Purpose
This study aims to standardize the simulation procedure in measuring DNA double-strand breaks (DSBs), by using advanced Monte Carlo toolkits, and newly introduced experimental methods for DNA DSB measurement.

Methods
For the experimental quantification of DNA DSB, an innovative DNA dosimeter was used to produce experimental data. GATE in combination with Geant4-DNA toolkit were exploited to simulate the experimental environment. The PDB4DNA example of Geant4-DNA was upgraded and investigated. Parameters of the simulation such energy threshold (ET) for a strand break and base pair threshold (BPT) for a DSB were evaluated, depending on the dose.

Results
Simulations resulted to minimum differentiation in comparison to experimental data for ET = 19 ± 1 eV and BPT = 10 bp, and high differentiation for ET<17.5 eV or ET>22.5 eV and BPT = 10 bp. There was also small differentiation for ET = 17.5 eV and BPT = 6 bp. Uncertainty has been kept lower than 3%.

Conclusions
This study includes first results on the quantification of DNA double-strand breaks. The energy spectrum of a LINAC was simulated and used for the first time to irradiate DNA molecules. Simulation outcome was validated on experimental data that were produced by a prototype DNA dosimeter.

The investigation of biological effects in living tissues requires the modeling of physical, chemical, and physico-chemical interactions. Strong effort has been given in the 3D modeling of DNA structure, such as to describe the cell nucleus. In 2015, a new application, Geant4-DNA was presented, enabling the atomic level description of DNA molecules and the possibility of evaluating the direct damage induced on the DNA molecule by ionizing radiation [1]. Recently, a DNA Double-Strand Break (DSB) dosimeter was developed for the detection and quantification of DNA-DSBs after irradiation[2]. Our goal is to validate the simulated data, and standardize the experimental procedure for measuring the biological damage.

In the present study, we investigated the PDB4DNA tool and developed a new G4-DNA class for the quantification of DSBs after irradiation. Experimental measures were used for testing the G4-DNA classes. A DNA molecule (1329bp, the largest in PDBlib) was irradiated with 3 different absorbed doses equal to 10, 25 and 50Gy. In our simulation study, we used a structure of a single DNA molecule (based on experimental data), and irradiated it multiple times to quantify the probability of DSBs.

The simulations, on G4-DNA DSB quantification, resulted in DSB probabilities equal to 9.0%, 17.0%, and 31% for doses 10Gy, 25Gy, and 50Gy respectively. Thus, the statistical difference between experimental and simulated DSBs was calculated to 8.09%, 9.23%, and 13.43% accordingly. Comparing our simulations with the standard used PDB4DNA class, differences varied from 40–70%.

This is a preliminary study for the modeling, and the quantification of DNA-DSBs based on experimental data. The limitations of this study need to be addressed, such as the modeling of multiple DNA molecules for accurate statistical simulations, and chemical reactions need to be taken into account for the total quantification of the biological damage on DNA structures.