Electron-Induced Damage by UV Photolysis of DNA Attached to Gold Nanoparticles.

Photolysis of DNA attached to gold nanoparticles (AuNPs) with ultraviolet (UV) photons induces DNA damage. The release of nucleobases (Cyt, Gua, Ade, and Thy) from DNA was the major reaction (99%) with an approximately equal release of pyrimidines and purines. This reaction contributes to the formation of abasic sites in DNA. In addition, liquid chromatography-mass spectrometry/MS (LC-MS/MS) analysis revealed the formation of reduction products of pyrimidines (5,6-dihydrothymidine and 5,6-dihydro-2'-deoxyuridine) and eight 2',3'- and 2',5'-dideoxynucleosides. In contrast, there was no evidence of the formation of 5-hydroxymethyluracil and 8-oxo-7,8-dihydroguanine, which are common oxidation products of thymine and guanine, respectively. Using appropriate filters, the main photochemical reactions were found to involve photoelectrons ejected from AuNPs by UV photons. The contribution of "hot" conduction band electrons with energies below the photoemission threshold was minor. The mechanism for the release of free nucleobases by photoelectrons is proposed to take place by the initial formation of transient molecular anions of the nucleobases, followed by dissociative electron attachment at the C1'-N glycosidic bond connecting the nucleobase to the sugar-phosphate backbone. This mechanism is consistent with the reactivity of secondary electrons ejected by X-ray irradiation of AuNPs attached to DNA, as well as the reactions of various nucleic acid derivatives irradiated with monoenergetic very-low-energy electrons (∼2 eV). These studies should help us to understand the chemistry of nanoparticles that are exposed to UV light and that are used as scaffolds and catalysts in molecular biology, curative agents in photodynamic therapy, and components of sunscreens and cosmetics.

Revealing the mechanism of damage to the carbonate ester in PADC polymeric nuclear track detector using low-energy electron stimulated desorption.

We investigate the mechanism of damage to the carbonate ester chemical functions in Poly allyl diglycol carbonate (PADC) induced by low-energy electrons (LEEs) of <50 eV, which are major components of the initial secondary products of ionizing radiation. PADC is the world's most widely used polymeric nuclear track detector (PNTD) for swift ion detection. Using diethylene glycol monoethyl ether acetate as a surrogate for PADC, we have measured for irradiation with low-energy electrons (LEEs) of <50 eV, the electron stimulated desorption (ESD) signal of O- from 3-monolayer thick films of DGMEA by time-of-flight mass spectrometry. We find that for electron irradiation at energies >6-9 eV, the instantaneous ESD yield of O- increases with the cumulative number of incident electrons (i.e., fluence), indicating that the additional O- signal derives from an electron-induced DGMEA product. From comparison with ESD measurements from films of acetic acid and acetaldehyde, we identify that the additional desorbed O- signal derives from oxygen atoms originally adjacent to the carbonyl bond in DGMEA. Since LEEs are the predominant secondary particles produced by ionizing radiation, this finding helps to better understand the mechanism of damage to carbonate ester in PADC, which is a key step for latent track formation in PADC.

Shape Resonances in DNA: Nucleobase Release, Reduction, and Dideoxynucleoside Products Induced by 1.3 to 2.3 eV Electrons.

Understanding the details of DNA damage caused by high-energy particles or photons is complicated by the multitude of reactive species, arising from the ionization and dissociation of H2O, DNA, and protein. In this work, oligonucleotides (ODNs) are irradiated with a beam of low-energy electrons of 1.3 to 2.3 eV, which can only induce damage via the decay of shape resonances into various dissociative electron attachment channels. Using LC-MS/MS analysis, the major products are the release of nonmodified nucleobases (NB; Cyt ≫ Thy ∼ Ade > Gua). Additional damage includes 5,6-dihydropyrimidines (dHT > dHU) and eight nucleosides with modified sugar moieties consisting of 2',3'- and 2',5'-dideoxynucleosides (ddG > ddA ∼ ddC > ddT). The distribution of products is remarkably different in a 16-mer ODN compared to that observed previously with thymidylyl-(3'-5')-thymidine. This difference is explained by electron delocalization occurring within a sufficiently long strand, the DEA theory of O'Malley, and recent time-dependent density functional theory calculations.

