Side-by-side comparison of DNA damage induced by low-energy electrons and high-energy photons with solid TpTpT trinucleotide

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 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.

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.

Harnessing the targeting potential of differential radiobiological effects of photon versus particle radiation for cancer treatment

Radiotherapy is one of the major modalities for malignancy treatment. High linear energy transfer (LET) charged-particle beams, like proton and carbon ions, exhibit favourable depth-dose distributions and radiobiological enhancement over conventional low-LET photon irradiation, thereby marking a new era in high precision medicine. Tumour cells have developed multicomponent signal transduction networks known as DNA damage responses (DDRs), which initiate cell-cycle checkpoints and induce double-strand break (DSB) repairs in the nucleus by nonhomologous end joining or homologous recombination pathways, to manage ionising radiation (IR)-induced DNA lesions. DNA damage induction and DSB repair pathways are reportedly dependent on the quality of radiation delivered. In this review, we summarise various types of DNA lesion and DSB repair mechanisms, upon irradiation with low and high-LET radiation, respectively. We also analyse factors influencing DNA repair efficiency. Inhibition of DNA damage repair pathways and dysfunctional cell-cycle checkpoint sensitises tumour cells to IR. Radio-sensitising agents, including DNA-PK inhibitors, Rad51 inhibitors, PARP inhibitors, ATM/ATR inhibitors, chk1 inhibitors, wee1 kinase inhibitors, Hsp90 inhibitors, and PI3K/AKT/mTOR inhibitors have been found to enhance cell killing by IR through interference with DDRs, cell-cycle arrest, or other cellular processes. The cotreatment of these inhibitors with IR may represent a promising therapeutic strategy for cancer.

Strand Breaks Induced by Very Low Energy Electrons: Product Analysis and Mechanistic Insight into the Reaction with TpT

Numerous experimental studies show that 5-15 eV electrons induce strand breaks in DNA at energies below the ionization threshold of DNA components. In this energy range, DNA damage arises principally by the formation of transient negative ions, decaying into dissociative electron attachment (DEA) and electronic excitation of dissociative states. Here, we carried out LC-MS/MS analysis of the degradation products arising from bombardment of TpT, a DNA model compound, irradiated with very low energy electrons (vLEEs; ∼1.8 eV). The formation of thymidine 5'-monophosphate (TMP5') together with 2',3'-dideoxythymidine (ddT3') can be explained by cleavage of the C3'-O bond of TpT, whereas thymidine 3'-monophosphate (TMP3') and 2',5'-dideoxythymidine (ddT5') are formed by cleavage of the C5'-O bond. The formation of ddT3' and ddT5' decreased upon irradiation of either TMP5' or TMP3', and even further in the case of thymidine, underlining the critical role of the phosphate group. Interestingly, the yield of TMP5' and TMP3' was higher than that of the corresponding ddT3' and ddT5' products, suggesting alternative fates of C3' and C5'-centered sugar radicals. In contrast, the release of thymine from TpT was minor (<20%) and did not result in the formation of expected products from DEA-mediated cleavage at the N-glycosidic bond. Lastly, vLEE induced the conversion of thymine to 5,6-dihydrothymine (5,6-dhT) within TpT, a reaction likely involving thymine anion radicals. In summary, we show that a major pathway of vLEEs involves DEA-mediated cleavage of the C3'-O and C5'-O bonds of TpT, resulting in the formation of specific fragments, which represent a prompt single strand break in DNA.

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.

Base Release and Modification in Solid-Phase DNA Exposed to Low-Energy Electrons

Ionization generates a large number of secondary low-energy electrons (LEEs) with a most probable energy of approximately 10 eV, which can break DNA bonds by dissociative electron attachment (DEA) and lead to DNA damage. In this study, we investigated radiation damage to dry DNA induced by X rays (1.5 keV) alone on a glass substrate or X rays combined with extra LEEs (average energy of 5.8 eV) emitted from a tantalum (Ta) substrate under an atmosphere of N₂ and standard ambient conditions of temperature and pressure. The targets included calf-thymus DNA and double-stranded synthetic oligonucleotides. We developed analytical methods to measure the release of non-modified DNA bases from DNA and the formation of several base modifications by LC-MS/MS with isotopic dilution for precise quantification. The results show that the yield of non-modified bases as well as base modifications increase by 20-30% when DNA is deposited on a Ta substrate compared to that on a glass substrate. The order of base release (Gua > Ade > Thy ∼ Cyt) agrees well with several theoretical studies indicating that Gua is the most susceptible site toward sugar-phosphate cleavage. The formation of DNA damage by LEEs is explained by DEA leading to the release of non-modified bases involving the initial cleavage of N1-C1', C3'-O3' or C5'-O5' bonds. The yield of base modifications was lower than the release of non-modified bases. The main LEE-induced base modifications include 5,6-dihydrothymine (5,6-dHT), 5,6-dihydrouracil (5-dHU), 5-hydroxymethyluracil (5-HmU) and 5-formyluracil (5-ForU). The formation of base modifications by LEEs can be explained by DEA and cleavage of the C-H bond of the methyl group of Thy (giving 5-HmU and 5-ForU) and by secondary reactions of H atoms and hydride anions that are generated by primary LEE reactions followed by subsequent reaction with Cyt and Thy (giving 5,6-dHU and 5,6-dHT).

