Low-energy (5-40 eV) electron-stimulated desorption of anions from physisorbed DNA bases

Electron stimulated desorption from condensed benzene

The electron induced dissociation of condensed benzene (C6H6) in thin films deposited on a Pt substrate is investigated by electron stimulated desorption (ESD) of anions and cations. The desorbed yields are recorded as a function of incident electron energy in the range of 10 to 950 eV for a fixed film thickness of 2 monolayers (ML) and for a fixed energy of 950 eV, as well as a function of film thickness from 0.5 to 8 monolayers (ML) for anions, and from 0.5 to 12ML for cations. Both energy and thickness dependencies are discussed in terms of the three main mechanisms yielding positively and/or negatively charged fragments: dissociative electron attachment (DEA), dipolar dissociation (DD) and dissociative ionization (DI) processes. At the probed energies, DD is the major mechanism, while DEA is predominantly induced by secondary electrons from the Pt substrate. Desorption of the parent positive ion is strongly suppressed. Similar qualitative behaviours are observed for the energy dependence of both anion and cation ESD yields, while some discrepancies exist in the thickness dependence, including a very significant systematic magnitude difference found between such ions formation. An estimation of the effective DD cross-section including the desorption probability is obtained. Feasible mechanisms behind the observed energy and thickness dependences for anion and cation yields are proposed. These results highlight the need for further investigations to better understand the underlying processes of electron induced dissociation in condensed matter.

Electron attachment to isolated and microhydrated favipiravir

Electron attachment and its equivalent in complex environments, single-electron reduction, are important in many biological processes. Here, we experimentally study the electron attachment to favipiravir, a well-known antiviral agent. Electron attachment spectroscopy is used to explore the energetics of associative (AEA) and dissociative (DEA) electron attachment to isolated favipiravir. AEA dominates the interaction and the yields of the fragment anions after DEA are an order of magnitude lower than that of the parent anion. DEA primary proceeds via decomposition of the CONH2 functional group, which is supported by reaction threshold calculations using ab initio methods. Mass spectrometry of small favipiravir-water clusters demonstrates that a lot of energy is transferred to the solvent upon electron attachment. The energy gained upon electron attachment, and the high stability of the parent anion were previously suggested as important properties for the action of several electron-affinic radiosensitizers. If any of these mechanisms cause synergism in chemo-radiation therapy, favipiravir could be repurposed as a radiosensitizer.

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

Electron and Positron Scattering by the Formamide Molecule

We report calculated elastic integral, differential, and momentum transfer cross sections for electron and positron collisions with the formamide (HCONH₂) molecule, for impact energies up to 10 eV. We have used the Schwinger multichannel method in the static-exchange and static-exchange plus polarization approximation for collisions of electrons and the static plus polarization approximation for collisions of positrons. The Born-closure procedure was applied to account for the long-range potential due to the permanent dipole moment of formamide. We obtained the well-characterized π* shape resonance located at around 2.38 eV, which belongs to the A″ symmetry of the C_s point group. Our integral and differential cross sections for collisions of electrons were compared with the data available in the literature and showed a good qualitative agreement. To the best of our knowledge, no experimental and theoretical data are currently available for positron-formamide collision, so our present cross sections were compared with the cross sections of formic acid, which is also polar and is isoeletronic to formamide.

Opportunities in the Synthesis and Design of Radioactive Thin Films and Nanoparticles

Studies of radioactive isotopes at the liquid-solid or gas-solid interface are enabling a detailed mechanistic understanding of the effects of radioactive decay on physical, biological, and chemical systems. In recent years, there has been a burgeoning interest in using radioactive isotopes for both imaging and therapeutic purposes by attaching them to the surface of colloidal nanoparticles. By merging the field of nanomedicine with the more mature field of internal radiation therapy, researchers are discovering new ways to diagnose and treat cancer. In this Perspective, we discuss state-of-the-art radioactive thin films as applied to both well-defined surfaces and more complex nanoparticles. We highlight the design considerations that are unique to radioactive films, which originate from the damaging and potentially self-destructive emissions produced during radioactive decay, and highlight future opportunities in the largely underexplored area between radioisotope chemistry and nanoscience.

Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA

The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A₄), d(A₈), d(A₁₂), d(A₁₆), and d(A₂₀)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A₄) to d(A₁₆), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A₂₀), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA₂₀ sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.