Low-Energy Electron Damage to Plasmid DNA in Thin Films: Dependence on Substrates, Surface Density, Charging, Environment, and Uniformity.

The interaction of low-energy electrons (LEEs) with DNA plays a significant role in the mechanisms leading to biological damage induced by ionizing radiation, particularly in radiotherapy, and its sensitization by chemotherapeutic drugs and nanoparticles. Plasmids constitute the form of DNA found in mitochondria and appear as a suitable model of genomic DNA. In a search for the best LEE targets, damage was induced to plasmids, in thin films in vacuum, by 6, 10, and 100 eV electrons under single collision conditions. The yields of single- and double-strand breaks, other cluster damage, isolated base lesions, and crosslinks were measured by electrophoresis and enzyme treatment. The films were deposited on oriented graphite or polycrystalline tantalum, with or without DNA autoassembly via diaminopropane (Dap) intercalation. Yields were correlated with the influence of vacuum, film uniformity, surface density, substrates, and the DNA environment. Aided by surface potential measurements and scanning electron microscopy and atomic force microscopy images, the lyophilized Dap-DNA films were found to be the most practical high-quality targets. These studies pave the way to the fabrication of LEE target-films composed of plasmids intercalated with biomolecules that could mimic the cellular environment; for example, as a first step, by replacing Dap with an amino acid.

Chemical transformation of molecular ices containing N2O and C2D2 by low energy electrons: New chemical species of astronomical interest.

We have employed electron stimulated desorption (ESD) and x-ray photoelectron spectroscopy (XPS) to study the chemical species generated from multilayer films of N2O, C2D2, and mixtures thereof (i.e., N2O/C2D2) by the impact of low energy electrons with energies between 30 and 70 eV. Our ESD results for pure films of N2O show the production of numerous fragment cations and anions, and of larger molecular ions, of sufficient kinetic energy to escape into vacuum, which are likely formed by ion-molecule scattering in the film. Ion-molecule scattering is also responsible for the production of cations from C2D2 films that contain as many as six or seven carbon atoms. Many of the same anions and cations desorb from N2O/C2D2 mixtures, as well as new species, which is the result of ion-molecule scattering in the film. Anion desorption signals further indicate the formation of C-N containing species within the irradiated films. XPS spectra of N1s, C1s, and O1s lines reveal the fragmentation of N-O bonds and gradual formation of molecules containing species containing O-C=O, C=O, and C-O functional groups. A comparison between ESD and XPS findings suggests that species observed in the ESD channel are primarily products of reactions taking place at the film-vacuum interface, while those observed in the XPS derive from reactions occurring within the solid.

Increased cognitive load during acquisition of a continuous task eliminates the learning effects of self-controlled knowledge of results.

Previous research has demonstrated that providing learners with self-control over some aspect of practice enhances motor learning (for a review see Wulf, 2007). One explanation for the self-control effect is that learners engage in deeper information processing when they are allowed to make choices during practice. Recent research has supported this line of thinking by showing that the self-control effect was eliminated for learners who engaged in a cognitive load task during the interval following completion of discrete task trials (Carter & Ste-Marie, 2017). The current study tested the effects of imposing a cognitive load task during the completion of continuous task trials. Participants (N = 48) were divided into self-control (SC), self-control with load (SCL), and two corresponding yoked (YK, YKL) groups. Participants learned a continuous tracing task and then performed 24-hour retention and transfer tests. Retention and transfer test movement times were significantly faster for SC compared to YK participants within the No Load condition but did not differ between these participants within the Load condition. Errors were similar among all groups in retention and transfer. These results provide support for the importance of information processing in regards to the self-controlled learning benefit.

Glycine formation in CO2:CH4:NH3 ices induced by 0-70 eV electrons.

