Single,double, and multiple double strand breaks induced in DNA by 3-100 eV electrons

Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.     

Comparison between X-ray photon and secondary electron damage to DNA in vacuum

Both monolayer and thick (20 microm) films of dry pGEM-3Zf(-) plasmid DNA deposited on tantalum foil were exposed to Al Kalpha X-rays (1.5 keV) for various times in an ultrahigh vacuum chamber. For monolayer DNA, the damage was induced mainly by low energy secondary electrons (SEs) emitted from the tantalum. For the thick films, DNA damage was induced chiefly by X-ray photons. Different forms of plasmid DNA were separated and quantified by agarose gel electrophoresis. The exposure curves for the formation of nicked circular (single strand break, SSB), linear (double strand break, DSB), and interduplex cross-link forms 1 and 2 were obtained for both monolayer and thick films of DNA, respectively. The lower limits of G values for SSB and DSB induced by SEs were derived to be 86 +/- 2 and 8 +/- 2 nmol J(-1), respectively. These values are 1.5 and 1.6 times larger than those obtained with 1.5 keV photons. The projected X-ray energy dependence of the low energy electron (LEE) enhancement factor for the SSB and DSB in monolayer DNA is also discussed. This new method of investigation of the SE-induced damage to large biomolecules allows direct comparison of the yield of products induced by high energy photons and LEEs under identical experimental conditions.     

FORMATION OF SINGLE AND DOUBLE STRAND BREAKS IN DNA ULTRAVIOLET IRRADIATED AT HIGH INTENSITY

The induction of single-strand breaks (SSB) by two quantum processes in DNA is well established. We now report that biphotonic processes result in double-strand breaks (DSB) as well. pUC19 and bacteriophage M13 RF DNA were irradiated using an excimer laser (248 nm) at intensities of 10(7), 10(9), 10(10) and 10(11) W/m2 and doses up to 30 kJ/m2. The proportion of DNA as supercoil, open circular, linear and short fragments was determined by gel electrophoresis. Linear molecules were noted at fluences where supercoiled DNA was still present. The random occurrence of independent SSB in proximity to each other on opposite strands (producing linear DNA) implies introduction of numerous SSB per molecule in the sample. If so, supercoiled DNA that has sustained no SSB should not be observed. A model accounting for the amounts of supercoiled, open circular, linear and shorter fragments of DNA due to SSB, DSB and Scissions (opposition of two independently occurring SSB producing an apparent DSB) was developed, our experimental data and those of others were fit to the model, and quantum yields determined for SSB and DSB formation at each intensity. Results showed that high intensity laser radiation caused an increase in the quantum yields for both SSB and DSB formation. The mechanism of DSB formation is unknown, and may be due to simultaneous cleavage of both strands in one biphotonic event or the biased introduction of an SSB opposite a preexisting SSB, requiring two biphotonic events.     

Evaluation of elastic‐scattering cross sections for electrons and positrons over a wide energy range

Quantification of surface‐ and bulk‐analytical methods, e.g. Auger‐electron spectroscopy (AES), X‐ray photoelectron spectroscopy (XPS), electron‐probe microanalysis (EPMA), and analytical electron microscopy (AEM), requires knowledge of reliable elastic‐scattering cross sections for describing electron transport in solids. Cross sections for elastic scattering of electrons and positrons by atoms, ions, and molecules can be calculated with the recently developed code ELSEPA (Elastic Scattering of Electrons and Positrons by Atoms) for kinetic energies of the projectile from 10 eV to 50 eV. These calculations can be made after appropriate selection of the basic input parameters: electron‐density distribution, a model for the nuclear‐charge distribution, and a model for the electron‐exchange potential (the latter option applies only to scattering of electrons). Additionally, the correlation‐polarization potential and an imaginary absorption potential can be considered in the calculations. We report comparisons of calculated differential elastic‐scattering cross sections (DCSs) for silicon and gold at selected energies (500 eV, 5 keV, 30 keV) relevant to AES, XPS, EPMA, and AEM, and at 100 MeV as a limiting case. The DCSs for electrons and positrons differ considerably, particularly for medium‐ and high‐atomic‐number elements and for kinetic energies below about 5 keV. The DCSs for positrons are always monotonically decreasing functions of the scattering angle, while the DCSs for electrons have a diffraction‐like structure with several minima and maxima. A significant influence of the electron‐exchange correction is observed at 500 eV. The correlation‐polarization correction is significant for small scattering angles at 500 eV, while the absorption correction is important at energies below about 10 keV. Copyright © 2005 John Wiley & Sons, Ltd.     