Dissociation dynamics in low energy electron attachment to ammonia using velocity slice imaging

The complete dissociation dynamics of low energy electron attachment to the ammonia molecule has been studied using velocity slice imaging (VSI) spectrometry. One low energy resonant peak around 5.5 eV and a broad resonance around 10.5 eV incident electron energies have been observed. The resonant states mainly dissociate via H- and NH2- fragments, though for the upper resonant state, the signature of NH- fragments is also predicted due to a three-body dissociation process. Kinetic energy and angular distributions of the NH2- fragment anions are measured simultaneously around the two resonances. Based on our experimental observations, we conclude that a temporary negative ion (TNI) state with A1 symmetry is responsible for the lower resonance. Whereas, we find strong evidence for the existence of a TNI state having A1 symmetry at the 10.5 eV resonance for the first time.

Concluding remarks for advances in ion spectroscopy Faraday Discussion

Because the Introductory Lecture of this Faraday Discussion emphasized the recent history and exciting developments in the fields of experimental methods and applications of gaseous ion spectroscopy, these Concluding Remarks are, by design, directed somewhat more toward the roles played by theory. In discussing both the experimental and theoretical studies of gaseous ions, it is important to recognize and appreciate the delicate balance workers in the field are pursuing in terms of methodological/tool development and applications to current-day pressing problems in chemistry, physics, materials science, and biology. Without both components of modern research in this field, progress will not be efficient. Substantial discussion is included about the reductive approach that is commonly used to attempt to connect studies of ions in the gas phase (i.e., as isolated species) with properties of these ions as they exist in nature. Issues of how small a model system can be, to what extent surroundings/solvation can be addressed, and how our experimental or theoretical tools might limit us are all discussed in some detail. The current ability of theory to assist in the interpretation of experimental spectral data on gaseous ions is discussed, as are several of the most pressing limitations of theory on this front. Finally, the author offers his thoughts about what advances/improvements in theory are needed and the outlook for when they might be expected, and urges the experimental community to remain in close contact with theory groups developing new methods so that progress can be optimized.

Clustered DNA Damage Induced by 2-20 eV Electrons and Transient Anions: General Mechanism and Correlation to Cell Death

The mechanisms of action of low-energy electrons (LEEs) generated in large quantities by ionizing radiation constitute an essential element of our understanding of early events in radiolysis and radiobiology. We present the 2-20 eV electron energy dependence of the yields of base damage (BD), BD-related cross-links (CLs), and non-double-strand break (NDSB) clustered damage induced in DNA. These new yield functions are generated by the impact of LEEs on plasmid DNA films. The damage is analyzed by gel electrophoresis with and without enzyme treatment. Maxima at 5 and 10 eV in BDs and BD-related CLs yield functions, and two others, at 6 and 10 eV, in those of NDSB clustered damage are ascribed to core-excited transient anions that decay into bond-breaking channels. The mechanism causing all types of DNA damages can be attributed to the capture of a single electron by a base followed by multiple different electron transfer pathways.

Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage

Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8 eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.

Energy Spectra of Protons and Generated Secondary Electrons around the Bragg Peak in Materials of Interest in Proton Therapy

The number and energy of secondary electrons generated around the trajectories of swift protons interacting with biological materials are highly relevant in proton therapy, due to the prominent role of low-energy electrons in the production of biodamage. For a given material, electron energy distributions are determined by the proton energy; and it is imperative that the distribution of proton energy at depths around the Bragg peak region be described as accurately as possible. With this objective, we simulated the energy distributions of proton beams of clinically relevant energies (50-300 MeV) at depths around the Bragg peak in liquid water and the water-equivalent polymer poly(methyl methacrylate) (PMMA). By using a simple model, this simulation has been conveniently extended to account for nuclear fragmentation reactions, providing depth-dose curves in excellent agreement with available experimental data. Special care has been taken to describe the electronic excitation spectrum of the target, taking into account its condensed phase nature. A predictive formula has been obtained for the mean value and the width of the proton energy distribution at the Bragg peak depth, quantities which are found to grow linearly with the initial energy of the beam, in good agreement with available data. To accurately characterize (in number and energy) the electrons generated around the proton paths, the energy distributions of the latter at each depth have been convoluted with the energy-dependent ionization inverse mean free paths. This results in a number of low-energy electrons around the Bragg peak larger than when only the proton beam average energy at the given depths is considered. The convoluted ionization inverse mean free path closely resembles the Bragg curve shape. The average energy of the secondary electrons is nearly constant (∼55 eV for liquid water and ∼43 eV for PMMA) in the plateau of the Bragg curve, independent of the proton incident energy and suddenly decaying once the Bragg peak is reached. These findings highlight the importance of a precise calculation of the proton beam energy distribution as a function of the target depth to reliably characterize the secondary electrons generated around the Bragg peak region.

