Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

PURPOSE: To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. METHODS: Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. RESULTS: When mediated by a DSB repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose-responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear quadratic model. CONCLUSIONS: Using a minimal number of assumptions, the kinetics and dose response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.     

Simulation of 125I-based radioprobing experiments to study DNA quadruplex structure and topology

Purpose: Certain guanine-rich DNA sequences have the capacity to fold into four-stranded structures stabilized by the stacking of square planar arrangements of four hydrogen-bonded guanine bases. However both the overall topology of folding and the more detailed three dimensional structure of these quadruplexes is difficult to determine or predict, and they can be polymorphic, altering radically depending on environmental conditions. Radioprobing experiments, in which Auger electrons emitted during the decay of a ¹²⁵I-containing base induce strand cleavage in a distance- and structure-dependent manner, have provided possible means of determining these details. Here we have used a combination of computer simulation methods to study the information obtained by one such experiment, reported in 2004.

Method: Models were constructed of three quadruplex topologies considered in the experiment, and one other topology proposed more recently. Molecular Dynamics simulations were used to equilibrate these structures and monitor how they evolved over several nanoseconds in solution. Snapshots from the trajectories were then subjected to Monte Carlo track structure prediction, from which theoretical cleavage patterns have been extracted.

Results: The four topologies were found to yield quite different cleavage patterns, which allow the presence of particular conformations in an experiment to be predicted.

Conclusion: Radioprobing, which is usable in biologically relevant environments, is sensitive enough to distinguish with some confidence between alternative folding topologies in a DNA structure. Monte Carlo track structure simulation can reinforce or question conclusions drawn from experiment, and Molecular Dynamics used with various restraints provides a practical means of guiding a model towards one that yields cleavage patterns closer to those found experimentally.     

Kinetics of DSB rejoining and formation of simple chromosome exchange aberrations

Purpose : To investigate the role of kinetics in the processing of DNA double strand breaks (DSB), and the formation of simple chromosome exchange aberrations following X-ray exposures to mammalian cells based on an enzymatic approach. Methods : Using computer simulations based on a biochemical approach, rate-equations that describe the processing of DSB through the formation of a DNA-enzyme complex were formulated. A second model that allows for competition between two processing pathways was also formulated. The formation of simple exchange aberrations was modelled as misrepair during the recombination of single DSB with undamaged DNA. Non-linear coupled differential equations corresponding to biochemical pathways were solved numerically by fitting to experimental data. Results : When mediated by a DSB-repair enzyme complex, the processing of single DSB showed a complex behaviour that gives the appearance of fast and slow components of rejoining. This is due to the time-delay caused by the action time of enzymes in biomolecular reactions. It is shown that the kinetic- and dose- responses of simple chromosome exchange aberrations are well described by a recombination model of DSB interacting with undamaged DNA when aberration formation increases with linear dose-dependence. Competition between two or more recombination processes is shown to lead to the formation of simple exchange aberrations with a dose-dependence similar to that of a linear-quadratic model. Conclusions : Using a minimal number of assumptions, the kinetics and dose-response observed experimentally for DSB rejoining and the formation of simple chromosome exchange aberrations are shown to be consistent with kinetic models based on enzymatic reaction approaches. A non-linear dose-response for simple exchange aberrations is possible in a model of recombination of DNA containing a DSB with undamaged DNA when two or more pathways compete for DSB repair.     

Calculated DNA damage from gadolinium Auger electrons and relation to dose distributions in a head phantom

PURPOSE: To calculate the number of 157Gadolinium (157Gd) neutron capture induced DNA double strand breaks (DSB) in tumor cells resulting from epithermal neutron irradiation of a human head when the peak tissue dose is 10 Gy. To assess the lethality of these Gd induced DSB. MATRIALS AND METHODS: DNA single and double strand breaks from Auger electrons emitted during 157Gd(n,gamma) events were calculated using an atomistic model of B-DNA with higher-order structure. When combined with gadolinium neutron capture reaction rates and neutron and photon physical dose rates calculated from the radiation transport through a model of the human head with explicit tumors, peak tissue dose can be related to the number of Auger electron induced DSB in tumor cell DNA. The lethality of these DNA DSB were assessed through a comparison with incorporated 125I decay cell survival curves and second comparison with the number of DSB resulting from neutron and photon interactions. RESULTS: These calculations on a molecular scale (microscopic calculations) indicate that for incorporated 157Gd, each neutron capture reaction results in an average of 1.56 +/- 0.16 DNA single strand breaks (SSB) and 0.21 +/- 0.04 DBS in the immediate vicinity (approximately 40 nm) of the neutron capture. In an example case of Gd Neutron Capture Therapy (GdNCT), a 1 cm radius midline tumor, peak normal tissue dose of 10 Gy, and a tumor concentration of 1000 ppm Gd, result in a maximum of 140 +/- 27 DSBs per tumor cell. CONCLUSIONS: The number of DSB from the background radiation components is one order of magnitude lower than the Gd Auger electron induced DSB. The cell survival of mammalian cell lines with a similar amount of complex DSB induced from incorporated 125I decay yield one to two magnitudes of cell killing. These two points indicate that gadolinium auger electrons could significantly contribute to cell killing in GdNCT.     

