Modeling Studies on Dicentrics Induction After Sub-Micrometer Focused Ion Beam Grid Irradiation

Abstract

The biophysical simulation tool PARTRAC contains modules for DNA damage response representing non-homologous end joining of DNA double-strand breaks (DSB) and the formation of chromosomal aberrations. Individual DNA ends from the induced DSB are followed regarding both their enzymatic processing and spatial mobility, as is needed for chromosome aberrations to arise via ligating broken ends from different chromosomes. In particular, by tracking the genomic locations of the ligated fragments and the positions of centromeres, the induction of dicentrics can be modelled. In recent experiments, the impact of spatial clustering of DNA damage on dicentric yields has been assessed in AL human-hamster hybrid cells: Defined numbers of 20 MeV protons (linear energy transfer, LET 2.6 keV/µm), 45 MeV Li ions (60 keV/µm) and 55 MeV C ions (310 keV/µm) focused to sub-µm spot sizes were applied with the ion microbeam SNAKE in diverse grid modes, keeping the absorbed dose constant. The impact of the µm-scaled spatial distribution of DSB (focusing effect) has thus been separated from nm-scaled DSB complexity (LET effect). The data provide a unique benchmark for the model calculations. Model and parameter refinements are described that enabled the simulations to largely reproduce both the LET-dependence and the focusing effect as well as the usual biphasic rejoining kinetics. The predictive power of the refined model has been benchmarked against dicentric yields for photon irradiation.

In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead

“…Shielding masks such as metal collimators have 1 to 2 µm-wide parallel slots that allow only stripes of the cell nucleus surface to be irradiated [32]. Ion microbeams can focus the irradiation spot size to sub-micrometer levels, generating high local damage density for studying the recruitment of damage repair proteins [34,35]. Laser micro irradiation is also a module integrated in many confocal microscopes, allowing the instant detection of DNA repair, via live cell imaging, by using the same instrument both to irradiate and monitor cellular responses [36][37][38][39].…”

Monte Carlo Modeling of DNA Lesions and Chromosomal Aberrations Induced by Mixed Beams of Alpha Particles and X-Rays

“…Details of the physical, chemical, and biological modules that were used to model the level of chromosomal aberrations are described elsewhere [19,27]. The parameters of the CA model were taken from Friedland et al [28] but disregarding the special DNA structure of the hybrid cell type in that study. The DSB was considered when two DNA breaks were separated by no more than 10 bp.…”

“…The motion of DNA ends is modeled considering chromatin mobility within time scales of a few hours. For a model validation, the number of dicentrics per cell was calculated with PARTRAC and compared with published results [27,28].…”

Internal microdosimetry of alpha-emitting radionuclides

“…Black symbols and lines: PART RAC calculation (Friedland et al 2017) with 10 bp maximum distance of breaks on opposite strands; multiple DSB within 25 bp distance are not resolved and scored as isolated ones. Result for electrons taken from calculations for 60 Co gamma rays (Friedland et al 2019) and later extended to nucleosomes (Pomplun and Terrissol 1994), 30-nm fiber structures (Holley and Chatterjee 1996), chromatin fiber loops (Friedland et al 1998) and chromosomes (Friedland et al 1999) as higher-order DNA structures. Nowadays, a sophisticated description of many structural DNA levels inside the cell nucleus is available for many track structure codes (Friedland et al 2008;Nikjoo and Girard 2012;Meylan et al 2016;Li et al 2015).…”