SmtDNA: A Geant4-DNA user application for evaluating radiation-induced damage in supercoiled mitochondrial DNA

Abstract

Background: There is no geometrical nucleotide resolution model which can be used in numerical simulations of the interaction between radiation and supercoiled mt-DNA to perform realistic evaluations of DNA–free radical reactions.Objectives: A new geometrical model of mitochondrial DNA (mt-DNA) is developed in Geant 4-DNA to investigate the radiation-induced damage on mt-DNA. The presented application can be used to modify both geometrical parameters and structural elements, and to evaluate the damage induced on the mt-DNA molecule by ionizing particles.Methods: Our model covers the organisation of a supercoiled human mitochondrial genetic system. The current model includes all 16,659 base pairs of human mitochondrial DNA. This new mtDNA model has been preliminarily tested in this work by determining SSB and DSB DNA damage yields and site-hit probabilities due to the impact of proton particles.Results: Determination of single-strand (SSBs) and double-strand breaks (DSBs) is designed using the locations of all hit sites. Estimation of single-strand breaks and double strand breaks yielded similar results with the increment of incident particle LET. The output results contain the information about the energy transfers in the backbone region of DNA double helix.Conclusions: Considerations seem to be consistent with the corresponding experimental determinations. This application can be used for the investigation of radiation-induced damage to the mitochondrial genome and in any problems that require a supercoiled geometrical model. This work is going to be extended to circular conformation in a parallel project in the near future.