Elastic scattering cross section models used for Monte Carlo simulation of electron tracks in media of biological and medical interest

PURPOSE: Elastic scattering is important for the spatial distribution of electrons penetrating matter, and thus for the distribution of deposited energy and DNA damage. Scattering media of interest are in particular liquid and gaseous water and gaseous nitrogen. The former are used as surrogates for tissue and cell environments (since more than 70% of the cell consists of water), while cross section data for nitrogen have been scaled and used as input in Monte Carlo (MC) codes simulating scattering in biologically relevant media. A short review is given of electron elastic scattering cross section models used in a biological and medical context and their experimental and theoretical background. CONCLUSIONS: Adequate theories and models exist for calculating elastic electron scattering in gaseous nitrogen and gaseous water (i.e., by free molecules) down to electron energies well below 100 eV. However, elastic electron scattering in liquid water at such low energies is apparently uncertain and not well understood. Further studies in the case of liquid water are thus motivated due to its biological importance.     

Track structure analysis illustrating the prominent role of low-energy electrons in radiobiological effects of low-LET radiations

Monte Carlo track structure methods have been used to illustrate the importance of low-energy electrons produced by low-LET radiations. It is shown that these low-energy secondary electrons contribute substantially to the dose in all low-LET irradiations and are particularly efficient at producing highly localized clusters of atomic damage which may be responsible for a major part of the biological effectiveness of low-LET radiations. The data generated by Monte Carlo track structure techniques and by earlier semi-analytical methods based on the LET concept have been compared in terms of cumulative and differential fractions of total dose absorbed as a function of electron energy. The data show that low-energy secondary electrons account for up to nearly 50% of the total dose imparted to a medium when irradiated with electrons or photons.     

Energy deposition in small cylindrical targets by ultrasoft x-rays

A Monte Carlo technique has been employed to calculate the energy deposition events in small cylindrical targets (less than or equal to 100 nm), including sizes which represent the DNA duplex, nucleosome and chromatin fibre, by simulated electron tracks from C (278 eV), A1 (1487 eV) and Ti (4509 eV) characteristic ultrasoft x-rays in water. Detailed examples of input data tables for the generation of electron tracks produced from the x-ray photon interactions are presented. Frequencies of energy deposition events per gray for target sizes from 1 to 100 nm are given and comparisons have been made with radiations of different qualities.     

Monte Carlo simulation of water radiolysis for low-energy charged particles

The paper describes the development of chemical modules simulating the prechemical and chemical stages of charged particle tracks in pure liquid water. These calculations are based on our physical track structure codes for electrons and ions (KURBUC, LEPHIST and LEAHIST) which provide the initial spatial distribution of H2O+, H2O* and subexcitation electrons at approximately 10(-15) s. We considered 11 species and 26 chemical reactions. A step-by-step Monte Carlo approach was adopted for the chemical stage between 10(-12) s and 10(-6) s. The chemistry codes enabled to simulate the non-homogeneous chemistry that pertains to electron, proton and alpha-particle tracks of various linear energy transfers (LET). Time-dependent yields of chemical species produced by electrons and ions of different energies were calculated. The calculated primary yields (G values at 10(-6) s) of 2.80 for OH and 2.59 for e(aq)- for 1 MeV electrons are in good agreement with the published values. The calculated G values at 10(-6) s for a wide range LETs from of 0.2 to 235 keV microm(-1) were obtained. The calculations show the LET dependence for OH and H2O2. The electron penetration ranges were calculated in order to discuss the role of low energy electrons.     

A Monte Carlo study of absorbed dose distributions in both the vapor and liquid phases of water by intermediate energy electrons based on different condensed-history transport schemes

Monte Carlo transport calculations of dose point kernels (DPKs) and depth dose profiles (DDPs) in both the vapor and liquid phases of water are presented for electrons with initial energy between 10 keV and 1 MeV. The results are obtained by the MC4 code using three different implementations of the condensed-history technique for inelastic collisions, namely the continuous slowing down approximation, the mixed-simulation with delta-ray transport and the addition of straggling distributions for soft collisions derived from accurate relativistic Born cross sections. In all schemes, elastic collisions are simulated individually based on single-scattering cross sections. Electron transport below 10 keV is performed in an event-by-event mode. Differences on inelastic interactions between the vapor and liquid phase are treated explicitly using our recently developed dielectric response function which is supplemented by relativistic corrections and the transverse contribution. On the whole, the interaction coefficients used agree to better than approximately 5% with NIST/ICRU values. It is shown that condensed phase effects in both DPKs and DDPs practically vanish above 100 keV. The effect of delta-rays, although decreases with energy, is sizeable leading to more diffused distributions, especially for DPKs. The addition of straggling for soft collisions is practically inconsequential above a few hundred keV. An extensive benchmarking with other condensed-history codes is provided.     

WormBot,an open-source robotics platform for survival and behavior analysis in C. elegans

GeroScience - Caenorhabditis elegans is a popular organism for aging research owing to its highly conserved molecular pathways, short lifespan, small size, and extensive genetic and reverse genetic...