Electron stimulated desorption from condensed pyrimidine and pyridazine

Low energy electron (LEE) interactions and the formation of transient negative ions play a dominant role in radiation-induced dissociation of condensed-phase biomolecules (e.g. in radiotherapy). Here we present data on the LEE-induced dissociation and desorption of the DNA/RNA-base and radiosensitizing agent analogues pyrimidine and pyridazine. Vapors of each molecule were condensed on either a Pt or Ar substrate to form a multilayer film or a submonolayer molecular target, respectively. These were irradiated with electrons of 0-80 eV and the desorbing anionic and cationic fragments analysed via time of flight mass spectrometry. The detected cations are the same species seen in gas-phase mass spectra, albeit of differing relative intensity. Anion yield functions exhibit strong maxima, indicating that transient negative ions contribute significantly, via dissociative electron attachment (DEA), to molecular dissociation below 20 eV. For both molecules, the <5 eV shape resonances, seen experimentally and predicted by theory, do not result in fragment desorption. The main anionic fragments are H^- and CN^- for both molecules, additionally the fragments C^-, CH^- C₂H^- and CHN^- desorb from pyrimidine and C^- and C₂H^- from pyridazine, with some resonances lying above the ionization limit. Pyrimidine shows higher anion desorption yields than pyridazine for all species except H^-. The anion signal also comprises dipolar dissociation (DD), investigated in both anionic and cationic yield functions. From analysis of anion and cation yields, fragmentation pathways are suggested. The direct ionization pathway provides information on the appearance energies for cations and their production processes in condensed phase.

Biomolecular damage induced by ionizing radiation: the direct and indirect effects of low-energy electrons on DNA

Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.

DNA strand breaks and crosslinks induced by transient anions in the range 2-20 eV

The energy dependence of the yields of single and double strand breaks (SSB and DSB) and crosslinks induced by electron impact on plasmid DNA films is measured in the 2-20 eV range. The yield functions exhibit two strong maxima, which are interpreted to result from the formation of core-excited resonances (i.e., transient anions) of the bases, and their decay into the autoionization channel, resulting in π → π* electronic transitions of the bases followed by electron transfer to the C-O σ* bond in the phosphate group. Occupancy of the σ* orbital ruptures the C-O bond of the backbone via dissociative electron attachment, producing a SSB. From a comparison of our results with those of other works, including theoretical calculations and electron-energy-loss spectra of the bases, the 4.6 eV peak in the SSB yield function is attributed to the resonance decay into the lowest electronically excited states of the bases; in particular, those resulting from the transitions 13A'(π2 → π3*) and 13A″(n2 → π3*) of thymine and 13A'(π → π*) of cytosine. The strongest peak at 9.6 eV in the SSB yield function is also associated with electron captured by excited states of the bases, resulting mostly from a multitude of higher-energy π → π* transitions. The DSB yield function exhibits strong maxima at 6.1 and 9.6 eV. The peak at 9.6 eV is probably related to the same resonance manifold as that leading to SSB, but the other at 6.1 eV may be more restricted to decay into the electronic state 13A' (π → π*) of cytosine via autoionization. The yield function of crosslinks is dominated by a broad peak extending over the 3.6-11.6 eV range with a sharper one at 17.6 eV. The different line shape of the latter function, compared to that of SSB and DSB, appears to be due to the formation of reactive radical sites in the initial supercoiled configuration of the plasmid, which react with the circular form (i.e., DNA with a SSB) to produce a crosslink.

Dissociative electron attachment to DNA-diamine thin films: impact of the DNA close environment on the OH- and O- decay channels

We measure the desorption of anions stimulated by the impact of 0-20 eV electrons on highly uniform thin films of plasmid DNA-diaminopropane. The results are accurately correlated with film thickness and composition by AFM and XPS measurements, respectively. Resonant structures in the H(-), O(-), and OH(-) yield functions are attributed to the decay of transient anions into the dissociative electron attachment (DEA) channel. The diamine induces ammonium-phosphate bridges along the DNA backbone, which suppresses the DEA O(-) channel and in counter-part increases considerably the desorption of OH(-). The close environment of the phosphate groups may therefore play an important role in modulating the rate and type of DNA damages induced by low energy electrons.

