This study investigates the genotoxicity of mercaptoacetic acid-coated CdSe-core quantum dots (MAA-QDs) and identifies the cadmium-mercaptoacetic acid (Cd-MAA) complex as a key contributor to DNA damage. The research used a plasmid-based transformation assay to evaluate the effects of MAA-QDs on DNA structure and biological activity. Incubation of DNA with varying concentrations of MAA-QDs caused significant changes in DNA configuration, including the conversion of covalently closed circular (CCC) DNA to open circular (OC) DNA, and a decrease in plasmid DNA transformation activity. These changes were concentration-dependent, indicating that MAA-QDs can damage DNA structure and biological function. Electrospray ionization mass spectrometry (ESI-MS) data suggested that the observed genotoxicity may be linked to the Cd-MAA complex formed in the solution of MAA-QDs. Circular dichroism (CD) and transformation assays indicated that the Cd-MAA complex interacts with DNA through groove-binding mode and preferentially binds to DNA fragments with high adenine and thymine content. The study also demonstrated that the plasmid transformation assay is an effective method for evaluating the genotoxicity of nanoparticles. The results suggest that the Cd-MAA complex formed in the solution of MAA-QDs has an innate tendency to damage plasmids with high AT content or AT-rich regions through a groove-binding mode, thereby affecting DNA biological activity. The study highlights the importance of understanding the genotoxic effects of quantum dots and provides a quantitative method for evaluating their toxicity. The findings also emphasize the need to consider the potential toxicity of quantum dots in biological applications and suggest strategies to minimize their genotoxicity, such as storing them uncoated and using sulfur compound coatings when necessary.This study investigates the genotoxicity of mercaptoacetic acid-coated CdSe-core quantum dots (MAA-QDs) and identifies the cadmium-mercaptoacetic acid (Cd-MAA) complex as a key contributor to DNA damage. The research used a plasmid-based transformation assay to evaluate the effects of MAA-QDs on DNA structure and biological activity. Incubation of DNA with varying concentrations of MAA-QDs caused significant changes in DNA configuration, including the conversion of covalently closed circular (CCC) DNA to open circular (OC) DNA, and a decrease in plasmid DNA transformation activity. These changes were concentration-dependent, indicating that MAA-QDs can damage DNA structure and biological function. Electrospray ionization mass spectrometry (ESI-MS) data suggested that the observed genotoxicity may be linked to the Cd-MAA complex formed in the solution of MAA-QDs. Circular dichroism (CD) and transformation assays indicated that the Cd-MAA complex interacts with DNA through groove-binding mode and preferentially binds to DNA fragments with high adenine and thymine content. The study also demonstrated that the plasmid transformation assay is an effective method for evaluating the genotoxicity of nanoparticles. The results suggest that the Cd-MAA complex formed in the solution of MAA-QDs has an innate tendency to damage plasmids with high AT content or AT-rich regions through a groove-binding mode, thereby affecting DNA biological activity. The study highlights the importance of understanding the genotoxic effects of quantum dots and provides a quantitative method for evaluating their toxicity. The findings also emphasize the need to consider the potential toxicity of quantum dots in biological applications and suggest strategies to minimize their genotoxicity, such as storing them uncoated and using sulfur compound coatings when necessary.