Circular Mitochondrial DNA: A Geant4‑DNA User Application for Evaluating Radiation‑induced Damage in Circular Mitochondrial DNA

Mohammad Bagher Tavakoli, Habiballah Moradi, Hossein Khanahmad, Mohsen Hosseini

DOI: 10.4103/jmss.JMSS_23_17

Abstract


The aim of this study was to develop a nucleotide geometrical model of the circular mitochondrial
DNA (mt‑DNA) structure using Geant4‑DNA toolkit to predict the radiation‑induced damages such
as single‑strand breaks (SSB), double‑strand breaks (DSB), and some other physical parameters. Our
model covers the organization of a circular human mt genetic system. The current model includes all
16,659 base pairs of human mt‑DNA. This new mt‑DNA 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. The accuracy of the geometry was determined by three‑dimensional visualization
in various ring element numbers. The hit locations were determined with respect to a reference
coordinate system, and the corresponding base pairs were stored in the ROOT output fle. The
coordinate determination according to the algorithm was consistent with the expected results. The
output results contain the information about the energy transfers in the backbone region of the DNA
double helix. The output fle was analyzed by root analyzing tools. Estimation of SSBs and DSBs
yielded similar results with the increment of incident particle linear energy transfer. In addition, these
values seem to be consistent with the corresponding experimental determinations. This model can
be used in numerical simulations of mt‑DNA radiation interactions to perform realistic evaluations
of DNA‑free radical reactions. This work will be extended to supercoiled conformation in the near
future.

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