<p>This research investigated the effects of DNA sequence on the single strand breaks (SSBs) and double strand breaks (DSBs) of DNA induced by Auger electron-emitting radionuclides in an atomic model of fibroblast cells using the Geant4-DNA toolkit. For this, two cells (C₁ and C₂) and their nuclei (N₁ and N₂), defined as homogeneous ellipsoids of liquid water of unit density, were considered. An atomic DNA model constructed in the Geant4-DNA toolkit was placed inside N₁ and N₂. While N₁ solely consisted of Cytosine-Guanine (C-G) sequences, N₂ contained a novel DNA sequence (damage-specific DNA-binding protein 2 (DDB2)), which has not been investigated to date. This sequence includes nucleotide motifs such as C-G, Adenine-Thymine (A-T), Guanine-Cytosine (G-C), and Thymine-Adenine (T-A). The total numbers of direct and indirect SSBs, DSBs, and hybrid DSBs (HDSBs), caused by five widely-used Auger electron-emitting radionuclides, including ^99mTc, ¹¹¹In, ¹²³I, ¹²⁵I, and ²⁰¹Tl were quantified at the cellular level. The results show that the total DNA damage, from greatest to least, corresponds to ²⁰¹Tl, ¹²⁵I, ¹²³I, ¹¹¹In, and ^99mTc. In addition, incorporating DDB2 base pairs (bp) into the DNA sequences increased the DNA damage by approximately 31% compared to the case with only C–G bp. The findings of the present study indicate that ²⁰¹Tl and ¹²⁵I, due to their higher decay yields of sub-1&#xa0;keV electron emissions (enabling highly localized energy deposition within the DNA strands), are more effective candidates for inducing DNA strand breaks in a single tumour cell compared to ¹²³I, ¹¹¹In, and ^99mTc.</p>