Mechanism and site of attack for direct damage to DNA by low-energy electrons

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.

Radiation-Induced Effect on Spin-Selective Electron Transfer through Self-Assembled Monolayers of ds-DNA

Stability of the DNA molecule is essential for the proper functioning and sustainability of all living organisms. In this study, we investigate the effect of gamma radiation (γ-radiation) on spin-selective electron transfer through double strand (ds)DNA molecules. Self-assembled monolayers (SAMs) of 21-base long DNA are prepared on Au-coated Ni thin film. We measure the spin polarization (%) of the SAMs of ds-DNA using the spin-dependent electrochemical technique. We use a Cs-based γ-radiation source to expose the SAMs of ds-DNA immobilized on thin films for various time intervals ranging from 0–30 min. The susceptibility of DNA to γ-radiation is measured by spin-dependent electrochemistry. We observe that the efficiency of spin filtering by ds-DNA gradually decreases when exposure (to γ-radiation) time increases, and drops below 1% after 30 min of exposure. The change in spin polarization value is related either to the conformational perturbation in DNA or to structural damage in DNA molecules caused by ionizing radiation.

Early Events in Radiobiology: Isolated and Cluster DNA Damage Induced by Initial Cations and Nonionizing Secondary Electrons

Radiobiological damage is principally triggered by an initial cation and a secondary electron (SE). We address the fundamental questions: What lesions are first produced in DNA by this cation or nonionizing SE? What are their relative contributions to isolated and potentially lethal cluster lesions? Five monolayer films of dry plasmid DNA deposited on graphite or tantalum substrates are bombarded by 0.1-100 eV electrons in a vacuum. From measurements of the current transmitted through the films, 3.5 and 4.5 cations per incident 60 and 100 eV electrons, respectively, are estimated to be produced and stabilized within DNA. Damage analysis at 6, 10, 20, 30, 60, and 100 eV indicates that essentially all lesions, but preferentially cluster damages, are produced by non-ionizing or weakly ionizing electrons of energies below 12 eV. Most of these lesions are induced within femtosecond times, via transient anions and electron transfer within DNA, with little contributions from the numerous cations.

Low energy secondary electron induced damage of condensed nucleotides

Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10^-18 cm²) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.

Efficient and surface site-selective ion desorption by positron annihilation

We compared positron- and electron-stimulated desorption (e⁺SD and ESD) of positive ions from a TiO₂(110) surface. Although desorption of O⁺ ions was observed in both experiments, the desorption efficiency caused by positron bombardment was larger by one order of magnitude than that caused by electron bombardment at an incident energy of 500 eV. e⁺SD of O⁺ ions remained highly efficient with incident positron energies between 10 eV and 600 eV. The results indicate that e⁺SD of O⁺ ions is predominantly caused by pair annihilation of surface-trapped positrons with inner-shell electrons. We also tested e⁺SD from water chemisorbed on the TiO₂ surface and found that the desorption of specific ions was enhanced by positron annihilation, above the ion yield with electron bombardment. This finding corroborates our conclusion that annihilation-site selectivity of positrons results in site-selective ion desorption from a bombarded surface.

Inducing chemical reactivity on specific sites of a molecule using the Coulomb interaction exerted by a low energy electron

Remarkable site-specificity in the resonant attachment of low energy electrons (LEEs) to molecular targets is proposed as an efficient method for inducing chemical reactivity on specific sites of molecules. The Coulomb interaction between the attached electron and the most polarizable molecular electrons localized on the attached site is the reason for site-specific chemical reactivity. The Coulombically induced site-specific chemical reactivity is best illustrated by the LEE induced chemical transformation of a weakly bound molecular complex into a strong covalent adduct. The chemical transformation occurs due to the Coulombically induced nucleophilicity on a specific molecular moiety in the complex. A simple strategy for inducing site-specific chemical reactivity using a LEE may find new avenues in chemical synthesis.

