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Non-thermal plasma has attracted strong interest in medicine and agriculture due to its ability to generate reactive oxygen and nitrogen species (RONS). These species can stimulate wound healing and seed germination, but at higher levels they induce DNA damage—useful in cancer therapy but harmful when healthy cells must be preserved. Direct study of DNA damage in cells is difficult because of repair processes and protective barriers. To address this, we applied a dual-model system combining plasmid DNA and human lymphocytes exposed to plasma from the RPS40 device. Using selective scavengers, we identified hydroxyl radicals, ozone, and reactive nitrogen species as key mediators of DNA strand breaks and structural changes. Our results support a mechanistic model in which long-lived plasma-derived species (NOx, ozone, acids) dissolve in water and subsequently generate short-lived radicals such as hydroxyl radicals and peroxynitrite. These reactive molecules then directly attack DNA. This integrated approach—linking plasmid and cellular assays with scavenger-based identification of RONS—offers a novel and cost-effective method for dissecting plasma–DNA interactions. The findings provide mechanistic insight into how plasma-activated water damages DNA, guiding the safer and more effective application of plasma technologies in biomedical and agricultural contexts.