What is the initial chemical precursor of DNA strand breaks generated by direct-type effects?

The present study tests the hypothesis that the majority of DNA strand breaks produced by direct-type effects are due to sugar free radical precursors and that these radicals are produced by direct ionization of the sugar-phosphate backbone or by hole transfer to the sugar from tightly bound water. Well-defined crystalline DNA samples of d(CGCG)(2), d(CGCACG:GCGTGC), d(GTGCGCAC)(2), and d((GCACGCGTGC)(2) were irradiated at 4 K, and their free radical dose response determined from 0 to 1800 kGy. A model is proposed that effectively describes the dose response curves. It includes the following parameters: the free radical concentration at saturation C(max), the free radical yields G(b) and G(s), and the destruction constants k(b) and k(s). The subscripts b and s refer to base-centered and sugar-centered radicals, respectively. In each of these systems, the free radical concentration exhibits a remarkable resistance to dose saturation up to at least 1500 kGy. As predicted, G(b) > G(s), the G(b)/G(s) ratio varying between 4 and 12. Likewise, k(b) > k(s), the k(b)/k(s) ratio varying between 28 and 81. The lower cross-section for destruction of the sugar-centered radicals is consistent with the expectation that they are relatively radiation resistant. G(b)/G is between 0.81 and 0.92, indicating that at low doses the bases trap out 80-90% of the total free radical population. The remaining 10-20% are located on the sugar. At high dose, a larger fraction of the radicals are trapped on the backbone as seen from the ratio C(mxS)/C(mxB), which ranges from 3.5 to 8. This unusually late onset of dose saturation closely parallels that observed for strand break products in earlier studies. There is, therefore, a good correlation between the dose response profiles of sugar-trapped radicals and strand breaks. These observations strongly support the hypothesis that sugar radicals are precursors to the majority of strand breaks produced by the direct-type effect in DNA.

Absolute cross sections for vibrational excitations of cytosine by low energy electron impact

The absolute cross sections (CSs) for vibrational excitations of cytosine by electron impact between 0.5 and 18 eV were measured by electron-energy loss (EEL) spectroscopy of the molecule deposited at monolayer coverage on an inert Ar substrate. The vibrational energies compare to those that have been reported from IR spectroscopy of cytosine isolated in Ar matrix, IR and Raman spectra of polycrystalline cytosine, and ab initio calculation. The CSs for the various H bending modes at 142 and 160 meV are both rising from their energy threshold up to 1.7 and 2.1 × 10(-17) cm(2) at about 4 eV, respectively, and then decrease moderately while maintaining some intensity at 18 eV. The latter trend is displayed as well for the CS assigned to the NH(2) scissor along with bending of all H at 179 meV. This overall behavior in electron-molecule collision is attributed to direct processes such as the dipole, quadrupole, and polarization contributions, etc. of the interaction of the incident electron with a molecule. The CSs for the ring deformation at 61 meV, the ring deformation with N-H symmetric wag at 77 meV, and the ring deformations with symmetric bending of all H at 119 meV exhibit common enhancement maxima at 1.5, 3.5, and 5.5 eV followed by a broad hump at about 12 eV, which are superimposed on the contribution due to the direct processes. At 3.5 eV, the CS values for the 61-, 77-, and 119-meV modes reach 4.0, 3.0, and 4.5 × 10(-17) cm(2), respectively. The CS for the C-C and C-O stretches at 202 meV, which dominates in the intermediate EEL region, rises sharply until 1.5 eV, reaches its maximum of 5.7 × 10(-17) cm(2) at 3.5 eV and then decreases toward 18 eV. The present vibrational enhancements, correspond to the features found around 1.5 and 4.5 eV in electron transmission spectroscopy (ETS) and those lying within 1.5-2.1 eV, 5.2-6.8 eV, and 9.5-10.9 eV range in dissociative electron attachment (DEA) experiments with cytosine in gas phase. While the ETS features are ascribed to shape resonances associated with the electron occupation of the second and third antibonding π-orbitals of the molecule in its ground state, the correspondence with DEA features suggests the existence of common precursor anion states decaying with certain probabilities into the vibrationally excited ground state.

Measurement of inelastic cross sections for low-energy electron scattering from DNA bases

PURPOSE

To determine experimentally the absolute cross sections (CS) to deposit various amount of energies into DNA bases by low-energy electron (LEE) impact.

