-value for films with thicknesses <30 nm thickness. Thus, the absolute values of the damage can be compared with that of films of any thickness under different experimental conditions.

Plume characteristics and dynamics of UV and IR laser-desorbed oligonucleotides

Laser desorption of dye-tagged oligonucleotides was studied using laser-induced fluorescence imaging. Desorption with ultra violet (UV) and infra-red (IR) lasers resulted in forward directed plumes of molecules. In the case of UV desorption, the initial shot desorbed approximately seven-fold more material than subsequent shots. In contrast, the initial shot in IR desorption resulted in the ejection of less material compared to subsequent shots and these plumes had a component directed along the path of the laser. Thermal equilibrium of the molecules in the plume was achieved after approximately 25 μs with a spread in molecular temperature which was described by a modified Maxwell-Boltzmann equation.

Comparison of DNA breaks at entrance channel and Bragg peak induced by fast C6+ ions--influence of the addition of platinum atoms on DNA

When energetic carbon ion beam (GeV range) goes through the matter, inelastic processes such as electronic ionization, molecular and nuclear fragmentation occur. For carbontherapy (hadrontherapy) purpose, it is of interest to compare the number of DNA breaks -single SSB or double DSB- for a given dose at the entrance channel and at the Bragg peak to look for a possible differential effect in the number of DNA breaks induced at these two locations. Samples of free plasmids DNA and complexes of plasmids DNA added with molecules containing platinum have been placed at different locations of an experimental setup simulating penetration depths of the ion beam in water and irradiated by carbon ions 290 MeV/amu. The DNA breaks have been quantified by subsequent electrophoresis on agarose gels. To disentangle the respective role of the direct and indirect effect, a free radical scavenger of hydroxyl radicals HO degree-dimethylsulfoxide DMSO- has been added in some of the experiments. In the range of Linear Energy Transfer-LET 13 - 110 keV/microm-, the number of the DSB was found to be constant versus the LET for a given dose. Contrary, the number of the SSB decreases at the Bragg peak compared to the entrance channel. In the presence of platinum, the number of single and double breaks was considerably enhanced, and follows a similar behaviour than in the free-DNA experiments. Quantitative results on DNA damages do not show significant enhancement due to the nuclear or to the molecular fragmentation in the present experiments.

Molecular simulations of ultra-low-energy nitrogen ion bombardment of A-DNA in vacuum

For investigating mechanisms involved in low-energy ion beam induced mutation, besides experiments using low-energy and low-fluence ions to bombard naked DNA, molecular simulations were carried out as an effort towards the insight in molecular interactions between ions and DNA. In the current study, Monte Carlo (MC) and molecular dynamics (MD) simulations were applied. The results of MC simulations provide some clues about the interaction energies and sites of preference of N-ion bombardment on an A-DNA short duplex strand. MD simulations of a single N-ion moving towards the same DNA strand with different linear velocities corresponding to bombardment energies of 0.1, 1, 10 and 100 eV revealed information about changes in bond lengths and visibly distorted structures of bombarded nucleotides. The simulations demonstrated that ion-bombardment-induced DNA change in structure was not a random but preferential effect.

DNA damage by low-energy ions

Ion-beam irradiation provides a promising treatment for some types of cancer. This promise is due mainly to the selective deposition of energy into a relatively small volume (the Bragg peak), thus reducing damage to healthy tissue. Recent observations that electrons with energies below the ionization potential of DNA can cause covalent damage to the bases and backbone have led to investigations into the ability of low-energy (<1 keV·Da−1) ion beams to damage double-stranded DNA. It has been clearly demonstrated that these low-energy ions induce a mixture of single- and double-strand breaks to dried DNA in vacuo. These effects depend upon the number of ions incident upon the DNA, the kinetic energy of the ions and on their charge state. This DNA damage may be important, as all radiotherapies will result in the production of low-energy secondary ions as radiation passes through tissues. Currently, their effects are neglected in treatment planning, and thus more work is required to quantify and understand DNA damage by low-energy ions.

Novel apparatus to measure hyperthermal heavy ion damage to DNA: strand breaks, base loss, and fragmentation

We have developed a novel apparatus that allows us to irradiate nonvolatile organic films of high mass (1-100 microg range) spread out over a large surface area (42 cm(2)) with low energy (kT-100 eV) heavy ions and to quantitatively analyze the film substance via standard biochemical techniques afterwards. Here we discuss the details of the apparatus and method and show that it allows us to measure substantial damage to double stranded DNA molecules (plasmids) and its fundamental subunits induced by heavy ions with unprecedented low energies, i.e., 2.5 eV/amu; these energies correspond to track end energies of stopping ions or secondary ions created along primary ion tracks. We find that hyperthermal Ar(+) ions interacting with plasmid DNA will lead to the formation of single and double strand breaks, as well as fragmentation of nucleosides, which also involve chemical modifications and site specific rupture along the N1-C1 glycosidic bond, resulting in base release. In cells, such localized clustered damage will enhance the severity of DNA strand lesions, thus making them harder to repair.

Ion-induced biomolecular radiation damage: from isolated nucleobases to nucleobase clusters

A large number of studies are devoted to the investigation of the biomolecular ionization and fragmentation dynamics underlying biological radiation damage. Most of these studies have been based on gas-phase collisions with isolated DNA building blocks. The radiobiological significance of these studies is often questioned because of the lack of a chemical environment. To clarify this aspect, we studied interactions of keV ions with isolated nucleobases and with nucleobase clusters by means of coincidence time-of-flight spectrometry. Significant changes already show up in the molecular fragmentation patterns of very small clusters.

Damage to plasmid DNA induced by low energy carbon ions

The damage induced in supercoiled plasmid DNA molecules by 1-6 keV carbon ions has been investigated as a function of ion exposure, energy and charge state. The production of short linear fragments through multiple double strand breaks has been demonstrated and exponential exposure responses for each of the topoisomers have been found. The cross section for the loss of supercoiling was calculated to be (2.2 +/- 0.5) x 10(-14) cm(2) for 2 keV C(+) ions. For singly charged carbon ions, increased damage was observed with increasing ion energy. In the case of 2 keV doubly charged ions, the damage was greater than for singly charged ions of the same energy. These observations demonstrate that ion induced damage is a function of both the kinetic and potential energies of the ion.

Quantification of ion-induced molecular fragmentation of isolated 2-deoxy-d-ribose molecules

Recent experiments on low energy ion-induced damage to DNA building blocks indicate that ion induced DNA damage is dominated by deoxyribose disintegration (Phys. Rev. Lett., 2005, 95, 153201). We have studied interactions of keV H+ and He(q+) with isolated deoxyribose molecules by means of high resolution time-of-flight spectrometry. Extensive statistical fragmentation of the molecules is observed. The fragment distribution is found to follow a power law dependence. The exponent can be used to characterize and quantify the molecular damage.