Glycine (Gly), the simplest amino-acid building-block of proteins, has been identified on icy dust grains in the interstellar medium, icy comets, and ice covered meteorites. These astrophysical ices contain simple molecules (e.g., CO2, H2O, CH4, HCN, and NH3) and are exposed to complex radiation fields, e.g., UV, γ, or X-rays, stellar/solar wind particles, or cosmic rays. While much current effort is focused on understanding the radiochemistry induced in these ices by high energy radiation, the effects of the abundant secondary low energy electrons (LEEs) it produces have been mostly assumed rather than studied. Here we present the results for the exposure of multilayer CO2:CH4:NH3 ice mixtures to 0-70 eV electrons under simulated astrophysical conditions. Mass selected temperature programmed desorption (TPD) of our electron irradiated films reveals multiple products, most notably intact glycine, which is supported by control measurements of both irradiated or un-irradiated binary mixture films, and un-irradiated CO2:CH4:NH3 ices spiked with Gly. The threshold of Gly formation by LEEs is near 9 eV, while the TPD analysis of Gly film growth allows us to determine the "quantum" yield for 70 eV electrons to be about 0.004 Gly per incident electron. Our results show that simple amino acids can be formed directly from simple molecular ingredients, none of which possess preformed C-C or C-N bonds, by the copious secondary LEEs that are generated by ionizing radiation in astrophysical ices.

Synthesis of complex organic molecules in simulated methane rich astrophysical ices.

It has been proposed that organic molecules required for life on earth may be formed by the radiation processing of molecular ices in space environments, e.g., within our solar system. Such processes can be studied in the laboratory with surface science analytical techniques and by using low-energy electron (LEE) irradiation to simulate the effects of the secondary electrons that are generated in great abundance whenever ionizing radiation interacts with matter. Here we present new measurements of 70 eV LEE irradiation of multilayer films of CH4, 18O2, and CH4/18O2 mixtures (3:1 ratio) at 22 K. The electron stimulated desorption (ESD) yields of cations and anions have been recorded as a function of electron fluence. At low fluence, the prompt desorption of more massive multi-carbon or C-O containing cationic fragments agrees with our earlier measurements. However, new anion ESD signals of C2-, C2H-, and C2H2- from CH4/18O2 mixtures increase with fluence, indicating the gradual synthesis (and subsequent electron-induced fragmentation) of new, more complex species containing several C and possibly O atoms. Comparisons between the temperature programed desorption (TPD) mass spectra of irradiated and unirradiated films show the electron-induced formation of new chemical species, the identities of which are confirmed by reference to the NIST database of electron impact mass spectra and by TPD measurements of films composed of the proposed products. New species observed in the TPD of irradiated mixture films include C3H6, C2H5OH, and C2H6. Furthermore, X-ray photoelectron spectroscopy of irradiated films confirms the formation of C-O, C=O, and O=C-O- bonds of newly formed molecules. Our experiments support the view that secondary LEEs produced by ionizing radiation drive the chemistry in irradiated ices in space, irrespective of the radiation type.

Loss of cellular transformation efficiency induced by DNA irradiation with low-energy (10 eV) electrons.

Low energy electrons (LEEs) of energies less than 20 eV are generated in large quantities by ionizing radiation in biological matter. While LEEs are known to induce single (SSBs) and double strand breaks (DSBs) in DNA, their ability to inactivate cells by inducing nonreparable lethal damage has not yet been demonstrated. Here we observe the effect of LEEs on the functionality of DNA, by measuring the efficiency of transforming Escherichia coli with a [pGEM-3Zf (-)] plasmid irradiated with 10 eV electrons. Highly ordered DNA films were prepared on pyrolitic graphite by molecular self-assembly using 1,3-diaminopropane ions (Dap(2+)). The uniformity of these films permits the inactivation of approximately 50% of the plasmids compared to <10% using previous methods, which is sufficient for the subsequent determination of their functionality. Upon LEE irradiation, the fraction of functional plasmids decreased exponentially with increasing electron fluence, while LEE-induced isolated base damage, frank DSB, and non DSB-cluster damage increased linearly with fluence. While DSBs can be toxic, their levels were too low to explain the loss of plasmid functionality observed upon LEE irradiation. Similarly, non-DSB cluster damage, revealed by transforming cluster damage into DSBs by digestion with repair enzymes, also occurred relatively infrequently. The exact nature of the lethal damage remains unknown, but it is probably a form of compact cluster damage in which the lesions are too close to be revealed by purified repair enzymes. In addition, this damage is either not repaired or is misrepaired by E. coli, since it results in plasmid inactivation, when they contain an average of three lesions. Comparison with previous results from a similar experiment performed with γ-irradiated plasmids indicates that the type of clustered DNA lesions, created directly on cellular DNA by LEEs, may be more difficult to repair than those produced by other species from radiolysis.