MATERIALS AND METHODS

Electron energy loss (EEL) spectra of DNA bases were recorded for different LEE impact energies on the molecules deposited at very low coverage on an inert argon (Ar) substrate. Following their normalisation to the effective incident electron current and molecular surface number density, the EEL spectra were then fitted with multiple Gaussian functions in order to delimit the various excitation energy regions. The CS to excite a molecule into its various excitation modes were finally obtained from computing the area under the corresponding Gaussians.

RESULTS

The EEL spectra and absolute CS for the electronic excitations of pyrimidine and the DNA bases thymine, adenine, and cytosine by electron impacts below 18 eV were reported for the molecules deposited at about monolayer coverage on a solid Ar substrate.

CONCLUSIONS

The CS for electronic excitations of DNA bases by LEE impact were found to lie within the 10(216) to 10(218) cm(2) range. The large value of the total ionisation CS indicated that ionisation of DNA bases by LEE is an important dissipative process via which ionising radiation degrades and is absorbed in DNA.

Low-energy electron-induced damage in a trinucleotide containing 5-bromouracil

The reaction of low-energy electrons (LEEs; 10 eV) with 5'-TpXpT-3' (TXT), where X is uracil (U), thymine (T), and 5-bromouracil (5BrU), was examined by HPLC-UV analysis. The presence of 5BrU increased total damage by >50%. The radiation products of T5BrUT included TUT (40%), free U, T, 5BrU (23%), and fragments (13%). These products may be explained by initial capture of LEEs by the nucleobase to form a transient anion, followed by transfer of the electron within the molecule and cleavage of susceptible bonds by dissociative electron attachment (C-Br, C-N, or C-O bonds). In addition, these products may arise from the uracilyl-5-yl (U-5-yl) radicals that undergo H-atom abstraction from the sugar moiety. Interestingly, several products contained two sites of cleavage (U, pUT, and TUp). The formation of these products was linear with dose, and thus, they arise from the single-electron reactions. To explain these products, we propose that the reaction of LEEs (10 eV) involves the coupling of two dissociative processes in the same molecule (for example, dissociative excitation and dissociative electron attachment). The latter reactions may contribute to the formation of clustered damage, which is the most deleterious damage induced by ionizing radiation.

Effect of morphology of thin DNA films on the electron stimulated desorption of anions

We present a comparison between the electron stimulated desorption (ESD) of anions from DNA samples prepared by lyophilization (an example of poorly organized or nonuniform films) and molecular self-assembly (well-ordered films). The lyophilization (or freeze- drying) method is perhaps the most frequently employed technique for forming DNA films for studies of low-energy electron (LEE) interactions leading to DNA damage; however, this technique usually produces nonuniform films with considerable clustering which may affect DNA configuration and enhance sample charging when the film is irradiated. Our results confirm the general validity of ESD measurements obtained with lyophilized samples, but also reveal limitations of lyophilization for LEE studies on DNA films. Specifically we observe some modulation of structures, associated with dissociative electron attachment, in the anion yield functions from different types of DNA film, confirming that conformational factors play a role in the LEE induced damage to DNA.

Photoelectron spectroscopic studies of 5-halouracil anions

The parent negative ions of 5-chlorouracil, UCl(-) and 5-fluorouracil, UF(-) have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl(-) and UF(-) and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr(-), we did not observe it, the mass spectrum exhibiting only Br(-) fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

Absolute cross sections for electronic excitations of cytosine by low energy electron impact

