Yield Of Single-strand Breaks Research Articles

Radiation-induced DNA damage by proton, helium and carbon ions in human fibroblast cell: Geant4-DNA and MCDS-based study

Background. Radiation-induced DNA damages such as Single Strand Break (SSB), Double Strand Break (DSB) and Complex DSB (cDSB) are critical aspects of radiobiology with implications in radiotherapy and radiation protection applications. Materials and Methods. This study presents a thorough investigation into the effects of protons (0.1–100 MeV/u), helium ions (0.13–100 MeV/u) and carbon ions (0.5–480 MeV/u) on DNA of human fibroblast cells using Geant4-DNA track structure code coupled with DBSCAN algorithm and Monte Carlo Damage Simulations (MCDS) code. Geant4-DNA-based simulations consider 1 μm × 1 μm × 0.5 μm water box as the target to calculate energy deposition on event-by-event basis and the three-dimensional coordinates of the interaction location, and then DBSCAN algorithm is used to calculate yields of SSB, DSB and cDSB in human fibroblast cell. The study investigated the influence of Linear Energy Transfer (LET) of protons, helium ions and carbon ions on the yields of DNA damages. Influence of cellular oxygenation on DNA damage patterns is investigated using MCDS code. Results. The study shows that DSB and SSB yields are influenced by the LET of the particles, with distinct trends observed for different particles. The cellular oxygenation is a key factor, with anoxic cells exhibiting reduced SSB and DSB yields, underscoring the intricate relationship between cellular oxygen levels and DNA damage. The study introduced DSB/SSB ratio as an informative metric for evaluating the severity of radiation-induced DNA damage, particularly in higher LET regions. Conclusions. The study highlights the importance of considering particle type, LET, and cellular oxygenation in assessing the biological effects of ionizing radiation.

Monte Carlo-Based Nanoscale Dosimetry Holds Promise for Radiopharmaceutical Therapy Involving Auger Electron Emitters.

Radiopharmaceutical therapy (RPT) is evolving as a promising strategy for treating cancer. As interest grows in short-range particles, like Auger electrons, understanding the dose-response relationship at the deoxyribonucleic acid (DNA) level has become essential. In this study, we used the Geant4-DNA toolkit to evaluate DNA damage caused by the Auger-electron-emitting isotope I-125. We compared the energy deposition and single strand break (SSB) yield at each base pair location in a short B-form DNA (B-DNA) geometry with existing simulation and experimental data, considering both physical direct and chemical indirect hits. Additionally, we evaluated dosimetric differences between our high-resolution B-DNA target and a previously published simple B-DNA geometry. Overall, our benchmarking results for SSB yield from I-125 decay exhibited good agreement with both simulation and experimental data. Using this simulation, we then evaluated the SSB and double strand break (DSB) yields caused by a theranostic Br-77-labeled poly ADP ribose polymerase (PARP) inhibitor radiopharmaceutical. The results indicated a predominant contribution of chemical indirect hits over physical direct hits in generating SSB and DSB. This study lays the foundation for future investigations into the nano-dosimetric properties of RPT.

Assessment of early DNA damage induced in human fibroblasts by four therapeutic radionuclides using Geant4-DNA

PurposeQuantifying the initial damage induction is necessary to understand the dependence of the late effects on radiation quality. This study was conducted to better understand the effects of therapeutic radionuclides on human cells and to improve the therapeutic efficacy of TRT. MethodsIn this study, early direct and indirect DNA damage induced by four widely used therapeutic radionuclides (Y-90, I-131, Lu-177, and I-125) in human fibroblasts was investigated using Geant4 DNA. The relative effects of direct and indirect damage induction on DNA and human cells were evaluated using complexity and source classification. In addition, we performed an analysis of the histogram of fragment length distribution for therapeutic radionuclides. ResultsThe results of this study showed that the highest single-strand break (SSB) and double-strand break (DSB) yields based on source classification are due to the relative effects of indirect damage induction on DNA and human cells. Radionuclide I-131 has the highest yield of SSB, while I-125 has the highest yield of DSB. On the other hand, Y-90 has the lowest SSB and DSB yield values. The study also revealed that I-125 has the highest fragment length distribution, while Y-90 has the lowest. ConclusionAmong the therapeutic radionuclides, I-131 and I-125 had the greatest effect on SSB and DSB yield values, respectively, while Y-90 had little effect.