Damage to model DNA fragments from very low-energy (<1 eV) electrons

Although electrons having enough energy to ionize or electronically excite DNA have long been known to cause strand breaks (i.e., bond cleavages), only recently has it been suggested that even lower-energy electrons (most recently 1 eV and below) can also damage DNA. The findings of the present work suggest that, while DNA bases can attach electrons having kinetic energies in the 1 eV range and subsequently undergo phosphate-sugar O-C sigma bond cleavage, it is highly unlikely (in contrast to recent suggestions) that electrons having kinetic energies near 0 eV can attach to the phosphate unit's P=O bonds. Electron kinetic energies in the 2-3 eV range are required to attach directly to DNA's phosphate group's P=O pi orbital and induce phosphate-sugar O-C sigma bond cleavages if the phosphate groups are rendered neutral (e.g., by nearby counterions). Moreover, significant activation barriers to C-O bond breakage render the rates of both such damage mechanisms (i.e., P=O-attached and base-attached) slow as compared to electron autodetachment and to other damage processes.     

Low energy electron and O- reactions in films of O2 coadsorbed with benzene or toluene

A detailed understanding of nascent reactive events leading to DNA damage is required to describe ionizing radiation effects on living cells. These early, sub-picosecond events involve mainly low energy (E < 20 eV) secondary electrons (SE), and low energy (E < 5 eV) secondary ion (and neutral) fragments; the latter are created either by the primary radiation, or by SE via dissociative electron attachment (DEA). While recent work has shown that SE initiate DNA strand break formation via DEA, the subsequent damage induced by the DEA ion fragments in DNA, or its basic components is unknown. Here, we report 0-20 eV electron impact measurements of anion desorption from condensed films containing O2 and either benzene (C6H6), or toluene (C6H5CH3); these molecules represent the most fundamental structural analogs of pyrimidine bases. Our experiments show that all of the observed OH- yields are the result of reactive scattering of 1-5 eV O- fragments produced initially by DEA to O2. These O- reactions involve hydrogen abstraction from benzene or toluene, and result in the formation of benzyl radicals, or toluene radicals centered on either the ring or exocyclic methyl group. O- scatters over nm distances comparable to DNA dimensions, and reactions involve a transient anion collision complex. Anion desorption is found to depend on both, the temperature of hydrocarbon film formation (morphology), and the order of overlayer adsorption, e.g. O2 on benzene, or benzene on O2. Our measurements support the notion that in irradiated DNA similar secondary-ion reactions can be initiated by the abundant secondary electrons, and may lead to clustered damage.     

Dissociative electron attachment to abasic DNA

Thin films of the short single DNA strand, GCAT, in which one of the bases has been removed were bombarded with 3 to 15 eV electrons. The yield functions of the H(-), O(-) and OH(-) ions desorbed from these films exhibit a broad peak near 9 eV, which is attributed to dissociative electron attachment to the basic molecules. Whereas removal of any one of the bases considerably decreases N-glycosidic and backbone C-O bond scission, the creation of basic sites does not appreciably modify bond rupture leading to anion electron stimulated desorption. These seemingly contradictory results make it possible to propose a detailed mechanism leading to the transfer of electrons in the range 5-13 eV within DNA.     