The absolute cross sections (CSs) for electronic excitations of cytosine by electron impact between 5 and 18 eV were measured by electron-energy-loss (EEL) spectroscopy of the molecule deposited at low coverage on an inert Ar substrate. The lowest EEL features found at 3.55 and 4.02 eV are ascribed to transitions from the ground state to the two lowest triplet 1 (3)A(')(π→π(∗)) and 2 (3)A(')(π→π(∗)) valence states of the molecule. Their energy dependent CSs exhibit essentially a common maximum at about 6 eV with a value of 1.84×10(-17) cm(2) for the former and 4.94×10(-17) cm(2) for the latter. In contrast, the CS for the next EEL feature at 4.65 eV, which is ascribed to the optically allowed transition to the 2 (1)A(')(π→π(∗)) valence state, shows only a steep rise to about 1.04×10(-16) cm(2) followed by a monotonous decrease with the incident electron energy. The higher EEL features at 5.39, 6.18, 6.83, and 7.55 eV are assigned to the excitations of the 3 (3,1)A(')(π→π(∗)), 4 (1)A(')(π→π(∗)), 5 (1)A(')(π→π(∗)), and 6 (1)A(')(π→π(∗)) valence states, respectively. The CSs for the 3 (3,1)A(') and 4 (1)A(') states exhibit a common enhancement at about 10 eV superimposed on a more or less a steep rise, reaching, respectively, a maximum of 1.27 and 1.79×10(-16) cm(2), followed by a monotonous decrease. This latter enhancement and the maximum seen at about 6 eV in the lowest triplet states correspond to the core-excited electron resonances that have been found by dissociative electron attachment experiments with cytosine in the gas phase. The weak EEL feature found at 5.01 eV with a maximum CS of 3.8×10(-18) cm(2) near its excitation threshold is attributed to transitions from the ground state to the 1 (3,1)A(")(n→π(∗)) states. The monotonous rise of the EEL signal above 8 eV is attributed to the ionization of the molecule. It is partitioned into four excitation energy regions at about 8.55, 9.21, 9.83, and 11.53 eV, which correspond closely to the ionization energies of the four highest occupied molecular orbitals of cytosine. The sum of the ionization CS for these four excitation regions reaches a maximum of 8.1×10(-16) cm(2) at the incident energy of 13 eV.

Influence of organic ions on DNA damage induced by 1 eV to 60 keV electrons

We report the results of a study on the influence of organic salts on the induction of single strand breaks (SSBs) and double strand breaks (DSBs) in DNA by electrons of 1 eV to 60 keV. Plasmid DNA films are prepared with two different concentrations of organic salts, by varying the amount of the TE buffer (Tris-HCl and EDTA) in the films with ratio of 1:1 and 6:1 Tris ions to DNA nucleotide. The films are bombarded with electrons of 1, 10, 100, and 60 000 eV under vacuum. The damage to the 3197 base-pair plasmid is analyzed ex vacuo by agarose gel electrophoresis. The highest yields are reached at 100 eV and the lowest ones at 60 keV. The ratios of SSB to DSB are surprisingly low at 10 eV (∼4.3) at both salt concentrations, and comparable to the ratios measured with 100 eV electrons. At all characteristic electron energies, the yields of SSB and DSB are found to be higher for the DNA having the lowest salt concentration. However, the organic salts are more efficient at protecting DNA against the damage induced by 1 and 10 eV electrons. DNA damage and protection by organic ions are discussed in terms of mechanisms operative at each electron energy. It is suggested that these ions create additional electric fields within the groove of DNA, which modify the resonance parameter of 1 and 10 eV electrons, namely, by reducing the electron capture cross-section of basic DNA units and the lifetime of corresponding transient anions. An interstrand electron transfer mechanism is proposed to explain the low ratios for the yields of SSB to those of DSB produced by 10 eV electrons.

Low-energy electron-induced DNA damage: effect of base sequence in oligonucleotide trimers

DNA damage induced by low-energy electrons (LEEs) has attracted considerable attention in recent years because LEEs represent a large percentage of the total energy deposited by ionizing radiation and because LEEs have been shown to damage DNA components. In this article, we have studied the effect of base sequences in a series of oligonucleotide trimers by the analysis of damage remaining within the nonvolatile condensed phase after LEE irradiation. The model compounds include TXT, where X represents one of the four normal bases of DNA (thymine (T), cytosine (C), adenine (A), and guanine (G)). Using HPLC-UV analysis, several known fragments were quantified from the release of nonmodified nucleobases (T and X) as well as from phosphodiester C-O bond cleavage (pT, pXT, Tp, and TXp). The total damage was estimated by the disappearance of the parent peaks in the chromatogram of nonirradiated and irradiated samples. When trimers were irradiated with LEE (10 eV), the total damage decreased 2-fold in the following order: TTT > TCT > TAT > TGT. The release of nonmodified nuclobases (giving from 17 to 24% of the total products) mainly occurred from the terminal sites of trimers (i.e., T) whereas the release of central nucleobases was minor (C) or not at all detected (A and G). In comparison, the formation of products arising from phosphodiester bond cleavage accounted for 9 to 20% of the total damage and it partitioned to the four possible sites of cleavage present in trimers. This study indicates that the initial LEE capture and subsequent bond breaking within the intermediate anion depend on the sequence and electron affinity of the bases, with the most damage attributed to the most electronegative base, T.

