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

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.

Damage Induced to DNA and Its Constituents by 0-3 eV UV Photoelectrons†

The complex physical and chemical interactions between DNA and 0-3 eV electrons released by UV photoionization can lead to the formation of various lesions such as base modifications and cleavage, crosslinks and single strand breaks. Furthermore, in the presence of platinum chemotherapeutic agents, these electrons can cause clustered lesions, including double strand breaks. We explain the mechanisms responsible for these damages via the production 0-3 eV electrons by UVC radiation, and by UV photons of any wavelengths, when they are produced by photoemission from nanoparticles lying within about 10 nm from DNA. We review experimental evidence showing that a single 0-3 eV electron can produce these damages. The foreseen benefits UV-irradiation of nanoparticles targeted to the cell nucleus are mentioned in the context of cancer therapy, as well as the potential hazards to human health when they are present in cells.

A Complete Cross Section Data Set for Electron Scattering by Pyridine: Modelling Electron Transport in the Energy Range 0-100 eV

Electron scattering cross sections for pyridine in the energy range 0–100 eV, which we previously measured or calculated, have been critically compiled and complemented here with new measurements of electron energy loss spectra and double differential ionization cross sections. Experimental techniques employed in this study include a linear transmission apparatus and a reaction microscope system. To fulfill the transport model requirements, theoretical data have been recalculated within our independent atom model with screening corrected additivity rule and interference effects (IAM-SCAR) method for energies above 10 eV. In addition, results from the R-matrix and Schwinger multichannel with pseudopotential methods, for energies below 15 eV and 20 eV, respectively, are presented here. The reliability of this complete data set has been evaluated by comparing the simulated energy distribution of electrons transmitted through pyridine, with that observed in an electron-gas transmission experiment under magnetic confinement conditions. In addition, our representation of the angular distribution of the inelastically scattered electrons is discussed on the basis of the present double differential cross section experimental results.

Optical Absorption Cross-Section of DNA Bases—Thymine and Guanine—in the Energy Region from 3.1 to 250 eV (5–400 nm)

(1) Background: Optical absorption cross-section—the absolute absorption intensity specific to each molecule—of nucleic acid bases enables us to estimate the reaction yields of DNA lesions induced by the exposure to not only photons but also ionizing radiations. However, it was unknown in the energy region exceeding ~10 eV (wavelength < ~120 nm). (2) Methods: Thin films of DNA bases—thymine and guanine—were prepared using a vacuum sublimation technique. Absorption spectra of these films were measured in the energy region from 3.1 to 250 eV (5–400 nm) at the synchrotron radiation facility UVSOR. (3) Results: The absorption spectra of both bases exhibited prominent absorption peaks around 20 eV and smaller peaks in the energy region below 10 eV. The determined optical oscillator strength distribution was verified to be reasonable based on the Thomas–Reiche–Kuhn oscillator strength sum rule. (4) Conclusion: Most of the oscillator strength distribution was positioned in the measured energy region, and therefore the absorption spectra significantly contributed to the quantitative study for the photo and radiation-chemical reactions of DNA.

Low energy (1-19 eV) electron scattering from condensed thymidine (dT) I: absolute vibrational excitation cross sections

Absolute cross sections (CSs) for vibrational excitation by electrons of energy between 1-19 eV scattering from condensed thymidine (dT) were measured by means of high-resolution electron energy loss spectroscopy (HREELS). The CSs were extracted from electron energy loss spectra of dT condensed on multilayers film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex molecules to be studied in condensed phase by HREELS. The magnitudes of the vibrational CSs lie within the 10-17 cm2 range. Structures observed in the energy dependence of the vibrational CSs under 3 eV and around 4 eV were compared with previous results of gas- and solid-phase studies on dT and related molecules (e.g., thymine and tetrahydrofuran). These structures were attributed to the formation of shape resonances.