Enhanced Single-Strand Breaks of a Nucleic Acid by Gold Nanoparticles under X-ray Irradiation

The hydroxyl radical concentration-dependent yield of single-strand breaks (SSBs), obtained through correction of scavenging and hindrance effects caused by gold nanoparticles (AuNPs), for fluorophore- and quencher-labeled DNA on AuNPs was 10 times that of free DNA based on fluorescence measurements of X-ray-irradiated DNA on AuNPs. By comparing the fluorescence data that revealed the number of SSBs with the results of mass spectrometry measurements that detected the total damage to DNA, we found that SSBs dominated DNA damage for DNA on AuNPs whereas non-SSB damage dominated for free DNA. The yield of RNA SSBs under X-ray irradiation was similar to that of DNA in the presence of AuNPs, whereas free RNA was more resistive to radiation than DNA. These results indicated the enhanced SSBs were likely catalyzed through the conversion from nucleobase damage to SSBs by AuNPs. The outcome of this work impacts materials and environmental science, sensing, nanotechnology, biology, and medicine.

Application of a simple DNA damage model developed for electrons to proton irradiation

Proton beam therapy allows irradiating tumor volumes with reduced side effects on normal tissues with respect to conventional x-ray radiotherapy. Biological effects such as cell killing after proton beam irradiations depend on the proton kinetic energy, which is intrinsically related to early DNA damage induction. As such, DNA damage estimation based on Monte Carlo simulations is a research topic of worldwide interest. Such simulation is a mean of investigating the mechanisms of DNA strand break formations. However, past modellings considering chemical processes and DNA structures require long calculation times. Particle and heavy ion transport system (PHITS) is one of the general-purpose Monte Carlo codes that can simulate track structure of protons, meanwhile cannot handle radical dynamics simulation in liquid water. It also includes a simple model enabling the efficient estimation of DNA damage yields only from the spatial distribution of ionizations and excitations without DNA geometry, which was originally developed for electron track-structure simulations. In this study, we investigated the potential application of the model to protons without any modification. The yields of single-strand breaks, double-strand breaks (DSBs) and the complex DSBs were assessed as functions of the proton kinetic energy. The PHITS-based estimation showed that the DSB yields increased as the linear energy transfer (LET) increased, and reproduced the experimental and simulated yields of various DNA damage types induced by protons with LET up to about 30 keV μm−1. These results suggest that the current DNA damage model implemented in PHITS is sufficient for estimating DNA lesion yields induced after protons irradiation except at very low energies (below 1 MeV). This model contributes to evaluating early biological impacts in radiation therapy.

TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields

Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R 2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R 2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.

Establishment of a Method for Investigating Direct and Indirect Actions of Ionizing Radiation Using Scavenger-free Plasmid DNA.