Absolute cross-sections for DNA strand breaks and crosslinks induced by low energy electrons

Absolute cross sections (CSs) for the interaction of low energy electrons with condensed macromolecules are essential parameters to accurately model ionizing radiation induced reactions. To determine CSs for various conformational DNA damage induced by 2-20 eV electrons, we investigated the influence of the attenuation length (AL) and penetration factor (f) using a mathematical model. Solid films of supercoiled plasmid DNA with thicknesses of 10, 15 and 20 nm were irradiated with 4.6, 5.6, 9.6 and 14.6 eV electrons. DNA conformational changes were quantified by gel electrophoresis, and the respective yields were extrapolated from exposure-response curves. The absolute CS, AL and f values were generated by applying the model developed by Rezaee et al. The values of AL were found to lie between 11 and 16 nm with the maximum at 14.6 eV. The absolute CSs for the loss of the supercoiled (LS) configuration and production of crosslinks (CL), single strand breaks (SSB) and double strand breaks (DSB) induced by 4.6, 5.6, 9.6 and 14.6 eV electrons are obtained. The CSs for SSB are smaller, but similar to those for LS, indicating that SSB are the main conformational damage. The CSs for DSB and CL are about one order of magnitude smaller than those of LS and SSB. The value of f is found to be independent of electron energy, which allows extending the absolute CSs for these types of damage within the range 2-20 eV, from previous measurements of effective CSs. When comparison is possible, the absolute CSs are found to be in good agreement with those obtained from previous similar studies with double-stranded DNA. The high values of the absolute CSs of 4.6 and 9.6 eV provide quantitative evidence for the high efficiency of low energy electrons to induce DNA damage via the formation of transient anions.

Electron-stimulated reactions in nanoscale water films adsorbed on α-Al2O3(0001)

100 eV electrons are stopped in the H₂O portion of the isotopically-layered nanoscale film on α-Al₂O₃(0001) but D₂ is produced at the D₂O/alumina interface by mobile electronic excitations and/or hydronium ions.

The relationship between interfacial bonding and radiation damage in adsorbed DNA

Illustration showing that secondary electrons have a higher damage probability for thiolated DNA as opposed to unthiolated DNA, due to the former's higher density of LUMO states, which leads to more efficient capture of the low energy electrons.

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.

Photoelectron spectroscopy and density functional theory studies on the uridine homodimer radical anions

We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine, (rU)(2)(●-). It features a broad band consisting of an onset of ∼1.2 eV and a maximum at the electron binding energy (EBE) ranging from 2.0 to 2.5 eV. Calculations performed at the B3LYP∕6-31++G∗∗ level of theory suggest that the PES is dominated by dimeric radical anions in which one uridine nucleoside, hosting the excess charge on the base moiety, forms hydrogen bonds via its O8 atom with hydroxyl of the other neutral nucleoside's ribose. The calculated adiabatic electron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimers show an excellent agreement with the experimental values. The anionic complexes consisting of two intermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers. Despite the fact that uracil-uracil anionic homodimers are additionally stabilized by barrier-free electron-induced proton transfer, their relative thermodynamic stabilities and the calculated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)(2)(●-).

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.

Density functional resonance theory of unbound electronic systems

Density functional resonance theory (DFRT) is a complex-scaled version of ground-state density functional theory (DFT) that allows one to calculate the in-principle exact resonance energies and lifetimes of metastable anions. In this formalism, the energy and lifetime of the lowest-energy resonance of unbound systems is encoded into a complex "density" that can be obtained via complex-coordinate scaling. This complex density is used as the primary variable in a DFRT calculation, just as the ground-state density would be used as the primary variable in DFT. As in DFT, there exists a mapping of the N-electron interacting system to a Kohn-Sham system of N noninteracting particles. This mapping facilitates self-consistent calculations with an initial guess for the complex density, as illustrated with an exactly solvable model system.

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.