eV-TEM: Transmission electron microscopy in a low energy cathode lens instrument

We are developing a transmission electron microscope that operates at extremely low electron energies, 0-40 eV. We call this technique eV-TEM. Its feasibility is based on the fact that at very low electron energies the number of energy loss pathways decreases. Hence, the electron inelastic mean free path increases dramatically. eV-TEM will enable us to study elastic and inelastic interactions of electrons with thin samples. With the recent development of aberration correction in cathode lens instruments, a spatial resolution of a few nm appears within range, even for these very low electron energies. Such resolution will be highly relevant to study biological samples such as proteins and cell membranes. The low electron energies minimize adverse effects due to radiation damage.

Stress-induced DNA damage biomarkers: applications and limitations

A variety of environmental stresses like chemicals, UV and ionizing radiation and organism's endogenous processes such as replication stress and metabolism can lead to the generation of reactive oxygen and nitrogen species (ROS/RNS) that can attack cellular vital components like DNA, proteins and lipid membranes. Among them, much attention has been focused on DNA since DNA damage plays a role in several biological disorders and aging processes. Thus, DNA damage can be used as a biomarker in a reliable and accurate way to quantify for example radiation exposure and can indicate its possible long term effects and cancer risk. Based on the type of DNA lesions detected one can hypothesize on the most probable mechanisms involved in the formation of these lesions for example in the case of UV and ionizing radiation (e.g., X- or α-, γ-rays, energetic ions, neutrons). In this review we describe the most accepted chemical pathways for DNA damage induction and the different types of DNA lesions, i.e., single, complex DNA lesions etc. that can be used as DNA damage biomarkers. We critically compare DNA damage detection methods and their limitations. In addition, we suggest the use of DNA repair gene products as biomarkes for identification of different types of stresses i.e., radiation, oxidative, or replication stress, based on bioinformatic approaches and meta-analysis of literature data.

Correlation between energy deposition and molecular damage from Auger electrons: A case study of ultra-low energy (5-18 eV) electron interactions with DNA

PURPOSE

The present study introduces a new method to establish a direct correlation between biologically related physical parameters (i.e., stopping and damaging cross sections, respectively) for an Auger-electron emitting radionuclide decaying within a target molecule (e.g., DNA), so as to evaluate the efficacy of the radionuclide at the molecular level. These parameters can be applied to the dosimetry of Auger electrons and the quantification of their biological effects, which are the main criteria to assess the therapeutic efficacy of Auger-electron emitting radionuclides.

METHODS

Absorbed dose and stopping cross section for the Auger electrons of 5-18 eV emitted by(125)I within DNA were determined by developing a nanodosimetric model. The molecular damages induced by these Auger electrons were investigated by measuring damaging cross section, including that for the formation of DNA single- and double-strand breaks. Nanoscale films of pure plasmid DNA were prepared via the freeze-drying technique and subsequently irradiated with low-energy electrons at various fluences. The damaging cross sections were determined by employing a molecular survival model to the measured exposure-response curves for induction of DNA strand breaks.

RESULTS

For a single decay of(125)I within DNA, the Auger electrons of 5-18 eV deposit the energies of 12.1 and 9.1 eV within a 4.2-nm(3) volume of a hydrated or dry DNA, which results in the absorbed doses of 270 and 210 kGy, respectively. DNA bases have a major contribution to the deposited energies. Ten-electronvolt and high linear energy transfer 100-eV electrons have a similar cross section for the formation of DNA double-strand break, while 100-eV electrons are twice as efficient as 10 eV in the induction of single-strand break.

CONCLUSIONS

Ultra-low-energy electrons (<18 eV) substantially contribute to the absorbed dose and to the molecular damage from Auger-electron emitting radionuclides; hence, they should be considered in the dosimetry calculation of such radionuclides. Moreover, absorbed dose is not an appropriate physical parameter for nanodosimetry. Instead, stopping cross section, which describes the probability of energy deposition in a target molecule can be an appropriate nanodosimetric parameter. The stopping cross section is correlated with a damaging cross section (e.g., cross section for the double-strand break formation) to quantify the number of each specific lesion in a target molecule for each nuclear decay of a single Auger-electron emitting radionuclide.