A Robust Procedure for Removing Background Damage in Assays of Radiation-Induced DNA Fragment Distributions

Integration of Monte Carlo simulations with PFGE experimental data yields constant RBE of 2.3 for DNA double-strand break induction by nitrogen ions between 125 and 225 keV/μm LET

The number of small radiation-induced DNA fragments can be heavily underestimated when determined from measurements of DNA mass fractions by gel electrophoresis, leading to a consequent underestimation of the initial DNA damage induction. In this study we reanalyzed the experimental results for DNA fragmentation and DNA double-strand break (DSB) yields in human fibroblasts irradiated with γ rays and nitrogen ion beams with linear energy transfer (LET) equal to 80, 125, 175 and 225 keV/μm, originally measured by Höglund et al. (Radiat Res 155, 818-825, 2001 and Int J Radiat Biol 76, 539-547, 2000). In that study the authors converted the measured distributions of fragment masses into DNA fragment distributions using mid-range values of the measured fragment length intervals, in particular they assumed fragments with lengths in the interval of 0-48 kbp had the mid-range value of 24 kbp. However, our recent detailed simulations with the Monte Carlo code PARTRAC, while reasonably in agreement with the mass distributions, indicate significantly increased yields of very short fragments by high-LET radiation, so that the actual average fragment lengths, in the interval 0-48 kbp, 2.4 kbp for 225 keV/μm nitrogen ions were much shorter than the assumed mid-range value of 24 kbp. When the measured distributions of fragment masses are converted into fragment distributions using the average fragment lengths calculated by PARTRAC, significantly higher yields of DSB related to short fragments were obtained and resulted in a constant relative biological effectiveness (RBE) for DSB induction yield of 2.3 for nitrogen ions at 125-225 keV/μm LET. The previously reported downward trend of the RBE values over this LET range for DSB induction appears to be an artifact of an inadequate average fragment length in the smallest interval.

3D visualisation of the stochastic patterns of the radial dose in nano-volumes by a Monte Carlo simulation of HZE ion track structure

The description of energy deposition by high charge and energy (HZE) nuclei is of importance for space radiation risk assessment and due to their use in hadrontherapy. Such ions deposit a large fraction of their energy within the so-called core of the track and a smaller proportion in the penumbra (or track periphery). We study the stochastic patterns of the radial dependence of energy deposition using Monte Carlo track structure codes RITRACKS and RETRACKS, that were used to simulate HZE tracks and calculate energy deposition in voxels of 40 nm. The simulation of a (56)Fe(26+) ion of 1 GeV u(-1) revealed zones of high-energy deposition which maybe found as far as a few millimetres away from the track core in some simulations. The calculation also showed that ∼43 % of the energy was deposited in the penumbra. These 3D stochastic simulations combined with a visualisation interface are a powerful tool for biophysicists which may be used to study radiation-induced biological effects such as double strand breaks and oxidative damage and the subsequent cellular and tissue damage processing and signalling.

Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC

This review describes the PARTRAC suite of comprehensive Monte Carlo simulation tools for calculations of track structures of a variety of ionizing radiation qualities and their biological effects. A multi-scale target model characterizes essential structures of the whole genomic DNA within human fibroblasts and lymphocytes in atomic resolution. Calculation methods and essential results are recapitulated regarding the physical, physico-chemical and chemical stage of track structure development of radiation damage induction. Recent model extension towards DNA repair processes extends the time dimension by about 12 orders of magnitude and paves the way for superior predictions of radiation risks.

Distribution of DNA fragment sizes after irradiation with ions

Ionizing radiation is responsible for production of double-strand breaks (DSBs) in a DNA structure. In contrast to sparsely ionizing radiation, densely ionizing radiation produces DSBs that are non-randomly distributed along the DNA molecule and can form clusters of various size. The paper discusses minimalistic models that describe observable patterns of fragment length in DNA segments irradiated with heavy ions and applies the formalism to interpret the recent experimental data collected by use of atomic force microscope (AFM).