Electron attachment to hydrated oligonucleotide dimers: guanylyl-3',5'-cytidine and cytidylyl-3',5'-guanosine

The dinucleoside phosphate deoxycytidylyl-3',5'-deoxyguanosine (dCpdG) and deoxyguanylyl-3',5'-deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5' end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3' end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine-containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The pi-stacking interaction between nucleobases G and C seems unlikely to improve the electron-capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron-capturing ability of cytosine should be attributed to the intensified proton accepting-donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O-C sigma bond and N-glycosidic bond breakage, might be expected for the radical anions of the guanosine-cytosine mixed oligonucleotides.

Electrochemical DNA biosensor for the detection of interaction between di[azino-di(5,6-azafluorene)-kappa2-NN'] dibromicoppers and DNA

A new Cu(II) complex CuL(2)Br(2) (L = azino-di(5,6-azafluorene)-kappa(2)-NN') was synthesized, and a new method of electrochemical probe has been proposed for the determination of hepatitis B virus (HBV) based on its interaction with [CuL(2)](2+). This ligand, containing functional groups, as well as planar aromatic domains, is capable of binding to double-stranded DNA (dsDNA) more efficiently than to single-stranded DNA (ssDNA). Emphasis has been placed on the elucidation of the nature of the interaction by electrochemical techniques. The electroactive [CuL(2)](2+) could be employed as an electrochemical indicator to detect hybridization events in DNA biosensors. These biosensors have been constructed by immobilization of a probe DNA sequence from HBV onto glassy carbon electrode (GCE). After hybridization with the complementary target sequence, [CuL(2)](2+) was accumulated within the dsDNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range. Using this approach, complementary target sequences of HBV can be quantified over the range of 1.74 x 10(-9) to 3.45 x 10(-7) M, with a detection limit of 8.32 x 10(-10) M and a linear correlation coefficient of 0.9936.In addition, this approach is capable of detecting hybridization of complementary sequences containing one or three mismatched bases.

Low-energy electron diffraction and induced damage in hydrated DNA

Elastic scattering of 5-30 eV electrons within the B-DNA 5'-CCGGCGCCGG-3' and A-DNA 5'-CGCGAATTCGCG-3' DNA sequences is calculated using the separable representation of a free-space electron propagator and a curved wave multiple scattering formalism. The disorder brought about by the surrounding water and helical base stacking leads to a featureless amplitude buildup of elastically scattered electrons on the sugar and phosphate groups for all energies between 5 and 30 eV. However, some constructive interference features arising from diffraction are revealed when examining the structural waters within the major groove. These appear at 5-10, 12-18, and 22-28 eV for the B-DNA target and at 7-11, 12-18, and 18-25 eV for the A-DNA target. Although the diffraction depends on the base-pair sequence, the energy dependent elastic scattering features are primarily associated with the structural water molecules localized within 8-10 A spheres surrounding the bases and/or the sugar-phosphate backbone. The electron density buildup occurs in energy regimes associated with dissociative electron attachment resonances, direct electronic excitation, and dissociative ionization. Since diffraction intensity can be localized on structural water, compound H2O:DNA states may contribute to energy dependent low-energy electron induced single and double strand breaks.

Comparisons of calculations with PARTRAC and NOREC: transport of electrons in liquid water

Monte Carlo computer models that simulate the detailed, event-by-event transport of electrons in liquid water are valuable for the interpretation and understanding of findings in radiation chemistry and radiation biology. Because of the paucity of experimental data, such efforts must rely on theoretical principles and considerable judgment in their development. Experimental verification of numerical input is possible to only a limited extent. Indirect support for model validity can be gained from a comparison of details between two independently developed computer codes as well as the observable results calculated with them. In this study, we compare the transport properties of electrons in liquid water using two such models, PARTRAC and NOREC. Both use interaction cross sections based on plane-wave Born approximations and a numerical parameterization of the complex dielectric response function for the liquid. The models are described and compared, and their similarities and differences are highlighted. Recent developments in the field are discussed and taken into account. The calculated stopping powers, W values, and slab penetration characteristics are in good agreement with one another and with other independent sources.