Absolute cross section for loss of supercoiled topology induced by 10 eV electrons in highly uniform /DNA/1,3-diaminopropane films deposited on highly ordered pyrolitic graphite.

It was recently shown that the affinity of doubly charged, 1-3 diaminopropane (Dap(2+)) for DNA permits the growth on highly ordered pyrolitic graphite (HOPG) substrates, of plasmid DNA films, of known uniform thickness [O. Boulanouar, A. Khatyr, G. Herlem, F. Palmino, L. Sanche, and M. Fromm, J. Phys. Chem. C 115, 21291-21298 (2011)]. Post-irradiation analysis by electrophoresis of such targets confirms that electron impact at 10 eV produces a maximum in the yield of single strand breaks that can be associated with the formation of a DNA(-) transient anion. Using a well-adapted deterministic survival model for the variation of electron damage with fluence and film thickness, we have determined an absolute cross section for strand-break damage by 10 eV electrons and inelastic scattering attenuation length in DNA-Dap complex films.

Oxygen attachment on alkanethiolate SAMs induced by low-energy electron irradiation.

Reactions of (18)O2 with self-assembled monolayer (SAM) films of 1-dodecanethiol, 1-octadecanethiol, 1-butanethiol, and benzyl mercaptan chemisorbed on gold were studied by the electron stimulated desorption (ESD) of anionic fragments over the incident electron energy range 2-20 eV. Dosing the SAMs with (18)O2 at 50 K results in the ESD of (18)O(-) and (18)OH(-). Electron irradiation of samples prior to (18)O2 deposition demonstrates that intensity of subsequent (18)O(-) and (18)OH(-) desorption signals increase with electron fluence and that in the absence of electron preirradiation, no (18)O(-) and (18)OH(-) ESD signals are observed, since oxygen is unable to bind to the SAMs. A minimum incident electron energy of 6-7 eV is required to initiate the binding of (18)O2 to the SAMs. O2 binding is proposed to proceed by the formation of CHx-1(•) radicals via resonant dissociative electron attachment and nonresonant C-H dissociation processes. The weaker signals of (18)O(-) and (18)OH(-) from short-chain SAMs are related to the latter's resistance to electron-induced damage, due to the charge-image dipole quenching and electron delocalization. Comparison between the present results and those for DNA oligonucleotides self-assembled on Au (Mirsaleh-Kohan, N. et al. J. Chem. Phys. 2012, 136, 235104) indicates that the oxygen binding mechanism is common to both systems.

Absolute cross section for low-energy-electron damage to condensed macromolecules: a case study of DNA.

Cross sections (CSs) for the interaction of low-energy electrons (LEE) with condensed macromolecules are essential parameters for accurate modeling of radiation-induced molecular decomposition and chemical synthesis. Electron irradiation of dry nanometer-scale macromolecular solid films has often been employed to measure CSs and other quantitative parameters for LEE interactions. Since such films have thicknesses comparable with electron thermalization distances, energy deposition varies throughout the film. Moreover, charge accumulation occurring inside the films shields a proportion of the macromolecules from electron irradiation. Such effects complicate the quantitative comparison of the CSs obtained in films of different thicknesses and limit the applicability of such measurements. Here, we develop a simple mathematical model, termed the molecular survival model, that employs a CS for a particular damage process together with an attenuation length related to the total CS, to investigate how a measured CS might be expected to vary with experimental conditions. As a case study, we measure the absolute CS for the formation of DNA strand breaks (SBs) by electron irradiation at 10 and 100 eV of lyophilized plasmid DNA films with thicknesses between 10 and 30 nm. The measurements are shown to depend strongly on the thickness and charging condition of the nanometer-scale films. Such behaviors are in accord with the model and support its validity. Via this analysis, the CS obtained for SB damage is nearly independent of film thickness and charging effects. In principle, this model can be adapted to provide absolute CSs for electron-induced damage or reactions occurring in other molecular solids across a wider range of experimental conditions.

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.

Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers.

We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H(-), CH(3)(-)/NH(-), O(-)/NH(2)(-), OH(-), CN(-), and Br(-) was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN(-) desorption. An increase in the yields of OH(-) is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2(')-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

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.

