**6. LEEs interaction with protein building blocks**

It is well known that within the cells, DNA is in close contact with, and packed by, chromo‐ somal proteins (histones). The attachment of proteins protects DNA from damage by com‐ paction (e.g., which restricts easy access by free radicals to DNA) and repairs some of the damage of electron/hydrogen donation [99]. LEE damage to proteins within cells should not, by itself, cause significant long‐term biological damages, because proteins can be replaced. However, due to the presence of histones and other chromosomal proteins in the vicinity of DNA, reactive species produced from LEE interactions with protein constituents (e.g., nearby amino acids) may in turn interact with DNA, causing indirect damage. Thus, from a radio‐ biological point of view, there is considerable interest in studying the action of LEEs on this important class of biomolecules [100]. Recent work has focused on the building blocks of proteins, that is, amino acids and small peptides, since the size and complexity of chromosomal proteins prevent direct detailed analysis of the fragmentation processes induced by LEEs [11, 39]. Indeed, measuring the fragmentation of amino acids and their analogs is no more complex than it is for DNA constituents (see Sections 4 and 5) [101–103], and can help elucidate the effects of electron irradiation in larger more complex proteins [103].

phoresis. This technique can identify supercoiled (SC), nicked circular (C), full‐length linear (L), cross‐linked (CL), and short linear forms of DNA, which can be assigned to undamaged DNA, SSBs, DSBs, several types of cross‐linked DNA, and multiple double‐strand breaks

Though it has been established that most of the strand breaks induced by ionizing radiation have been repaired by a DNA ligation step, a DSB represents a particularly detrimental lesion that poses a serious threat to the cell, since it usually cannot be easily repaired [88]. Indeed, even a single DSB can lead to cell death if left unrepaired or, more worryingly, it can cause

The results obtained for LEE‐irradiated supercoiled plasmid DNA in several investigations are well described in the literature and summarized in authoritative review articles [10, 11, 35]. These studies have shown that SSBs can occur as a result of DEA at electron energies well below electronic excitation and ionization thresholds (0.8–10 eV) [83, 90]. The results of Martin et al. [90] reveal two resonant peaks at 0.8 and 2.2 eV in the SSB yield function (i.e., the number of strand breaks versus the incident electron energy) via the formation of TMAs. These findings are consistent with theoretical calculations indicating that SSBs induced by near‐zero energy electrons are thermodynamically feasible [91–93]. Theoretical simulations of electron scatter‐ ing and electron capture via "shape" resonances support the role of LEEs in DNA strand breaks [94]. Theoretical calculations on scattering and attachment of LEEs to DNA components up to

supercoiled plasmid DNA have been intensively reviewed in recent years [95, 96].

**6. LEEs interaction with protein building blocks**

Another spatially resolved technique that exploits the use of graphene‐coated Au thin films and surface‐enhanced Raman spectroscopy (SERS) has recently emerged. Utilizing this technique, the sequence dependence of DNA damage at excitation energies < 5 eV can be studied [97]. Currently, Ptasińska and coworkers are performing a quantitative and qualitative investigation of the various types of damages to dry and hydrated DNA induced by exposure to helium and nitrogen atmospheric pressure plasma jets (APPJs). Since an APPJ contains multiple reactive species, including LEEs, also found in radiation chemistry, exposure to these plasma jets provides information on both the direct and indirect pathways to damaging DNA. Ptasińska and coworkers have employed nitrogen APPJ to induce DNA damage in SCC‐25 oral cancer cells, and have thus provided new insight into radiation damage to a cellular system

It is well known that within the cells, DNA is in close contact with, and packed by, chromo‐ somal proteins (histones). The attachment of proteins protects DNA from damage by com‐ paction (e.g., which restricts easy access by free radicals to DNA) and repairs some of the damage of electron/hydrogen donation [99]. LEE damage to proteins within cells should not, by itself, cause significant long‐term biological damages, because proteins can be replaced. However, due to the presence of histones and other chromosomal proteins in the vicinity of DNA, reactive species produced from LEE interactions with protein constituents (e.g., nearby

(MDSBs), respectively [87].

194 Radiation Effects in Materials

[98].

mutagenesis and cancer if repaired improperly [89].