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.

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.

Induction of strand breaks by low-energy electrons (8-68 eV) in a self-assembled monolayer of oligonucleotides: effective cross sections and attenuation lengths

Self-assembled monolayers of 5'-32P-labeled 3'-thiolated oligonucleotides chemisorbed on gold were bombarded by low-energy electrons (LEE) of 8-68 eV. Shorter 5'-32P-oligonucleotides produced by LEE-induced strand breaks were separated with denaturing polyacrylamide gel electrophoresis and quantified by phosphor imaging. The yields of short oligonucleotides (y) decrease exponentially with their length (n), following the equation y=ae-bn, where a and b are constants, which are related to the average effective cross section per nucleotide for DNA strand break (sigmaeff) and the attenuation length (AL=1b) of LEE, respectively. The AL decreases with LEE energies from 2.5+/-0.6 nm at 8 eV to 0.8+/-0.1 nm at 68 eV, whereas sigmaeff increases from (3+/-1)x10(-18) to (5.1+/-1.6)x10(-17) cm2 within the same energy range. The energy dependence of sigmaeff shows a resonance peak of (2.8+/-0.9)x10(-17) cm2 at 18 eV superimposed on a monotonically rising curve. Transient electron attachment to a sigma* anion state of the deoxyribose group, followed by dipolar dissociation into H- and the corresponding positive-ion radical, leading to C-O bond cleavage, is proposed to account for this maximum.

DNA immobilization chemical interference due to aggregates study by Dip and Drop approach

In the present manuscript, we report the studies and observations for chemical interference due to aggregates formation during covalent immobilization of thiolated lambda-DNA between gold microelectrodes. Dip and Drop approaches were employed to study DNA immobilization using thiolated oligos (oligoA 5' GGGCGGCGACCT 3' and oligoB 5' AGGTCGCCGCCC 3'). As a result of aggregation, less interference was observed in Dip approach as compared to Drop approach. Atomic Force Microscopy (AFM) analysis of piranha treated gold surface revealed 47.5% increase in height roughness, contributing in interference by creating active sites. Cyclic voltammetry (CV) studies ascertain the multitude of adsorption states existing in long strand of DNA on surface. Surface coverage was found to be approximately 72% (1.35x10(10) molecules/cm(2)), and approximately 42% (7.89x10(9) molecules/ cm(2)) in Dip and Drop approach, respectively. Dip approach can be used as a measure to minimize interference due to aggregation.

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.

Dissociative electron attachment to hydrated single DNA strands

The present experiments concern electron interactions with a film of short single strands of DNA covered by 3 monolayers of water, which corresponds to 5.25 water molecules per nucleotide. We report on the desorption of H{-}, O{-}, OH{-} from this target induced by 3-20 eV electrons. Below 15 eV, these anions emanate principally from a new type of dissociative core-excited transient anions formed via electron capture by a DNA- H2O complex. A smaller portion of the H{-} desorption signal arises from weakly bonded H2O molecules. The overall anion yield from DNA is increased by a factor of 1.6 owing to the presence of water.

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.

Collision-induced dissociation of hydrated adenosine monophosphate nucleotide ions: protection of the ion in water nanoclusters

Fragmentation of singly charged anions of adenosine 5'-monophosphate (AMP-) induced by collisions with neutral atoms (Ne, Na) has been studied at a collision energy of 50 keV. The experiments were performed with isolated AMP- as well as with AMP- anions nanosolvated in a cluster with a given number m of water molecules. In the first case, the dominant fragmentation channels concern the loss of adenine, PO3- and H2PO4-. In the latter, loss of water molecules becomes the dominating process, and the AMP- ion is fully protected when m is larger than approximately 13. The observed fragment distributions are well described with the model of an evaporative ensemble.