Experimental and theoretical analysis for total electron scattering cross sections of benzene

Measurements of the total electron scattering cross sections (TCSs) from benzene, in the impact energy range of 1-1000 eV, are presented here by combining two different experimental systems. The first utilizes a magnetically confined electron transmission beam for the lower energies (1-300 eV), while the second utilizes a linear transmission beam apparatus for the higher energies (100-1000 eV). These cross sections have also been calculated by means of two different theoretical methods, the Schwinger Multichannel with Pseudo Potential (SMCPP) procedure, employing two different approaches to account for the polarization of the target for impact energies between 0.1 and 15 eV, and the Independent Atom Model with the Screening Corrected Additivity Rule including Interference effect (IAM-SCAR+I) paradigm to cover the 10-10 000 eV impact energy range. The present results are compared with available theoretical and experimental data, with the level of accord being good in some cases and less satisfactory in others, and some predicted resonances have been identified. In particular, we found a π^* shape resonance at 1.4 eV and another feature in the energy region 4.6-4.9 eV interpreted as a π^* resonance (²B_2g symmetry), which is a mixture of shape and a core excited resonance, as well as a Feshbach resonance at 5.87 eV associated with the 3s (a_1g) Rydberg state. A Born-type formula to extrapolate TCS values for energies above 10 000 eV is also given. This study provides a complete set of TCS data, with uncertainty limits within 10%, ready to be used for modeling electron transport applications.

Clustered DNA Damages induced by 0.5 to 30 eV Electrons

Low-energy electrons (LEEs) of energies ≤30 eV are generated in large quantities by ionizing radiation. These electrons can damage DNA; particularly, they can induce the more detrimental clustered lesions in cells. This type of lesions, which are responsible for a large portion of the genotoxic stress generated by ionizing radiation, is described in the Introduction. The reactions initiated by the collisions of 0.5-30 eV electrons with oligonucleotides, duplex DNA, and DNA bound to chemotherapeutic platinum drugs are explained and reviewed in the subsequent sections. The experimental methods of LEE irradiation and DNA damage analysis are described with an emphasis on the detection of cluster lesions, which are considerably enhanced in DNA-Pt-drug complexes. Based on the energy dependence of damage yields and cross-sections, a mechanism responsible for the clustered lesions can be attributed to the capture of a single electron by the electron affinity of an excited state of a base, leading to the formation of transient anions at 6 and 10 eV. The initial capture is followed by electronic excitation of the base and dissociative attachment-at other DNA sites-of the electron reemitted from the temporary base anion. The mechanism is expected to be universal in the cellular environment and plays an important role in the formation of clustered lesions.

Absolute cross sections for chemoradiation therapy: Damages to cisplatin-DNA complexes induced by 10 eV electrons

In chemoradiation therapy, the synergy between the radiation and the chemotherapeutic agent (CA) can result in a super-additive treatment. A priori, this increased effectiveness could be estimated from model calculations, if absolute cross sections (ACSs) involved in cellular damage are substantially higher, when the CA binds to DNA. We measure ACSs for damages induced by 10 eV electrons, when DNA binds to the CA cisplatin as in chemotherapy. At this energy, DNA is damaged essentially by the decay of core-excited transient anions into bond-breaking channels. Films of cisplatin-DNA complexes of ratio 5:1 with thicknesses 10, 15, and 20 nm were irradiated in vacuum during 5-30 s. Conformation changes were quantified by electrophoresis and yields extrapolated from exposure-response curves. Base damages (BDs) were revealed and quantified by enzymatic treatment. The ACSs were generated from these yields by two mathematical models. For 3197 base-pair plasmid DNA, ACS for single strand breaks, double strand breaks (DSBs), crosslinks, non-DSB cluster damages, and total BDs is 71 ± 2, 9.3 ± 0.4, 10.1 ± 0.3, 8.2 ± 0.3, and 115 ± 2 ×10^-15 cm², respectively. These ACSs are higher than those of nonmodified DNA by factors of 1.6 ± 0.1, 2.2 ± 0.1, 1.3 ± 0.1, 1.3 ± 0.3, and 2.1 ± 0.4, respectively. Since LEEs are produced in large quantities by radiolysis and strongly interact with biomolecules, we expect such enhancements to produce substantial additional damages in the DNA of the nucleus of cancer cells during concomitant chemoradiation therapy. The increase damage appears sufficiently large to justify more elaborate simulations, which could provide a quantitative evaluation of molecular sensitization by Pt-CAs.