In the recent years, several investigations have employed soft ionization techniques, such as matrix‐assisted laser desorption ionization (MALDI) [104–107], electrospray ionization (ESI) [108, 109], and collision‐induced dissociation (CID) [110–114], to study the ionization and fragmentation of different amino acids and small peptides in the gas phase. Gas‐phase investigations of LEE‐induced damage to protein subunits have been reported for the amino acids alanine [115], tyrosine [116], glycine [117, 118], proline [119, 120], cysteine [121], and serine [122,123], as well as small peptides, such as dialanine [124] and amino acid esters [125]. For all cases, the anion yield functions (i.e., ion yields measured as a function of electron energy) exhibited localized maxima at energies below 15 eV, indicating the formation of TMAs. It has been established that no intact parent anion is observable on mass spectrometric timescales after capture of a free electron, and that the most probable reaction corresponds to the loss of a hydrogen atom from a carboxyl group to form for a molecule "M," the dehydro‐ genated anion (M–H)‾ at energies of around 1.5 eV [120, 123, 126, 127]. Early DEA studies ascribed this process to initial electron attachment into a *π*\* orbital of the (C=O) bond in the COOH group, which couples to the repulsive *σ*\* (O–H) orbital [118]. However, recent calcu‐ lations questioned this DEA mechanism [126]; instead, it was suggested that direct electron capture into the purely repulsive short‐lived *σ*\* (O–H) orbital, which is a very broad resonance of more than 5 eV width, could be responsible for the loss of the hydrogen [126].

In the condensed phase, analyzing LEE‐stimulated desorption of anions from physisorbed thin films of glycine, alanine, cysteine, tryptophan, histidine, and proline [128, 129] indicated that H‾ was the major desorption fragment, as CH3‾, O‾, and OH‾ were the fragments produced with lower signals in all named amino acids. Similar results were observed in ESD experiments from LEE‐bombarded chemisorbed films, prepared by self‐assembled monolayers (SAMs) of two different chains of Lys amide molecules [129]. For this model of a segment of a peptide backbone, the desorbed signals were dependent on the length of the amino acid sequence.

Amino acids are also suitable model molecules for investigating the interactions of biomole‐ cules with metallic surfaces, particularly silver and gold. Of the 20 naturally occurring amino acids, only cysteine contains a thiol (-SH) group, which allows it to bind to the metal by forming a S-Metal bond [130, 131]. This characteristic makes cysteine an ideal model to investigate protein interactions with gold surfaces including those of gold nanoparticles [132, 133]. A detailed study on electron attachment to L‐cysteine/Au(111) was recently reported by Alizadeh et al. [134, 135] who measured anion yields desorbed from chemisorbed (SAMs) and physi‐ sorbed thin films bombarded with sub‐20 eV energy electrons. These ESD measurements showed that LEEs are able to effciently decompose this amino acid via DEA and dipolar dissociation (DD), when the molecule is chemisorbed via the SH group to a gold surface.

Regarding the protective effect of amino acids on DNA against LEEs, Solomun et al. [136] reported that the single‐strand DNA‐binding *E. coli* protein can effectively inhibit the forma‐ tion of SSBs by 3‐eV electrons in oligonucleotides. Ptasińska et al. [137] subsequently investi‐ gated by post‐irradiation analysis with HPLC‐UV, the molecular fragmentation induced by 1‐ eV electrons in films comprising the GCAT tetramer and one of the two amino acids, glycine and arginine. At low ratios (*R*) of amino acid to GCAT (i.e., *R* < 1), particularly for glycine, the total oligonucleotide fragmentation yield unexpectedly increased. At higher ratios (1 ≤ *R* ≤ 4), protection of DNA from damage by electrons was observed for both glycine and arginine. Therefore, the amino acid probably reduced electron capture by GCAT and/or the lifetime of the TMA that initiates DEA process. A similar conclusion regarding the stability of the amino acid side chain–nucleobase complexes can be deduced from the theoretical studies of Wang et al. [138]. Wang and coworkers performed calculations at the B3LYP/6‐311G(d,p)‐level anionic hydrogen‐bonded complexes formed between the amino acid side chains and the nucleobase guanine.

Furthermore, by studying via first‐principles molecular dynamics simulations a model system composed of thymine and glycine, Kohanoff et al. [139] recently investigated the protection of DNA by amino acids against the effects of LEEs. They considered thymine–glycine dimers and a condensed‐phase model consisting of one thymine molecule solvated in amorphous glycine. These results indicated that at room temperature, the amino acid chemically and physically performs the role of a protective agent for the nucleobase. In a chemical mechanism, the excess electron is first captured by the thymine; then, a proton is transferred in a barrierless way from a neighboring hydrogen‐bonded glycine. Reducing the net partial charge on the thymine molecule stabilizes the excess electron. In the physical mechanism, glycine molecule acts as an electron scavenger to capture the excess electron directly, which prevents the electron to be localized in DNA. Protecting the nucleobase via the latter mechanism requires a predisposition for proton transfer to the oxygen in the carboxylic acid group of one of the involved amino acids. Consequently, raising the free‐energy barrier associated with strand breaks, prompted by these mechanisms, can halt further reactions of the excess electron within the strand of DNA, for instance, transferring the electron to the backbone which leads to induce a strand break in DNA. Increasing the ratio of amino acid to nucleic acid will enhance the protecting role of amino acids, and accordingly will decrease the induction of DNA strand breaks by LEEs, as shown experimentally [137, 139].