In this study, an improved method using scavenger-free plasmid DNA was established to accurately determine yields of DNA damage induced by direct and indirect actions of ionizing radiation. The scavenger-free plasmid DNA was obtained by dialysis over 5-7 days, and the DNA solvent was replaced with phosphate buffer to completely remove impurities, which could be scavengers of radicals produced as a result of water radiolysis. DNA samples of films and dilute aqueous solutions were used to separately evaluate contributions of the direct and indirect actions of X rays (150-160 kVp). The irradiated DNA was analyzed by agarose gel electrophoresis to quantify strand-break yields. The yields of single-strand breaks (SSBs), n(SSB), were determined to be (6.5 ± 2.0) × 10-10 and (3.1 ± 0.9) × 10-7 SSBs/Gy/Da for the film and solution samples, respectively, showing a significant contribution of hydroxyl radicals (•OH) compared with direct energy depositions from ionizing radiation to DNA. As observed in SSBs, the yields of double-strand breaks (DSBs), n(DSB), were (5.6 ± 1.1) × 10-11 and (1.3 ± 0.2) × 10-8 DSBs/Gy/Da for the film and solution samples, respectively. The yield ratio of DSBs to SSBs, that is, n(DSB)/n(SSB), was 0.091 ± 0.026 for the film samples, while it was much lower for the solution samples (0.045 ± 0.010), indicating that direct actions result in more localized strand breaks relative to indirect actions. Base excision repair enzymes, namely, endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg), were utilized after irradiations to convert base lesions and apurinic/apyrimidinic (AP) sites into strand breaks. The amounts of Nth and Fpg for the conversion were optimized to a few units per µg of DNA, although the optimal concentrations can differ among conditions.

Quantifying the DNA-damaging Effects of FLASH Irradiation With Plasmid DNA

To investigate a plasmid DNA nicking assay approach for isolating and quantifying the DNA-damaging effects of ultrahigh-dose-rate (ie, FLASH) irradiation relative to conventional dose-rate irradiation. We constructed and irradiated phantoms containing plasmid DNA to nominal doses of 20 Gy and 30 Gy using 16 MeV electrons at conventional (0.167 Gy/s) and FLASH (46.6 Gy/s and 93.2 Gy/s) dose rates. We delivered conventional dose rates using a standard clinical Varian iX linear accelerator and FLASH dose rates (FDRs) using a modified Varian 21EX C-series linear accelerator. We ran the irradiated DNA and controls (0 Gy) through an agarose gel electrophoresis procedure that sorted and localized the DNA into bands associated with single strand breaks (SSBs), double strand breaks (DSBs), and undamaged DNA. We quantitatively analyzed the gel images to compute the relative yields of SSBs and DSBs and applied a mathematical model of plasmid DNA damage as a function of dose to compute the relative biological effectiveness (RBE) of SSB and DSB (RBESSB and RBEDSB) damage for a given endpoint and FDR. Both RBESSB and RBEDSB were less than unity with the FDR irradiations, indicating FLASH sparing. With regard to the more deleterious DNA DSB damage, the DSB RBEs of FLASH beams at dose rates of 46.6 Gy/s and 93.2 Gy/s relative to the conventional 16 MeV beam dose rate were 0.54 ± 0.15 and 0.55 ± 0.17, respectively. This study demonstrated the feasibility of using a DNA-based phantom to isolate and assess the FLASH sparing effect on DNA. We also found that FLASH irradiation causes less damage to DNA compared with a conventional dose rate. This result supports the notion that the protective effect of FLASH irradiation occurs at least partially via fundamental biochemical processes.

TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation

The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependent G values in pure liquid water for ·OH, e– aq, and H2 with published experimental data. For H2O2 and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by 137Cs γ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependent G values and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for ·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.

A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation - Part II: sensitivity and uncertainty analysis.