Inelastic electron interaction (attachment/ionization) with deoxyribose

We have investigated experimentally the formation of anions and cations of deoxyribose sugar (C(5)H(10)O(4)) via inelastic electron interaction (attachment/ionization) using a monochromatic electron beam in combination with a quadrupole mass spectrometer. The ion yields were measured as a function of the incident electron energy between about 0 and 20 eV. As in the case of other biomolecules (nucleobases and amino acids), low energy electron attachment leads to destruction of the molecule via dissociative electron attachment reactions. In contrast to the previously investigated biomolecules dehydrogenation is not the predominant reaction channel for deoxyribose; the anion with the highest dissociative electron attachment (DEA) cross section of deoxyribose is formed by the release of neutral particles equal to two water molecules. Moreover, several of the DEA reactions proceed already with "zero energy" incident electrons. In addition, the fragmentation pattern of positively charged ions of deoxyribose also indicates strong decomposition of the molecule by incident electrons. For sugar the relative amount of fragment ions compared to that of the parent cation is about an order of magnitude larger than in the case of nucleobases. We determined an ionization energy value for C(5)H(10)O(4) (+) of 10.51+/-0.11 eV, which is in good agreement with ab initio calculations. For the fragment ion C(5)H(6)O(2) (+) we obtained a threshold energy lower than the ionization energy of the parent molecular ion. All of these results have important bearing for the question of what happens in exposure of living tissue to ionizing radiation. Energy deposition into irradiated cells produces electrons as the dominant secondary species. At an early time after irradiation these electrons exist as ballistic electrons with an initial energy distribution up to several tens of electron volts. It is just this energy regime for which we find in the present study rather characteristic differences in the outcome of electron interaction with the deoxyribose molecule compared to other nucleobases (studied earlier). Therefore, damage induced by these electrons to the DNA or RNA strands may start preferentially at the ribose backbone. In turn, damaged deoxyribose is known as a key intermediate in producing strand breaks, which are the most severe form of lesion in radiation damage to DNA and lead subsequently to cell death.     

Low-energy electron-induced single strand breaks in 2'-deoxycytidine-3'-monophosphate using the local complex potential based time-dependent wave packet approach

Recent experimental and theoretical investigations on resonant electron scattering off DNA and DNA fragments using low-energy electrons (LEEs), to propose the mechanism for single strand breaks (SSBs) and double strand breaks (DSBs), have received considerable attention. It is our purpose here to understand theoretically the comprehensive route to SSB in a selected DNA fragment, namely, 2'-deoxycytidine-3'-monophosphate (3'-dCMPH), induced by LEE (0-3 eV) scattering using the local complex potential based time-dependent wave packet (LCP-TDWP) approach. To the best of our knowledge, there is no time-dependent quantum mechanical study that has been reported in the literature for this DNA fragment to date. Initial results obtained from our calculation in the gas phase provide a good agreement with experimental observation and show the plausibility of SSB at 0.75 eV, which is very close to the highest SSB yield reported from the experimental measurement (0.8 eV) on plasmid DNA in the condensed phase.     

Low energy electron induced damage to plasmid DNA pQE30

Low energy electrons (LEEs) are produced in copious amounts by the primary radiation used in radiation therapy. The damage caused to the DNA by these secondary electrons in the energy range 5-22 eV has been studied to understand their possible role in radiation induced damage. Electrons are irradiated on dried films of plasmid DNA (pQE30) and analysed using agarose gel electrophoresis. Single strand breaks (SSBs) induced by LEE to supercoiled plasmid DNA show resonance structures at 7, 12, and 15 eV for low doses and 6, 10, and ～18 eV at saturation doses. The present measurements have an overall agreement with the literature that LEEs resonantly induce SSBs in DNA. Resonant peaks in the SSBs induced by LEEs at 7, 12, and 15 eV with the lowest employed dose in the current study are somewhat different from those reported earlier by two groups. The observed differences are perhaps related to the irradiation dose, conditions and the nature of DNA employed, which is further elaborated.     

