Computer Simulation of Short DNA Fragments Induced by High-LET Charged Particles

The formation of short DNA fragments, up to 3 kbp, induced in chromatin by nitrogen (LET 97 keV/μm) and iron (LET 190 keV/μm) ions was studied by computer simulation. Chromatin models with different structure parameters and Monte Carlo track structure simulation were used to assess the impact of chromatin fiber structure and LET on the DNA fragment size distribution. For the structures modeled (different types of solenoids, a chain of nucleosomes), the fragment size distribution had a maximum in the region of ~100 bp corresponding to the formation of DNA breaks in two neighboring turns of the helix on the nucleosome. For the solenoid type of chromatin, the calculation predicted the peak in the region around 1000 bp, corresponding to the formation of DNA breaks in two neighboring turns of the solenoid. Additionally, the assumption of the variety of chromatin structures under irradiation was studied. It allowed to explain the experimentally observed size distributions of the short DNA fragments induced by high-LET charged particles.