Calculations of deoxyribonucleic acid (DNA) damages involve many parameters in the computation process. As these parameters are often subject to uncertainties, it is of central importance to comprehensively quantify their impacts on DNA single-strand break (SSB) and double-strand break (DSB) yields. This has been a challenging task due to the required large number of simulations and the relatively low computational efficiency using CPU-based MC packages. In this study, we present comprehensive evaluations on sensitivities and uncertainties of DNA SSB and DSB yields on 12 parameters using our GPU-based MC tool, gMicroMC. We sampled one electron at a time in a water sphere containing a human lymphocyte nucleus and transport the electrons and generated radicals until 2Gy dose was accumulated in the nucleus. We computed DNA damages caused by electron energy deposition events in the physical stage and the hydroxyl radicals at the end of the chemical stage. We repeated the computations by varying 12 parameters: (a) physics cross section, (b) cutoff energy for electron transport, (c)-(e) three branching ratios of hydroxyl radicals in the de-excitation of excited water molecules, (f) temporal length of the chemical stage, (g)-(h) reaction radii for direct and indirect damages, (i) threshold energy defining the threshold damage model to generate a physics damage, (j)-(k) minimum and maximum energy values defining the linear-probability damage model to generate a physics damage, and (l) probability to generate a damage by a radical. We quantified sensitivity of SSB and DSB yields with respect to these parameters for cases with 1.0 and 4.5keV electrons. We further estimated uncertainty of SSB and DSB yields caused by uncertainties of these parameters. Using a threshold of 10% uncertainty as a criterion, threshold energy in the threshold damage model, maximum energy in the linear-probability damage model, and probability for a radical to generate a damage were found to cause large uncertainties in both SSB and DSB yields. The scaling factor of the cross section, cutoff energy, physics reaction radius, and minimum energy in the linear-probability damage model were found to generate large uncertainties in DSB yields. We identified parameters that can generate large uncertainties in the calculations of SSB and DSB yields. Our study could serve as a guidance to reduce uncertainties of parameters and hence uncertainties of the simulation results.

An investigation of the physics mechanism based on DNA damage produced by protons and alpha particles in a realistic DNA model

The direct effect of monoenergetic protons and alpha particles on DNA molecules, as the biological endpoint, were investigated using the Geant4-DNA extensions of the Geant4 Toolkit. two different geometries of B-DNA were simulated to confirm the importance of DNA geometry, namely an atomic model of the Protein Data Bank (PDB) and a simple water cylinder. A direct damage is produced when incident radiations deposit energy in the DNA molecule. Further, the yields of DNA Direct Single-Strand Breaks (SSB), Double-Strand Breaks (DSB), and Total-Strand Breaks (TSB) were calculated for protons and alpha particles with different incident energies. The relative biological effectiveness for the induction of direct DNA double-strand breaks (RBEDSB) was evaluated in the human cell. The SSBevent ratio was determined for each incident particle. The results from the models indicated that TSB, SSB, and DSB yields are higher for simple geometry, compared to the atomic model, and a strong dependence was found by selecting the DNA geometrical model. The SSB yield incorporated the weak dependence of SSB on the type and energy of the incident particles. In addition, based on the results, the TSB yield was approximately independent of the linear energy transfer (LET) of the incident energies while the DSB yield increased as a function of the LET. Further, the results demonstrated that the DSB yield and RBEDSB of the protons were higher for iso-LET ions, compared to the alpha particles. Finally, the contribution of secondary electrons to the creation of DSBs was equal to 83 and 74% for protons and alpha particles at the same LET value, respectively.

HOW DETECTION OF PLASMID DNA FRAGMENTATION AFFECTS RADIATION STRAND BREAK YIELDS.

A compromised detection of radiation-induced plasmid DNA fragments results in underestimation of calculated damage yields. Electrophoretic methods are easy and cheap, but they can only detect a part of the fragments, neglecting the shortest ones. These can be detected with atomic force microscopy, but at the expense of time and price. Both methods were used to investigate their capabilities to detect the DNA fragments induced by high-energetic heavy ions. The results were taken into account in calculations of radiation-induced yields of single and double strand breaks. It was estimated that the double strand break yield is twice as high when the fragments are at least partially detected with the agarose electrophoresis, compared to when they were completely omitted. Further increase by 13% was observed when the measured fragments were corrected for the fraction of the shortest fragments up to 300 base pairs, as detected with the atomic force microscopy. The effect of fragment detection on the single strand break yield was diminished.

Efficiency of radiation-induced base lesion excision and the order of enzymatic treatment

Purpose: To clarify whether initial base excision repair processes at clustered DNA damage sites comprising multiple base lesions affect subsequent excision processes via the formation of additional strand breaks by glycosylase and apurinic/apyrimidinic (AP) endonuclease base excision enzymes.Materials and methods: Plasmid DNA (pUC18) as a model DNA molecule was exposed to high-linear-energy-transfer (LET) ionizing radiation (He2+ or C6+ ions) or low-LET ionizing radiation (X-rays) under various conditions to produce varied radical-scavenging effects. pUC18 was then treated sequentially or simultaneously with two bacterial base excision enzymes (glycosylases), namely, endonuclease III and formamidopyrimidine-DNA glycosylase, which convert pyrimidine (or abasic [AP] site) and purine (or AP site) lesions to single-strand breaks (SSB), respectively. Yields of additional SSB or double-strand breaks (DSB) as digestion products were examined after changing the order of enzymatic treatment.Results: There were few differences among the enzymatic treatments, indicating that treatment order did not affect the final yields of additional SSB or DSB formed by glycosylase activity. This suggests that of the total damage, the fraction of clustered damage sites with a persistent base lesion dependent on the order of glycosylase treatment was insignificant if present.Conclusion: Base lesion clusters induced by high- or low-LET radiation appear three or more base pairs apart, and are promptly converted to a DSB by glycosylase, regardless of the order of enzymatic treatment.

The effect of dimethyl sulfoxide on the induction of DNA strand breaks in plasmid DNA and colony formation of PC Cl3 mammalian cells by alpha-, beta-, and Auger electron emitters (223)Ra, (188)Re, and (99m)Tc.

BackgroundDNA damage occurs as a consequence of both direct and indirect effects of ionizing radiation. The severity of DNA damage depends on the physical characteristics of the radiation quality, e.g., the linear energy transfer (LET). There are still contrary findings regarding direct or indirect interactions of high-LET emitters with DNA. Our aim is to determine DNA damage and the effect on cellular survival induced by 223Ra compared to 188Re and 99mTc modulated by the radical scavenger dimethyl sulfoxide (DMSO).MethodsRadioactive solutions of 223Ra, 188Re, or 99mTc were added to either plasmid DNA or to PC Cl3 cells in the absence or presence of DMSO. Following irradiation, single strand breaks (SSB) and double strand breaks (DSB) in plasmid DNA were analyzed by gel electrophoresis. To determine the radiosensitivity of the rat thyroid cell line (PC Cl3), survival curves were performed using the colony formation assay.ResultsExposure to 120 Gy of 223Ra, 188Re, or 99mTc leads to maximal yields of SSB (80 %) in plasmid DNA. Irradiation with 540 Gy 223Ra and 500 Gy 188Re or 99mTc induced 40, 28, and 64 % linear plasmid conformations, respectively. DMSO prevented the SSB and DSB in a similar way for all radionuclides. However, with the α-emitter 223Ra, a low level of DSB could not be prevented by DMSO. Irradiation of PC Cl3 cells with 223Ra, 188Re, and 99mTc pre-incubated with DMSO revealed enhanced survival fractions (SF) in comparison to treatment without DMSO. Protection factors (PF) were calculated using the fitted survival curves. These factors are 1.23 ± 0.04, 1.20 ± 0.19, and 1.34 ± 0.05 for 223Ra, 188Re, and 99mTc, respectively.ConclusionsFor 223Ra, as well as for 188Re and 99mTc, dose-dependent radiation effects were found applicable for plasmid DNA and PC Cl3 cells. The radioprotection by DMSO was in the same range for high- and low-LET emitter. Overall, the results indicate the contribution of mainly indirect radiation effects for each of the radionuclides regarding DNA damage and cell survival. In summary, our findings may contribute to fundamental knowledge about the α-particle induced DNA damage.Electronic supplementary materialThe online version of this article (doi:10.1186/s13550-016-0203-x) contains supplementary material, which is available to authorized users.

Proton and light ion RBE for the induction of direct DNA double strand breaks.

To present and characterize a Monte Carlo (MC) tool for the simulation of the relative biological effectiveness for the induction of direct DNA double strand breaks (RBEDSB (direct)) for protons and light ions. The MC tool uses a pregenerated event-by-event tracks library of protons and light ions that are overlaid on a cell nucleus model. The cell nucleus model is a cylindrical arrangement of nucleosome structures consisting of 198 DNA base pairs. An algorithm relying on k-dimensional trees and cylindrical symmetries is used to search coincidences of energy deposition sites with volumes corresponding to the sugar-phosphate backbone of the DNA molecule. Strand breaks (SBs) are scored when energy higher than a threshold is reached in these volumes. Based on the number of affected strands, they are categorized into either single strand break (SSB) or double strand break (DSB) lesions. The number of SBs composing each lesion (i.e., its size) is also recorded. RBEDSB (direct) is obtained by taking the ratio of DSB yields of a given radiation field to a (60)Co field. The MC tool was used to obtain SSB yields, DSB yields, and RBEDSB (direct) as a function of linear energy transfer (LET) for protons ((1)H(+)), (4)He(2+), (7)Li(3+), and (12)C(6+) ions. For protons, the SSB yields decreased and the DSB yields increased with LET. At ≈24.5 keV μm(-1), protons generated 15% more DSBs than (12)C(6+) ions. The RBEDSB (direct) varied between 1.24 and 1.77 for proton fields between 8.5 and 30.2 keV μm(-1), and it was higher for iso-LET ions with lowest atomic number. The SSB and DSB lesion sizes showed significant differences for all radiation fields. Generally, the yields of SSB lesions of sizes ≥2 and the yields of DSB lesions of sizes ≥3 increased with LET and increased for iso-LET ions of lower atomic number. On the other hand, the ratios of SSB to DSB lesions of sizes 2-4 did not show variability with LET nor projectile atomic number, suggesting that these metrics are independent of the radiation quality. Finally, a variance of up to 8% in the DSB yields was observed as a function of the particle incidence angle on the cell nucleus. This simulation effect is due to the preferential alignment of ion tracks with the DNA nucleosomes at specific angles. The MC tool can predict SSB and DSB yields for light ions of various LET and estimate RBEDSB (direct). In addition, it can calculate the frequencies of different DNA lesion sizes, which is of interest in the context of biologically relevant absolute dosimetry of particle beams.

Microdosimetry of DNA conformations: relation between direct effect of (60)Co gamma rays and topology of DNA geometrical models in the calculation of A-, B- and Z-DNA radiation-induced damage yields.

In order to obtain the energy deposition pattern of ionizing radiation in the nanometric scale of genetic material and to investigate the different sensitivities of the DNA conformations, direct effects of (60)Co gamma rays on the three A, B and Z conformations of DNA have been studied. For this purpose, single-strand breaks (SSB), double-strand breaks (DSB), base damage (BD), hit probabilities and three microdosimetry quantities (imparted energy, mean chord length and lineal energy) in the mentioned DNA conformations have been calculated and compared by using GEometry ANd Tracking 4 (Geant4) toolkit. The results show that A-, B- and Z-DNA conformations have the highest yields of DSB (1.2 Gy(-1) Gbp(-1)), SSB (25.2 Gy(-1) Gbp(-1)) and BD (4.81 Gy(-1) Gbp(-1)), respectively. Based on the investigation of direct effects of radiation, it can be concluded that the DSB yield is largely correlated to the topological characteristics of DNA models, although the SSB yield is not. Moreover, according to the comparative results of the present study, a reliable candidate parameter for describing the relationship between DNA damage yields and geometry of DNA models in the theoretical radiation biology research studies would be the mean chord length (4 V/S) of the models.

DNA Strand Breaks Induced by 0–1.5 eV UV Photoelectrons under Atmospheric Pressure

Vacuum experiments with monoenergetic low-energy electrons (LEEs) impacting on biomolecules have revealed basic mechanisms of radiobiological damage. To move closer to cellular conditions, we explore the possibility of damaging DNA at standard atmospheric pressure with electrons of 0–1.5 eV. These electrons are produced by UV light incident on a tantalum or n-Si substrate, onto which a five-monolayer film of DNA is deposited. Total conformational damage, cross-links, and double- and single-strand breaks (SSBs) are measured as a function of LEE fluence. The photoelectron energy distribution can be modified by changing the work function of the substrate or the photon energy. In a N2 atmosphere with a tantalum substrate, the yields of SSBs (5 ± 2 × 10–14 electron–1 molecule–1) and their number per energy deposited (46 ± 36 × 10–4/eV) are in good agreement with those obtained, under similar conditions, by monoenergetic 0.5–1.0 eV electron impact in vacuo and 1.5 KeV X-ray photoelectrons at atmospheric pressur...

Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures

Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for 60Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.

Breaking DNA strands by extreme-ultraviolet laser pulses in vacuum.

Ionizing radiation induces a variety of DNA damages including single-strand breaks (SSBs), double-strand breaks (DSBs), abasic sites, modified sugars, and bases. Most theoretical and experimental studies have been focused on DNA strand scissions, in particular production of DNA double-strand breaks. DSBs have been proven to be a key damage at a molecular level responsible for the formation of chromosomal aberrations, leading often to cell death. We have studied the nature of DNA damage induced directly by the pulsed 46.9-nm (26.5eV) radiation provided by an extreme ultraviolet (XUV) capillary-discharge Ne-like Ar laser (CDL). Doses up to 45 kGy were delivered with a repetition rate of 3 Hz. We studied the dependence of the yield of SSBs and DSBs of a simple model of DNA molecule (pBR322) on the CDL pulse fluence. Agarose gel electrophoresis method was used for determination of both SSB and DSB yields. The action cross sections of the single- and double-strand breaks of pBR322 plasmid DNA in solid state were determined. We observed an increase in the efficiency of strand-break induction in the supercoiled DNA as a function of laser pulse fluence. Results are compared to those acquired at synchrotron radiation facilities and other sources of extreme-ultraviolet and soft x-ray radiation.

⁹⁹mTc pyrene derivative complex causes double-strand breaks in dsDNA mainly through cluster-mediated indirect effect in aqueous solution.

Radiation therapy for cancer patients works by ionizing damage to nuclear DNA, primarily by creating double-strand breaks (DSB). A major shortcoming of traditional radiation therapy is the set of side effect associated with its long-range interaction with nearby tissues. Low-energy Auger electrons have the advantage of an extremely short effective range, minimizing damage to healthy tissue. Consequently, the isotope 99mTc, an Auger electron source, is currently being studied for its beneficial potential in cancer treatment. We examined the dose effect of a pyrene derivative 99mTc complex on plasmid DNA by using gel electrophoresis in both aqueous and methanol solutions. In aqueous solutions, the average yield per decay for double-strand breaks is 0.011±0.005 at low dose range, decreasing to 0.0005±0.0003 in the presence of 1 M dimethyl sulfoxide (DMSO). The apparent yield per decay for single-strand breaks (SSB) is 0.04±0.02, decreasing to approximately a fifth with 1 M DMSO. In methanol, the average yield per decay of DSB is 0.54±0.06 and drops to undetectable levels in 2 M DMSO. The SSB yield per decay is 7.2±0.2, changing to 0.4±0.2 in the presence of 2 M DMSO. The 95% decrease in the yield of DSB in DMSO indicates that the main mechanism for DSB formation is through indirect effect, possibly by cooperative binding or clustering of intercalators. In the presence of non-radioactive ligands at a near saturation concentration, where radioactive Tc compounds do not form large clusters, the yield of SSB stays the same while the yield of DSB decreases to the value in DMSO. DSBs generated by 99mTc conjugated to intercalators are primarily caused by indirect effects through clustering.