On the mechanism of anion desorption from DNA induced by low energy electrons

Our knowledge of the mechanisms of radiation damage to DNA induced by secondary electrons is still very limited, mainly due to the large sizes of the system involved and the complexity of the interactions. To reduce the problem to its simplest form, we investigated specific electron interactions with one of the most simple model system of DNA, an oligonucleotide tetrameter compound of the four bases. We report anion desorption yields from a thin solid film of the oligonucleotide GCAT induced by the impact of 3-15 eV electrons. All observed anions (H-, O-, OH-, CN-, and OCN-) are produced by dissociative electron attachment to the molecule, which results in desorption peaks between 6 and 12 eV. Above 14 eV nonresonant dipolar dissociation dominates the desorption yields. By comparing the shapes and relative intensities of the anion yield functions from GCAT physisorbed on a tantalum substrate with those obtained from isolated DNA basic subunits (i.e., bases, deoxyribose, and phosphate groups) from either the gas phase or condensed phase experiments, it is possible to obtain more details on the mechanisms involved in low energy electron damage to DNA, particularly on those producing single strand breaks.     

On the formation of ozone in oxygen-rich solar system ices via ionizing radiation

The irradiation of pure molecular oxygen (O(2)) and carbon dioxide (CO(2)) ices with 5 keV H(+) and He(+) ions was investigated experimentally to simulate the chemical processing of oxygen rich planetary and interstellar surfaces by exposure to galactic cosmic ray (GCR), solar wind, and magnetospheric particles. Deposited at 12 K under ultra-high vacuum conditions (UHV), the irradiated condensates were monitored on-line and in situ in the solid-state by Fourier transform infrared spectroscopy (FTIR), revealing the formation of ozone (O(3)) in irradiated oxygen ice; and ozone, carbon monoxide (CO), and cyclic carbon trioxide (c-CO(3)) in irradiated carbon dioxide. In addition to these irradiation products, evolution of gas-phase molecular hydrogen (H(2)), atomic helium (He) and molecular oxygen (O(2)) were identified in the subliming oxygen and carbon dioxide condensates by quadrupole mass spectrometry (QMS). Temporal abundances of the oxygen and carbon dioxide precursors and the observed molecular products were compiled over the irradiation period to develop reaction schemes unfolding in the ices. These reactions were observed to be dependent on the generation of atomic oxygen (O) by the homolytic dissociation of molecular oxygen induced by electronic, S(e), and nuclear, S(n), interaction with the impinging ions. In addition, the destruction of the ozone and carbon trioxide products back to the molecular oxygen and carbon dioxide precursors was promoted over an extended period of ion bombardment. Finally, destruction and formation yields were calculated and compared between irradiation sources (including 5 keV electrons) which showed a surprising correlation between the molecular yields (～10(-3)-10(-4) molecules eV(-1)) created by H(+) and He(+) impacts. However, energy transfer by isoenergetic, fast electrons typically generated ten times more product molecules per electron volt (～10(-2)-10(-3) molecules eV(-1)) than exposure to the ions. Implications of these findings to Solar System chemistry are also discussed.     

Phosphodiester and N-glycosidic bond cleavage in DNA induced by 4-15 eV electrons

Thin molecular films of the short single strand of DNA, GCAT, were bombarded under vacuum by electrons with energies between 4 and 15 eV. Ex vacuo analysis by high-pressure liquid chromatography of the samples exposed to the electron beam revealed the formation of a multitude of products. Among these, 12 fragments of GCAT were identified by comparison with reference compounds and their yields were measured as a function of electron energy. For all energies, scission of the backbone gave nonmodified fragments containing a terminal phosphate, with negligible amounts of fragments without the phosphate group. This indicates that phosphodiester bond cleavage by 4-15 eV electrons involves cleavage of the C-O bond rather than the P-O bond. The yield functions exhibit maxima at 6 and 10-12 eV, which are interpreted as due to the formation of transient anions leading to fragmentation. Below 15 eV, these resonances dominate bond dissociation processes. All four nonmodified bases are released from the tetramer, by cleavage of the N-glycosidic bond, which occurs principally via the formation of core-excited resonances located around 6 and 10 eV. The formation of the other nonmodified products leading to cleavage of the phosphodiester bond is suggested to occur principally via two different mechanisms: (1) the formation of a core-excited resonance on the phosphate unit followed by dissociation of the transient anion and (2) dissociation of the CO bond of the phosphate group formed by resonance electron transfer from the bases. In each case, phosphodiester bond cleavage leads chiefly to the formation of stable phosphate anions and sugar radicals with minimal amounts of alkoxyl anions and phosphoryl radicals.     

