Charged particle radiation can, directly and indirectly, affect cells by breaking DNA strands. This effect includes DNA single-strand breaks (SSB) and DNA double-strand breaks (DSB), which may cause cell death and mitotic failure. Thus, using short-range charged particles such as Auger electrons (AEs) not only leads to the destruction of the target cell but also prevents the nearby healthy cells from exposing to ionizing radiation. In this study, two spherical cells (C and C
2
) and their cell nucleus, both made of liquid water, were modeled. An atomic DNA model constructed in the Geant4-DNA Monte Carlo (MC) simulation toolkit was placed inside the nucleus of the C and C
2
cells. The number of direct and indirect SSB, DSB, and hybrid DSB (HDSB), caused by some of the most widely-used Auger electron-emitting (AEE) radionuclides, including
99m
Tc,
111
In,
123
I,
125
I, and
201
Tl, distributed within different compartments of the C cell, was calculated in the C and C
2
cells, considering the distance between the surface of the two cells ranges from 0 to 5 μm. The present work aimed to investigate the biological effects of AEE radionuclides and their potential for cancer treatment through targeted radiation therapy. The results indicate the impact of
201
Tl >
125
I >
123
I >
111
In >
99m
Tc on DNA damage when the target is C (first spherical cell). On the other hand, for C
2
at distances of 0 to 5 μm, the impact of
99m
Tc >
123
I >
111
In >
201
Tl >
125
I on DNA damage is observed.