Total dissociative electron attachment cross sections for molecular constituents of DNA

Total cross sections for the dissociative electron attachment process are presented for the DNA bases thymine, cytosine, and adenine and for three compounds used as surrogates for the ribose and phosphate groups, tetrahydrofuran, 3-hydroxytetrahydrofuran, and trimethylphosphate, respectively. Cross section magnitudes are obtained by observation of positive ion production and normalization to ionization cross sections calculated elsewhere using the binary-encounter-Bethe method. The average cross section of the three bases is 3-10 times smaller than the effective cross section per nucleotide reported for single strand breaks in surface-bound supercoiled DNA. Consequently, damage to the bases alone does not appear to account for the major portion of the strand breaks. The presence of an OH group on the ribose surrogate considerably enhances its cross section. Model compounds in which protonation or OH groups are used to terminate bonds may therefore display larger cross sections than in DNA itself.

Dissociative electron attachment to phosphoric acid esters: the direct mechanism for single strand breaks in DNA

We use dibutyl phosphate to simulate the behavior of the phosphate group in DNA towards the attack of low energy electrons. We find that the compound undergoes effective dissociative electron attachment within a low energy resonant feature at 1 eV and a further resonance peaking at 8 eV. The dissociative electron attachment (DEA) reactions are associated with the direct cleavage of the C-O and the P-O bond but also the excision of the PO-, PO3-, H2PO3- units. For the phosphate group coupled in the DNA network these reactions represent single strand breaks. We hence propose that the most direct mechanism of single strand breaks occurring in DNA at subexcitation energies (< 4 eV) is due to DEA directly to the phosphate group.

Low-energy electron stimulated desorption of neutrals from multilayers of SiCl4 on Si(111)

The interaction of low-energy electrons with multilayers of SiCl(4) adsorbed on Si(111) leads to production and desorption of Cl((2)P(32)), Cl((2)P(12)), Si, and SiCl. Resonant structure in the yield versus incident electron energy (E(i)) between 6 and 12 eV was seen in all neutral channels and assigned to dissociative electron attachment (DEA), unimolecular decay of excited products produced via autodetachment and direct dissociation. These processes yield Cl((2)P(32)) and Cl((2)P(12)) with nonthermal kinetic energies of 425 and 608 meV, respectively. The Cl((2)P(12)) is produced solely at the vacuum surface interface, whereas the formation of Cl((2)P(32)) likely involves subsurface dissociation, off-normal trajectories, and collisions with neighbors. Structure in the Cl((2)P(32)) yield near 14 and 25 eV can originate from excitation of electrons in the 2e, 7t(2) and 6t(2), 6a(1) levels, respectively. Although the 14 eV feature was not present in the Cl((2)P(12)) yield, the broad 25 eV feature, which involves complex Auger filling of holes in the 6t(2) and 6a(1) levels of SiCl(4), is observed. Direct ionization, exciton decay, and DEA from secondary electron scattering all occur at E(i)>14 eV. Si and SiCl were detected via nonresonant ionization of SiCl(x) precursors that are produced via the same states and mechanisms that yield Cl. The Si retains the kinetic energy profile of the desorbed precursors.

Where is the Sodium in Self-Assembled Monolayers of Single-Stranded DNA?

Monolayers of single-stranded DNA (ssDNA) immobilized on surfaces form the basis of a number of important biotechnology applications, including DNA microarrays and biosensors. The organization of ssDNA as layer on a solid substrate allows one to investigate various properties of the DNA in a controlled manner and to use DNA for analytical applications as well as for exploring futuristic schemes for molecular electronics. It is commonly assumed that the adsorbed DNA layer contains some structural water and the cations. Here we show, based on XPS studies, that when monolayers of ssDNA are formed from sodium phosphate buffer and washed thoroughly, no Na+ signal is detected. A finite concentration of ions is observed when the DNA is made from a solution of Mg2+ ions, but it is still only a fifth of what it would be if all the phosphate ions were fully neutralized by the metal cations.