Precise and fast secondary ion mass spectrometry depth profiling of polymer materials with large Ar cluster ion beams

We demonstrate depth profiling of polymer materials by using large argon (Ar) cluster ion beams. In general, depth profiling with secondary ion mass spectrometry (SIMS) presents serious problems in organic materials, because the primary keV atomic ion beams often damage them and the molecular ion yields decrease with increasing incident ion fluence. Recently, we have found reduced damage of organic materials during sputtering with large gas cluster ions, and reported on the unique secondary ion emission of organic materials. Secondary ions from the polymer films were measured with a linear type time‐of‐flight (TOF) technique; the films were also etched with large Ar cluster ion beams. The mean cluster size of the primary ion beams was Ar₇₀₀ and incident energy was 5.5 keV. Although the primary ion fluence exceeded the static SIMS limit, the molecular ion intensities from the polymer films remained constant, indicating that irradiation with large Ar cluster ion beams rarely leads to damage accumulation on the surface of the films, and this characteristic is excellently suitable for SIMS depth profiling of organic materials. Copyright © 2009 John Wiley & Sons, Ltd.     

Bringing electrons and microarray technology together

Low-energy secondary electrons are the most abundant radiolysis species which are thought to be able to attach to and damage DNA via formation and decay of localized molecular resonances involving DNA components. In this study, we analyze the consequences of low-energy electron impact on the ability of DNA to hybridize (i.e., to form the duplex). Specifically, single-stranded thymine DNA oligomers tethered to a gold surface are irradiated with very low-energy electrons (E = 3 eV, which is below the 7.5 eV ionization threshold of DNA) and subsequently exposed to a dye-marked complementary strand to quantify by a fluorescence method the electron induced damage. The damage to (dT)25 oligomers is detected at quite low electron doses with only about 300 electrons per oligomer being sufficient to completely preclude its hybridization. In the microarray format, the method can be used for a rapid screening of the sequence dependence of the DNA-electron interaction. We also show for the first time that the DNA reactions at surfaces can be imaged by secondary electron (SE) emission with both high analytical and spatial sensitivity. The SE micrographs indicate that strand breaks induced by the electrons play a significant role in the reaction mechanism.     

Large damage threshold and small electron escape depth in X-ray absorption spectroscopy of a conjugated polymer thin film

The information depth of near-edge X-ray absorption fine structure spectroscopy in the total electron yield mode (TEY-NEXAFS) is given by the escape depth of the TEY electrons z(TEY). This is determined by the effective ranges both of the inelastically scattered secondary electrons and of the primary excited electron before they thermalize below the vacuum level. For regioregular poly(3-hexylthiophene) (rreg-P3HT) thin films, we have measured the total electron emission efficiency to be 0.028 +/- 0.005 e/ph at an incident photon energy of 320 eV. The range of the primary electron was computed using optical dielectric-loss theory to be 7.5 nm. The range of the secondary electrons was then found by modeling to be 3.0 nm. This gives z(TEY) to be 2.5 nm, which is considerably less than the often-assumed value of 10 nm in the literature. It is also considerably smaller than the computed electron-electron scattering inelastic mean free path in the material, which suggests the predominance of electron-phonon scattering. Thus, TEY-NEXAFS has sufficient surface sensitivity to probe the frontier molecular layers of these organic conjugated polymers. In a second aspect of this report, the rreg-P3HT films have been characterized by in-situ core and valence photoemission spectroscopies and by ex-situ microattenuated total-reflection vibrational spectroscopy as a function of irradiation dose. No damage was observed in composition, bonding, orientation, and surface morphology under typical TEY-NEXAFS spectral acquisition conditions. For an integrated TEY that exceeds 2 x 10(-3) C cm(-2), however, the material degrades via alkyl side-chain dehydrogenation to unsaturated units, cross linking, ring opening of the backbone, and sulfur extrusion. Given that secondary electrons are the dominant cause of radiation damage, this exposure threshold measured by integrated TEY should also be valid at other X-ray energies.     