Modeling Cell Reactions to Ionizing Radiation: From a Lesion to a Cancer

This article focuses on the analytic modeling of responses of cells in the body to ionizing radiation. The related mechanisms are consecutively taken into account and discussed. A model of the dose- and time-dependent adaptive response is considered for 2 exposure categories: acute and protracted. In case of the latter exposure, we demonstrate that the response plateaus are expected under the modelling assumptions made. The expected total number of cancer cells as a function of time turns out to be perfectly described by the Gompertz function. The transition from a collection of cancer cells into a tumor is discussed at length. Special emphasis is put on the fact that characterizing the growth of a tumor (ie, the increasing mass and volume), the use of differential equations cannot properly capture the key dynamics-formation of the tumor must exhibit properties of the phase transition, including self-organization and even self-organized criticality. As an example, a manageable percolation-type phase transition approach is used to address this problem. Nevertheless, general theory of tumor emergence is difficult to work out mathematically because experimental observations are limited to the relatively large tumors. Hence, determination of the conditions around the critical point is uncertain.

Absolute cross section for DNA damage induced by low-energy (10 eV) electrons: Experimental refinements and sample characterization by AFM

This work describes multiple experimental improvements for measuring absolute cross sections of DNA damage induced by low-energy electrons in nanometer-thick films in vacuum. Measurements of such cross sections are particularly sensitive to film thickness and uniformity. Using atomic force microscopy in 70% ethanol, we present a novel and effective method to determine plasmid DNA film thickness and uniformity that combines height histograms and force-distance curves. We also investigate film deposition with DNA intercalated with 1,3-diaminopropane (Dap) on tantalum-coated substrates as a convenient and cost-effective alternative to the previously-used graphite substrate. The tantalum substrate permits deposition of films very similar to those formed on graphite. Using these refinements and further optimizations of the experimental procedure, we measure an absolute cross section of (7.4 ± 2.3) × 10^-18 cm² per nucleotide for conformational damage to a 3197 base-pair plasmid, induced by 10 eV electrons, which we believe should be considered as a reference value.

Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer

In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.

Radiation damage during in situ electron microscopy of DNA-mediated nanoparticle assemblies in solution

Oligonucleotide-nanoparticle conjugates, also called programmable atom equivalents, carry promise as building blocks for self-assembled colloidal crystals, reconfigurable or stimuli responsive functional materials, as well as bio-inspired hierarchical architectures in wet environments. In situ studies of the DNA-mediated self-assembly of nanoparticles have so far been limited to reciprocal space techniques. Liquid-cell electron microscopy could enable imaging such systems with high resolution in their native environment but to realize this potential, radiation damage to the oligonucleotide linkages needs to be understood and conditions for damage-free electron microscopy identified. Here, we analyze in situ observations of DNA-linked two-dimensional nanoparticle arrays, along with control experiments for different oligonucleotide configurations, to identify the mechanisms of radiation damage for ordered superlattices of DNA-nanoparticle conjugates. In a biological context, the results point to new avenues for studying direct and indirect radiation effects for small ensembles of DNA in solution by tracking conjugated nanoparticles. By establishing low-dose conditions suitable for extended in situ imaging of programmable atom equivalents, our work paves the way for real-space observations of DNA-mediated self-assembly processes.

Direct electron irradiation of DNA in a fully aqueous environment. Damage determination in combination with Monte Carlo simulations

We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si₃N₄ membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D_1/2 = 1.7 ± 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.

Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology

During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG)₂ is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A)₂ confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT)₂ to 5'-(GGG ATT)₄ ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K⁺ ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy.