Yield Of Strand Breaks Research Articles

Conformation-Dependent DNA Damage Induced by Gold Nanoparticles

The sensitivity of two conformations of plasmid DNA, the A and B forms, to strand break formation induced by gold nanoparticles (GNPs) is investigated by varying the GNP to DNA ratio in solution and the degree of DNA hydration. Decreasing DNA hydration via lyophilisation or by replacement of water with ethanol in solution modifies its conformation from the B to the A form. The yields of single strand breaks (SSB) are found to be highly dependent on the amount of DNA in the A configuration. The damage also increases with the amount of GNPs bound to DNA. At a ratio of two GNPs for one plasmid in an 80%-ethanol, 20%-water solution, 50% of the initial supercoiled population is converted to SSB. Thus, close contact with GNPs causes extensive damage to DNA in the A form. Since during transcription the DNA-RNA duplexes adopt an A form, GNPs could be genotoxic. Our results suggest that GNPs may have potential as chemotherapeutic agents if conjugated to nuclear targeting ligands. Considering their additional radiotherapeutic properties, targeted GNPs could also become highly effective in the treatment of cancer with concomitant chemoradiation therapy.

Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid

We quantified the damage yields produced in plasmid DNA by γ-irradiation in the presence of low concentrations (10–100μM) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield of DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins.By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 50–60% of base lesions and AP-sites were repaired by 10μM ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.

Hypoxic radiosensitization by nitric oxide

Purpose Nitric oxide (NO) radiosensitizes mammalian cells significantly more efficiently than oxygen but the mechanism of this effect is unknown. We have studied the effect of NO on radiation-induced single strand breaks in plasmid DNA, changes to DNA bases, cellular double strand breaks and cell survival to gain further information into the mechanisms of radiosensitization. Results The yields of plasmid DNA strand breaks are reduced in the presence of NO when compared with the yield induced by hydroxyl radical alone – post-irradiation treatment with DNA glycosylases however revealed that damaged nucleotides are formed in the presence of NO as seen through the formation of additional strand breaks. NO reacts with radiation-induced dGMP (2’-deoxyguanosine monophosphate) radicals to produce specific guanine modifications. Chemical mechanisms for these changes have been proposed. V79-4 cells are radiosensitized by NO more efficiently in exponential growth; these cells also exhibit enhanced γH2AX staining, a marker for double strand breaks (DSB). The maximum numbers of foci are formed later and remain longer after NO damage relative to DSB generated in anoxia, suggesting formation of replication-induced DSB. Conclusions It is tentatively proposed that NO may radiosensitize cells by causing specific DNA damage which is difficult to repair - future studies will focus on identifying NO-induced DNA lesions in irradiated cells and increasing our understanding into how these lesions may enhance DNA damage following replication and repair.

SU-E-T-05: Comparing DNA Strand Break Yields for Photons under Different Irradiation Conditions with Geant4-DNA.

To validate and scrutinize published DNA strand break data with Geant4-DNA and a probabilistic model. To study the impact of source size, electronic equilibrium and secondary electron tracking cutoff on direct relative biological effectiveness (DRBE). Geant4 (v4.9.5) was used to simulate a cylindrical region of interest (ROI) with r = 15 nm and length = 1.05 mm, in a slab of liquid water of 1.06 g/cm3 density. The ROI was irradiated with mono-energetic photons, with a uniformly distributed volumetric isotropic source (0.28, 1.5 keV) or a plane beam (0.662, 1.25 MeV), of variable size. Electrons were tracked down to 50 or 10 eV, with G4-DNA processes and energy transfer greater than 10.79 eV was scored. Based on volume ratios, each scored event had a 0.0388 probability of happening on either DNA helix (break). Clusters of at least one break on each DNA helix within 3.4 nm were found using a DBSCAN algorithm and categorized as double strand breaks (DSB). All other events were categorized as single strand breaks (SSB). Geant4-DNA is able to reproduce strand break yields previously published. Homogeneous irradiation conditions should be present throughout the ROI for DRBE comparisons. SSB yields seem slightly dependent on the primary photon energy. DRBEs show a significant increasing trend for lower energy incident photons. A lower electron cutoff produces higher SSB yields, but decreases the SSB/DSB yields ratio. The probabilistic and geometrical DNA models can predict equivalent results. Using Geant4, we were able to reproduce previously published results on the direct strand break yields of photon and study the importance of irradiation conditions. We also show an ascending trend for DRBE with lower incident photon energies. A probabilistic model coupled with track structure analysis can be used to simulate strand break yields. NSERC, CIHR.

Evaluation of the mean energy deposit during the impact of charged particles on liquid water

The DNA strand break yield due to the impact of ionizing particles on living beings is closely related to the number of inelastic events per unit absorbed dose produced by these particles. The higher this number, the higher the probability of causing DNA strand breaks per unit absorbed dose. In a previous work, it was found that the total number of events produced by primary particles and the secondary electrons is almost independent of the type and energy of the incident particle (or LET). This finding could be supported by a quasi-constant mean energy deposit by inelastic event (). In this work, was defined and determined for electrons and the non-negative charge states of hydrogen (H0, +) and helium (He0, +, 2 +) species impacting on liquid water. Ionization, excitation and charge transfer (up to two-electron transfers) processes have been included in present calculations. We found that, for liquid water, is within 13.7 ± 4.1 eV, 14.2 ± 1.7 eV and 13.8 ± 1.4 eV for electrons, hydrogen and helium species, respectively, with impact energies changing over three orders of magnitude. Unlike the mean excitation energy, the mean energy deposit per inelastic event depends not only on the target molecule but also on the projectile features. However, this dependence is relatively weak. This fact supports the quasi-independent number of inelastic events per unit absorbed dose found previously when charged particles impact on matter.

Yield of Single- and Double-Strand Breaks and Nucleobase Lesions in Fully Hydrated Plasmid DNA Films Irradiated with High-LET Charged Particles

We measured the yield and spectrum of strand breaks and nucleobase lesions produced in fully hydrated plasmid DNA films to determine the linear energy transfer (LET) dependence of DNA damage induced by ion-beam irradiation in relation to the change in the atomic number of ions. The yield of isolated damage was revealed as a decrease in prompt SSBs with increasing LET of He(2+), C(5+,6+) and Ne(8+,10+) ions. On the other hand, the yields of prompt DSBs increased with increasing ion LET. SSBs were additionally induced in ion-irradiated DNA film by treatment with two kinds of base excision repair proteins (glycosylases), Nth and Fpg, indicating that base lesions are produced in the hydrated DNA film. This result shows that nucleobase lesions are produced via both chemical reactions with diffusible water radicals, such as OH radicals, and direct energy deposition onto DNA and the hydrated water layer. Nth-sensitive sites deduced to be pyrimidine lesions, such as 5,6-dihydrothymine (DHT), showed a relatively larger yield than Fpg-sensitive sites deduced to be purine lesions, such as 7,8-dihydro-8-oxo-2'deoxyguanine (8-oxoGua), for all ion exposures tested. The yield of SSBs or DSBs observed by enzyme treatment decreased noticeably with increasing LET for all tested ions. These results indicated that higher-LET ions preferentially produce a complex type of damage that might compromise the activities of the glycosylases used in this study. These findings are biologically important since, under cell mimicking conditions, persistent DNA damage occurs in part due to direct energy deposition on the DNA or hydrated water shell that is specifically induced by dense ionization in the track.

Estimation of the RBE of mammography-quality beams using a combination of a Monte Carlo code with a B-DNA geometrical model

The PENELOPE code is used to determine direct strand break yields corresponding to photons from a 60Co source and 28 and 30 kV x-ray beams impacting on a B-DNA geometrical model, which accounts for five organizational levels of the human genetic material. Direct single, double and total strand break probabilities are determined in a liquid water homogeneous medium with 1.06 g cm−3 density. The spectra produced by the x-ray beams at various depths in the phantom have been used to study the dependence of the damage yield on the depth. The relative biological effectiveness (RBE) is also estimated using the 60Co radiation qualities as the reference. According to this work, the damage probabilities and thus the RBE are, within the uncertainties, similar for both x-ray energies and are independent of the depth into the phantom. Furthermore, the total strand break yield is invariant with respect to the energy of the incident photons. The RBE for low-energy x-ray beams determined here (1.3 ± 0.1) is lower than that reported by Kellerer, taking into account that he used a 200 kV radiation as the reference quality. However, our RBE values are consistent with those determined by Kühne et al (2005 Radiat. Res. 164 669–76), which used the same biological endpoint and reference quality as our study. Also, our RBE values are similar to those determined by Verhaegen and Reniers (2004 Radiat. Res. 162 592–9).

On the role of low-energy electrons in the radiosensitization of DNA by goldnanoparticles

Four different gold nanoparticle (GNP) preparations, includingnaked GNPs and GNPs coated either with thiolated undecane (S-C11H23), or with dithiolated diethylenetriaminepentaacetic (DTDTPA) or gadolinium (Gd)DTDTPA chelating agents, were synthesized. The average diameters, for each type ofnanoparticle, are 5 nm, 10 and 13 nm, respectively. Dry films of plasmid DNA pGEM-3Zf(−), DNA with bound GNPs and DNA with coated GNPs were bombardedwith 60 keV electrons. The yields of single and double strand breaks weremeasured as a function of exposure by electrophoresis. The binding of just oneGNP without coating to DNA containing 3197 base pairs increases singleand double strand breaks by a factor of 2.3 while for GNPs coated with S-C11H23 this factor is reduced to 1.6. The GNPs coated with DTDTPA and DTDTPA:Gd in thesame ratio with the DNA, produce essentially no increment in damage. These results couldbe explained by the attenuation by the coatings of the intensity of the low-energyphotoelectrons emitted from the GNPs. Thus, coatings of GNPs may considerablyattenuate the short-range low-energy electrons emitted from gold, leading to a considerabledecrease of radiosensitization. According to our results, the highest radiosensitizationshould be obtained with GNPs having the shortest possible ligand, directed to the DNA ofcancer cells.

Direct observation of ultrafast-electron-transfer reactions unravels high effectiveness of reductive DNA damage

Both water and electron-transfer reactions play important roles in chemistry, physics, biology, and the environment. Oxidative DNA damage is a well-known mechanism, whereas the relative role of reductive DNA damage is unknown. The prehydrated electron (e(pre)-), a novel species of electrons in water, is a fascinating species due to its fundamental importance in chemistry, biology, and the environment. e(pre)- is an ideal agent to observe reductive DNA damage. Here, we report both the first in situ femtosecond time-resolved laser spectroscopy measurements of ultrafast-electron-transfer (UET) reactions of e(pre)- with various scavengers (KNO(3), isopropanol, and dimethyl sulfoxide) and the first gel electrophoresis measurements of DNA strand breaks induced by e(pre)- and OH(•) radicals co-produced by two-UV-photon photolysis of water. We strikingly found that the yield of reductive DNA strand breaks induced by each e(pre)- is twice the yield of oxidative DNA strand breaks induced by each OH(•) radical. Our results not only unravel the long-standing mystery about the relative role of radicals in inducing DNA damage under ionizing radiation, but also challenge the conventional notion that oxidative damage is the main pathway for DNA damage. The results also show the potential of femtomedicine as a new transdisciplinary frontier and the broad significance of UET reactions of e(pre)- in many processes in chemistry, physics, biology, and the environment.

The invariance of the total direct DNA strand break yield

The invariance of the total direct strand break yield when DNA is irradiated by different types of particles and energies has been reported by previous works. This study is intended to explain the physical causes of this behavior. The GEANT4-DNA extension of the GEANT4 general purpose Monte Carlo simulation toolkit has been used to determine direct strand break yields induced by protons and alpha particles impacting on a B-DNA geometrical model, including five organization levels of the human genetic material. The linear energy transfer (LET) of such particles ranges from 4.8 keV/microm (10 MeV protons) to about 235 keV/microm (2 MeV alpha particles), at 5.225 pm depth (near the center of the region of interest). Direct total, single and double strand break probabilities have been determined in a liquid water homogeneous medium with a 1.06 g/cm3 density. The energetic spectra of single strand breaks (SSB), the number of energy deposition events, and the SSB/event ratio were determined. The target-hit probability was found to be independent of both the type and the energy of the incident particle, even if this latter is a secondary electron. This probability is determined by the geometrical properties of the system. The total strand break yield and the number of energy deposition events required to reach a certain absorbed dose were found nearly independent of the type and energy of the incident ion (proton or alpha). In contrast, the double strand break (DSB) yield was found strongly dependent on the LET of the incident radiation. The SSB generation process is homogeneous and independent of the LET of the particles involved, at least within the proton and alpha particle energy range here studied. The target-hit probability is only determined by the ratio between the total volume occupied by targets and that of the ROI where the radiation deposits its energy. The maximum separation distance between two adjacent SSBs to produce a DSB is the parameter that breaks the homogeneity of the target-hit process, making the DSB production process strongly heterogeneous.

Abstract 4903: Identification of damage products derived from C3′-deoxy-3′-thymidinyl radical, a proposed intermediate from DNA-LEEs interactions

Abstract Radiotherapy uses ionizing radiation (IR) to target deoxyribonucleic acids (DNA) among other biological molecules for cancer treatment. As a result genotoxic, mutagenic and recombinogenic lesions can be formed. Oxidative damage to DNA through IR is partially produced by the secondary particles created along the ionization track. Secondary low-energy electrons (LEEs, 1-20 eV) are the most abundant secondary species produced by primary IR. Although it has been established that LEEs can produce substantial yields of DNA single and double strand breaks, the mechanism of their formation has not been established. Elucidation of the mechanism of damage by LEEs is essential for the development of global models of cellular radiolysis and more efficient methods of cancer radiotherapy. It was proposed that LEE can add to DNA constituents resulting in the formation of transient molecular anion intermediates that eventually lead to bond dissociation. It is believed that carbon-centered radicals on the sugar moiety are a major reactive intermediate formed in this process. One of these is the C3′-deoxy-3′-thymidinyl radical. The synthesis of C3′-deoxy-3′-(selenophenyl)thymidine as a precursor of this radical has been completed. Initial photolysis experiments for photochemical generation of the radical of interest were performed and the formation of the radical intermediate of interest has been established. Identification of damage products derived from this intermediate in nucleosides is currently in progress. The modified nucleoside was incorporated into oligonucleotides using reverse DNA synthesis. Photochemical generation of the C3′-deoxy-3′-thymidinyl radical within DNA was achieved using ultraviolet light (≥ 320nm). Identification of the damage products obtained from the generation of the C3’ radical is currently in progress. Oligonucleotides sequences with different base context were synthesized in order to investigate the effect of sequence on the distribution of damage products. The effect of the concentration of GSH on the damage product distribution is also under investigation. Through these efforts a link will be established between the products of LEEs and the deleterious effects of radiation in cancer radiotherapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4903. doi:10.1158/1538-7445.AM2011-4903

Protection by organic ions against DNA damage induced by low energy electrons.

It is well known that electrons below 15 eV induce strand breaks in DNA essentially via the formation of transient anions which decay by dissociative electron attachment (DEA) or into dissociative electronics states. The present article reports the results of a study on the influence of organic ions on this mechanism. tris and EDTA are incorporated at various concentrations within DNA films of different thicknesses. The amino group of tris molecules and the carboxylic acid function of ethylenediamine tetra-acetic acid (EDTA) molecules together can be taken as simple model for the amino acids components of proteins, such as histones, which are intimately associated with the DNA of eukaryotic cells. The yield of single strand breaks induced by 10 eV electrons is found to decrease dramatically as a function of the number of organic ions/nucleotide. As few as 2 organic ions/nucleotide are sufficient to decrease the yield of single strand breaks by 70%. This effect is partly explained by an increase in multiple inelastic electrons scattering with film thickness but changes in the resonance parameters can also contribute to DNA protection. This can occur if the electron captures cross section and the lifetime of the transient anions (i.e., core-excited resonances) formed at 10 eV are reduced by the presence of organic ions within the grooves of DNA. Moreover, it is proposed that the tris molecules may participate in the repair of DNA anions [such as G(-H)(-)] induced by DEA on DNA bases.

A nanodosimetric model of radiation-induced clustered DNA damage yields

We present a nanodosimetric model for predicting the yield of double strand breaks (DSBs) and non-DSB clustered damages induced in irradiated DNA. The model uses experimental ionization cluster size distributions measured in a gas model by an ion counting nanodosimeter or, alternatively, distributions simulated by a Monte Carlo track structure code developed to simulate the nanodosimeter. The model is based on a straightforward combinatorial approach translating ionizations, as measured or simulated in a sensitive gas volume, to lesions in a DNA segment of one–two helical turns considered equivalent to the sensitive volume of the nanodosimeter. The two model parameters, corresponding to the probability that a single ion detected by the nanodosimeter corresponds to a single strand break or a single lesion (strand break or base damage) in the equivalent DNA segment, were tuned by fitting the model-predicted yields to previously measured double-strand break and double-strand lesion yields in plasmid DNA irradiated with protons and helium nuclei. Model predictions were also compared to both yield data simulated by the PARTRAC code for protons of a wide range of different energies and experimental DSB and non-DSB clustered DNA damage yield data from the literature. The applicability and limitations of this model in predicting the LET dependence of clustered DNA damage yields are discussed.

Characterization of condensed plasmid DNA models for studying the direct effect of ionizing radiation

We have examined the changes in physical properties of aqueous solutions of the plasmid pUC18 that take place on the addition of the cationic oligopeptide penta-arginine. An increase in sedimentation rate and static light scattering, and changes in the nucleic acid CD spectrum all suggest that this ligand acts to condense the plasmid. Dynamic light scattering suggests the hydrodynamic radii of the condensate particles are a few micrometers, ca. 50-fold larger than that of the monomeric plasmid. Condensation of the plasmid also produces a ca. 100-fold decrease in the strand break yield produced by gamma irradiation. This extensive protection against reactive intermediates in the bulk of the solution implies that condensed plasmid DNA may offer a model system with which to study the direct effect of ionizing radiation (ionization of the DNA itself). The use of peptide ligands as condensing agents in this application is attractive because the derivatives of several amino acids (particularly tryptophan and tyrosine) have been shown to modify the radiation chemistry of DNA extensively.

A new calculation on spectrum of direct DNA damage induced by low-energy electrons

In this work, direct DNA damage induced by low-energy electrons (<5 keV) is simulated using Monte Carlo methods, and the resulting yield of various strand breaks and base damages in cellular environment is presented. The simulation is based on a new inelastic cross section for the production of electron track structure in liquid water, and on ionization cross sections of DNA bases to generate base radical. Especially, a systematic approach of simulating detailed base damage is suggested. This approach includes improvement of a volume model of DNA, generation of the DNA base sequence, conversion of ionization events in liquid water at hit site to the ionization interaction of electrons with DNA bases and development of an algorithm to convert a base radical to a damage. The results obtained in terms of strand breaks are compared with those of experiments and other theoretical calculations, and good agreement was obtained. The yield of detailed base damages and clustered DNA damages caused by the combination of various strand breaks and base damages is presented, and the corresponding distribution characteristics are analyzed. The influence of the relative content of base pairs A-T and G-C in a DNA segment on the yield of both strand breaks and base damages is also explored. The present work provides fundamental information on DNA damage and represents the first effort toward the goal of obtaining the spectrum of clustered DNA damage including detailed base damages, for the mechanistic interpretation and prediction of radiation effects.

Induction of DNA Strand Breaks, Base Lesions and Clustered Damage Sites in Hydrated Plasmid DNA Films by Ultrasoft X Rays around the Phosphorus K Edge

To characterize the DNA damage induced by K-shell ionization of phosphorus atom in DNA backbone on the level of hydration, the yields of DNA strand breaks and base lesions arising from the interaction of ultrasoft X rays with energies around the phosphorus K edge were determined using dry and fully hydrated pUC18 plasmid DNA samples. Base lesions and bistranded clustered DNA damage sites were revealed by postirradiation treatment with the base excision repair proteins endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). The yield of prompt single-strand breaks (SSBs) with dry DNA irradiated at the phosphorus K resonance energy (2153 eV) is about one-third that below the phosphorus K edge (2147 eV). The yields of prompt double-strand breaks (DSBs) were found to be less dependent on the X-ray energy, with the yields being about two times lower when irradiated at 2153 eV. Heat-labile sites were not produced in detectable amounts. The yields of base lesions were dependent on the energy of the X rays, especially when the DNA was fully hydrated. Bistranded clustered DNA damage sites, revealed enzymatically as additional DSBs, were produced in dry as well as in hydrated DNA with all three energies of X rays. The yields of these enzyme-sensitive sites were also lower when irradiated at the phosphorus K resonance energy. On the other hand, the yields of prompt SSBs and enzyme-sensitive sites for the two off-resonance energies were, larger than those determined previously for gamma radiation. The results indicate that the photoelectric effect caused by X rays and dense ionization and excitation events along the tracks of low-energy secondary electrons are more effective at inducing SSBs and enzyme-sensitive sites. The complex types of damage, prompt and enzymatically induced DSBs, are preferentially induced by phosphorus K resonance at 2153 eV rather than simple SSBs and isolated base lesions, particularly in hydrated conditions. It is concluded that not only the phosphorus K resonance and resulting emission of low-energy LMM-Auger electrons ( approximately 120 eV) but also the level of hydration plays an important role in the induction of complex damage in plasmid DNA.

Mechanisms of Strand Break Formation in DNA due to the Direct Effect of Ionizing Radiation: The Dependency of Free Base Release on the Length of Alternating CG Oligodeoxynucleotides

The question of how NA base sequence influences the yield of DNA strand breaks produced by the direct effect of ionizing radiation was investigated in a series of oligodeoxynucleotides of the form (d(CG)(n))(2) and (d(GC)(n))(2). The yields of free base release from X-irradiated DNA films containing 2.5 waters/nucleotide were measured by HPLC as a function of oligomer length. For (d(CG)(n))(2), the ratio of the Gua yield to Cyt yield, R, was relatively constant at 2.4-2.5 for n = 2-4 and it decreased to 1.2 as n increased from 5 to 10. When Gua was moved to the 5' end, for example going from d(CG)(5) to d(GC)(5), R dropped from 1.9 +/- 0.1 to 1.1 +/- 0.1. These effects are poorly described if the chemistry at the oligomer ends is assumed to be independent of the remainder of the oligomer. A mathematical model incorporating charge transfer through the base stack was derived to explain these effects. In addition, EPR was used to measure the yield of trapped-deoxyribose radicals at 4 K following X-irradiation at 4 K. The yield of free base release was substantially greater, by 50-100 nmol/J, than the yield of trapped-deoxyribose radicals. Therefore, a large fraction of free base release stems from a nonradical intermediate. For this intermediate, a deoxyribose carbocation formed by two one-electron oxidations is proposed. This reaction pathway requires that the hole (electron loss site) transfers through the base stack and, upon encountering a deoxyribose hole, oxidizes that site to form a deoxyribose carbocation. This reaction mechanism provides a consistent way of explaining both the absence of trapped radical intermediates and the unusual dependence of free base release on oligomer length.

LET dependence of the yield of DNA strand breaks and base lesions induced in fully hydrated plasmid DNA films by ion particles

LET dependence of the yield of DNA strand breaks and base lesions induced in fully hydrated plasmid DNA films by ion particles

Variation of strand break yield for plasmid DNA irradiated with high-Z metal nanoparticles.

Using agarose gel electrophoresis, we measured the effectiveness of high-Z metal particles of different sizes on SSB and DSB yields for plasmid DNA irradiated with 160 kVp X rays. For plasmid samples prepared in Tris-EDTA buffer, gold nanoparticles were shown to increase G'(SSB) typically by a factor of greater than 2 while G'(DSB) increased by a factor of less than 2. Similar dose-modifying effects were also observed using gold microspheres. Addition of 10(-1) M DMSO typically decreased damage yields by a factor of less than 0.5. Plasmid samples prepared in PBS showed significantly different damage yields compared to those prepared in Tris-EDTA (P < 0.001) with G'(SSB) and G'(DSB) increasing by factors of 100 and 48, respectively. Furthermore, addition of gold nanoparticles to samples prepared in PBS decreased G'(SSB) and G'(DSB) by factors of 0.2 and 0.3, respectively. The results show plasmid damage yields to be highly dependent on differences in particle size between the micro- and nanometer scale, atomic number (Z) of the particle, and scavenging capacity of preparation buffers. This study provides further evidence using a plasmid DNA model system for the potential of high-Z metal nanoparticles as local dose-modifying agents.

Induction of single strand breaks, and base lesions in plasmid DNA films induced by carbon, nitrogen, and oxygen KLL Auger process

Purpose: To reveal the reaction process in DNA by Auger electrons using the observed single strand breaks (SSB) and base lesions induced by monochromatic ultrasoft X-rays in dry plasmid DNA film. Desorbed ions from DNA and 2-deoxy-D-ribose thin films were also measured to ascertain the decomposition site in DNA.Materials and methods: Dry plasmid DNA (pUC18) films were irradiated with synchrotron monochromatic ultrasoft X-rays (USX). Two photon energies, 270, and 560 eV, were chosen for the irradiation experiments. Irradiated plasmid DNA was analyzed by agarose gel electrophoresis. The yield of base lesions was determined by the post-irradiation-treatment of the DNA with enzymatic probes (formamidpyrimidine DNA glycosylase [Fpg] and endonuclease III [Nth]). Desorbed ions induced by 540 eV USX irradiation from calf thymus DNA and 2-deoxy-D-ribose thin films were detected by quadrupole-mass spectrometer.Results: Yield of strand breaks and base lesions were obtained by 270 and 560 eV photon energies, respectively. Each yield showed characteristic of the photon energy spectrum. The characteristics of the desorbed ion mass spectra from 2-deoxy-D-ribose and DNA films were strikingly similar with each other.Conclusions: In this paper we report, for the first time, the yields of base lesions and SSB induced by monochromatic USX. The yield of SSB induced by core-ionization of carbon, nitrogen, and oxygen was two times more frequent than that of valence-electrons. From the comparison of desorbed ion mass spectra of 2-deoxy-D-ribose with DNA films we predict these breaks are likely to be induced by the decomposition of the sugar sites in DNA backbone.