Low energy electron stimulated desorption from DNA films dosed with oxygen

Desorption of anions stimulated by 1-18 eV electron impact on self-assembled monolayer (SAM) films of single DNA strands is measured as a function of film temperature (50-250 K). The SAMs, composed of 10 nucleotides, are dosed with O(2). The OH(-) desorption yields increase markedly with exposure to O(2) at 50 K and are further enhanced upon heating. In contrast, the desorption yields of O(-), attributable to dissociative electron attachment to trapped O(2) molecules decrease with heating. Irradiation of the DNA films prior to the deposition of O(2) shows that this surprising increase in OH(-) desorption, at elevated temperatures, arises from the reaction of O(2) with damaged DNA sites. These results thus appear to be a manifestation of the so-called "oxygen fixation" effect, well known in radiobiology.     

Low-energy electron-induced processes in fluorinated copper phthalocyanine films observed by F- desorption: why so little damage?

As an indication of damage induced by hot electrons in an organic electronic material, the desorption of F- ions from a thin perfluorinated copper phthalocyanide film on SiO2 under low-energy (0-25 eV) electron impact has been recorded mass spectrometrically. Yields and damage cross sections are very low. No strong features due to negative ion resonances are found in the electron energy dependence of the desorption yield; rather the yield function rises from a threshold at about 5-6 eV continuously (with some weak structure) throughout the measured range. We discuss these findings in terms of the electronic structure of the film, as well as parameters influencing the relevant bond breaking process. We emphasize the strong influence of energy redistribution, which quenches normally long-lived negative ion resonances and selects localized and strongly repulsive excitations, as often observed in electronically induced bond breaking at surfaces. The improved understanding should be helpful in the selection of low-damage materials for organic semiconductor devices and for selection of operation parameters.     

Formation and emission of tetraalkylammonium salt molecular ions sputtered from a gelatin matrix

A gelatin matrix was simultaneously doped with nine equimolar, homologous, tetraalkylammonium salts ranging in mass from 210 to 700 Da. Bombardment of the sample with kiloelectronvolt ions resulted in a nonidentical distribution of relative cation intensities with a maximum at m/z 242 for samples with a total salt concentration of 0.004 g of salt/g of gelatin. A rapid increase in relative intensities with increasing mass is observed for the low mass salts and is believed to be linked to changes in the ionization efficiencies. The changes in ionization efficiencies are likely related to decreasing coulombic attractive forces between the organic cation and the counterion. Disappearance cross-sections, determined from decay curves, indicate that sputter-induced damage increases with increasing mass of the cation. Fragment-to-intact cation ratios also suggest that damage accumulates fastest in the heaviest salts. These observations indicate that desorption yields of the organic salts in a gelatin matrix decrease with increasing mass. In addition, suppression of lower mass tetraalkylammonium salt intact cation intensities was observed for salt-in-gelatin concentrations greater than 10⁻³ g/g.     

Fermi-shuttle processes in the electron emission by ion impact: Contribution to radiation damages

Secondary electrons, formed in biological tissues by high-energy particle impact, significantly contribute to the fragmentation of small molecules and to single- and double-strand brakes in DNA. Differential spectra of electrons emitted in the collisions of decelerating swift ions are of vital importance for estimating ion impact radiation damages. We demonstrate that the so-called Fermi-shuttle-type acceleration mechanism can produce a significant enhancement in the emission of high-energy secondary electrons. Double differential cross-sections for electron emission, measured in the collisions of N⁺ and N₂⁺ ions with Ar targets at 750 keV/u impact energy, clearly show this effect. The measured cross-sections are in good agreement with the theoretical results of CTMC calculations. Multiple scattering contribution to the Ar spectra above 300 eV is proved to be significant.