Protection by organic ions against DNA damage induced by low energy electrons

It is well known that electrons below 15 eV induce strand breaks in DNA essentially via the formation of transient anions which decay by dissociative electron attachment (DEA) or into dissociative electronics states. The present article reports the results of a study on the influence of organic ions on this mechanism. tris and EDTA are incorporated at various concentrations within DNA films of different thicknesses. The amino group of tris molecules and the carboxylic acid function of ethylenediamine tetra-acetic acid (EDTA) molecules together can be taken as simple model for the amino acids components of proteins, such as histones, which are intimately associated with the DNA of eukaryotic cells. The yield of single strand breaks induced by 10 eV electrons is found to decrease dramatically as a function of the number of organic ions/nucleotide. As few as 2 organic ions/nucleotide are sufficient to decrease the yield of single strand breaks by 70%. This effect is partly explained by an increase in multiple inelastic electrons scattering with film thickness but changes in the resonance parameters can also contribute to DNA protection. This can occur if the electron captures cross section and the lifetime of the transient anions (i.e., core-excited resonances) formed at 10 eV are reduced by the presence of organic ions within the grooves of DNA. Moreover, it is proposed that the tris molecules may participate in the repair of DNA anions [such as G(-H)(-)] induced by DEA on DNA bases.

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.

Bond selective dissociative electron attachment to thymine

Free-electron attachment to thymine and partially deuterated thymine, where D replaces H at all carbon atoms, is studied in the electron energy range from about 0 to 15 eV. The formation of fragment anions that are formed by the loss of one or two H (D) atoms is analyzed as a function of the incident electron energy using a crossed electron/neutral beam apparatus in combination with a quadrupole mass spectrometer. By using partially deuterated thymine and quantum-chemical calculation a bond selectivity for the loss of one and two hydrogen atoms is observed that is determined only by the kinetic energy of the incident electron.

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.

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.

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.

Low-Energy (3−24 eV) Electron Damage to the Peptide Backbone

We report the mass spectrometric measurement of anions desorbed by 3-24 eV electron impact on thin films of formamide-1-d (DCONH2) and on the self-assembled monolayer (SAM) of two different Lys amide molecules used as a molecular model of the peptide backbone. In the present SAM configuration, the amides are elevated from a gold substrate by hydrocarbon chains to remove the effects of the metal substrate. Electron irradiation produces H- and D- from the formamide-1-d film and H-, CH3-, O-, and OH- from the SAM Lys amides. Below 13 eV, the dependence of the anion yields on the incident electron energy exhibits structures indicative of the dissociative electron attachment process, which is responsible for molecular fragmentation via the initial formation of core-excited anions. Above 13 eV, anion desorption is dominated principally by non-resonant dipolar dissociation. Our results suggest that the sensitivity of the peptide backbone to secondary electrons produced by ionizing radiation depends on the chemical environment (i.e., the amino acids sequence).

Electron-Attachment Resonances of Glycine Zwitterions from Quantum Scattering Calculations: Modeling Macrosolvation Effects

A computational study of the quantum dynamics for low-energy electrons scattered by the isolated zwitterionic species of the glycine molecule is carried out using a model interaction potential described in the main text. The macroscopic effects of water solvation on the target molecule in the electron scattering problem are described through a continuum polarizable model (CPCM) which modifies the target molecular structure. In such a way, realistic molecular orbitals depicting the glycine zwitterion in solution are used to model the electron-molecule interaction. The results of the calculations indicate the presence of five different transient negative ions (TNIs) formed at energies from the threshold and up to about 6 eV. Although no nuclear motion was explicitly considered in the ensuing decay processes, the analysis of the nodal structures and density distributions for the resonant excess electron wavefunctions over the molecular space suggests possible anionic fragmentations that produce (Gly-H)-, H-, -CO2-, and -NH3. The likely consequences of such releases into the medium are briefly discussed.