X-ray photoelectron spectroscopy analysis of gold surfaces after removal of thiolated DNA oligomers by ultraviolet/ozone treatment.

Well-ordered films of molecular DNA can be formed by the attachment of thiolated DNA oligonucleotides to a supporting gold substrate. The gold substrate represents a significant fraction of the total cost of preparing such films, and it is thus important to determine whether such substrates can be reused. Here, we investigate with X-ray photoelectron spectroscopy the suitability of UV/ozonolysis previously employed to remove alkanethiols from gold, for removing 40-mer, single- and double-stranded synthetic DNA. We find that while UV/O(3) can indeed remove thiolated DNA from gold slides, the treatment times required permit the implantation of additional organic contaminants.

Electron induced dissociation in condensed-phase nitromethane I: desorption of ionic fragments.

Low energy electron induced dissociation of condensed nitromethane was investigated by measuring the electron stimulated desorption of anions and cations from multilayer films of CH(3)NO(2) and CD(3)NO(2), using a recently constructed, high sensitivity time of flight mass spectrometer. The desorbed yields were measured as a function of incident electron energy in the range between 1 to 20 eV and as function of coverage on Pt and Xe substrates. In anion desorption experiments, the following ions were observed: H(-) (D(-)), O(-), OH(-) (OD(-)), CN(-), NCO(-), NO(2)(-), CHNO(2)(-) (CDNO(2)(-)), CH(2)NO(2)(-) (CD(2)NO(2)(-)). Resonant structure seen in all anion yield functions, is attributed to dissociative electron attachment (DEA), though certain anion signals [e.g., OH(-) (OD(-)) and CH(2)NO(2)(-) (CD(2)NO(2)(-))] are likely the result of reactive scattering by O(-) ions. The dominant desorbed cation signals are CD(3)(+) and NO(+), and the appearance potentials of these species were measured to be 12.2 and 11.5 eV, respectively. The present measurements provide information on how the electron-induced dissociation processes of this proto-typical explosive molecule are modulated by the condensed environment and on how initial dissociation events occurring on a particular molecule, may induce further dissociation.

Cross sections for electron trapping by DNA and its component subunits I: Condensed tetrahydrofuran deposited on Kr.

We report cross sections for electron capture processes occurring in condensed tetrahydrofuran (THF) for incident electron energies in the range of 0-9 eV. The charge trapping cross section for 6-9 eV electrons is very small, and an upper limit of 4 x 10(-19) cm2 is estimated from our results. This latter is thus also an upper bound for the cross section for dissociative electron attachment process that is known to occur at these energies for condensed THF. At energies close to zero eV electron trapping proceeds via intermolecular stabilization. The cross section for this process is strongly dependent on the quantity of deposited THF. Since THF may model the furyl ring found in deoxyribose, these measurements indicate that this ring likely plays little role in either initiating or enhancing strand break damage via the attachment of the low energy secondary electrons produced when DNA is exposed to ionizing radiation.

Intrinsic and extrinsic factors in anion electron-stimulated desorption: D- from deuterated hydrocarbons condensed on Kr and water ice films.

The results of D(-) ion desorption induced by 3-20 eV electrons incident on condensed CD(4), C(2)D(6), C(3)D(8), C(2)D(4), and C(2)D(2) are presented. These compounds were deposited in submonolayer amounts on the surfaces of multilayer solid films of Kr and nonporous and porous amorphous ice. While desorption of the D(-) anions proceeds via well-known processes, i.e., dissociative electron attachment (DEA) and dipolar dissociation, significant perturbations of these processes due to presence of the different film substrates are observed. We have shown that it is possible to distinguish between the character and nature of these perturbations. The presence of the nonporous ice perturbs the D(-) desorption intensity by affecting the intrinsic properties of the intermediate anion states through which dissociation proceeds. On the other hand, the presence of the porous ice introduces extrinsic effects, which can affect electron energy losses prior to their interaction with the hydrocarbon molecule and/or the energies and intensities of the fragment species after dissociation. Simple mechanisms responsible for the observed variations in the intensities of desorbed anionic signals are proposed and discussed. Electron transfer from transient anion states to electron states of the substrate film or nearby hydrocarbon molecules appear as the most efficient mechanism to reduce the magnitude of the DEA process.