Cross sections for low-energy electron scattering from adenine in the condensed phase

Measurements of the vibrational and electronic excitation of a sub-monolayer up to a monolayer film of adenine were performed with a high resolution electron energy-loss (HREEL) spectrometer. The integral cross sections (over the half-space angle) for excitation of the normal vibrational modes of the ground electronic state and electronically excited states are calculated from the measured reflectivity EEL spectra. Most cross sections for vibrational excitation are of the order of 10(-17) cm(2), the largest being the out-of-plane wagging of the amino-group and the six-member ring deformations. A wide resonance feature appears in the incident energy dependence of the vibrational cross sections at 3-5 eV, while a weak shoulder is present in this dependence for combined ring deformations and bending of hydrogen atoms. For the five excited electronic states, at 4.7, 5.0, 5.5, 6.1 and 6.6 eV, the cross sections are of the order of 10(-18) cm(2), except in the case of the state at the energy of 6.1 eV, for which it is two to three times higher.

Successive Attachment of Electrons to Protonated Guanine: (G+H)• Radicals and (G+H)- Anions

The structures, energetics, and vibrational frequencies of nine hydrogenated 9H-keto-guanine radicals (G+H)(*) and closed-shell anions (G+H)(-) are predicted using the carefully calibrated (Chem. Rev. 2002, 102, 231) B3LYP density functional method in conjunction with a DZP++ basis set. These radical and anionic species come from consecutive electron attachment to the corresponding protonated (G+H)(+) cations in low pH environments. The (G+H)(+) cations are studied using the same level of theory. The proton affinity (PA) of guanine computed in this research (228.1 kcal/mol) is within 0.7 kcal/mol of the latest experiment value. The radicals range over 41 kcal/mol in relative energy, with radical r1, in which H is attached at the C8 site of guanine, having the lowest energy. The lowest energy anion is a2, derived by hydride ion attachment at the C2 site of guanine. No stable N2-site hydride should exist in the gas phase. Structure a9 was predicted to be dissociative in this research. The theoretical adiabatic electron affinities (AEA), vertical electron affinities, and vertical detachment energies were computed, with AEAs ranging from 0.07 to 3.12 eV for the nine radicals.

Hydrogen Atom and Hydride Anion Addition to Adenine: Structures and Energetics

The radicals and anions derived from the 9H tautomer of adenine by adding a hydrogen atom to one of the four double bonds of the adenine framework have been studied. Computations were carried out using a carefully calibrated density functional (B3LYP) method and basis set (DZP++). Optimized geometries, energies, and vibrational frequencies are predicted for eight radicals and anions. The radicals are found to lie in a range of 22 kcal mol(-1), with the radical derived by addition to the C(8) carbon atom being the lowest lying energetically. The anions are predicted to be bound species in the gas phase with an energetic range of 43 kcal mol(-1). Anions produced by addition of a hydride ion to adenine carbon atoms are found to be the most favorable. Six of the anions are predicted to be stable species with respect to electron detachment. The adiabatic electron affinities, vertical electron affinities, and vertical detachment energies are computed for the first time. Electron affinities for these radicals range from 0.0 to 2.0 eV. Radicals produced by addition to a nitrogen atom have near-zero adiabatic electron affinities, while radicals produced by addition at carbon atoms have considerably higher electron affinities.

The deprotonated guanine-cytosine base pair

Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26-27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine-cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal x mol(-1), vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal x mol(-1) lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H...O2 distance dramatically reduced from 1.88 to 1.58 A, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a "reverse wobble" incorporating two N-H...N hydrogen bonds. Three different types of relaxation energies (4.3-54 kcal x mol(-1)) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.

Absolute electronic excitation cross sections for low-energy electron (5–12eV) scattering from condensed thymine

The absolute cross sections for electronic excitations of thymine by electron impact between 5 and 12 eV are determined by means of electron-energy loss (EEL) spectroscopy for the molecule deposited at submonolayer coverage on an inert Ar substrate. The lowest EEL features at 3.7 and 4.0 eV are attributed to the excitation of the triplet 1 3A'(pi --> pi*) and 1 3A''(n --> pi*) valence states of the molecule. The higher EEL features located at 4.9, 6.3, 7.3, and 9 eV with a weak shoulder around 6 eV are ascribed mostly to triplet valence (pi --> pi*) excitation manifold of the molecule. The energy dependence of the cross section for both the lowest triplet valence excitations shows essentially a peak at about 5 eV reaching a value of 2.9 x 10(-17) cm2. The cross sections for the higher EEL features are generally characterized by a common broad maximum around 8 eV. The latter reaches a value of 1.36 x 10(-16) cm2 for the combined 6 and 6.3 eV excitation region. The maxima in the present cross sections are found to correspond to the resonances that have been reported at about the same energies in the O- yield from electron impact on thymine in the gas phase.