Synthetic lethality is a genetic concept in which cell death is induced by the combination of mutations in two sensitive genes, while mutation of either gene alone is not sufficient to affect cell survival. Synthetic lethality can be also achieved "chemically" by combination of drug-like molecules targeting distinct but cooperative pathways. Previously, we reported that the small molecule pyridostatin (PDS) stabilizes G-quadruplexes in cells and elicits a DNA damage response (DDR) by causing the formation of DNA double strand breaks (DSB). We hypothesize that cell death mediated by ligand-induced G-quadruplex stabilization could be potentiated in cells deficient in DNA damage repair genes. Here, we demonstrated that PDS acts synergistically both with NU7441, an inhibitor of the DNA-PK kinase crucial for non-homologous end joining (NHEJ) repair of DNA DSBs, and BRCA2-deficient cells that are genetically impaired in homologous recombination-mediated DSB repair (HR). G-quadruplex targeting ligands have potential as cancer therapeutic agents, acting synergistically with inhibition or mutation of the DNA damage repair machinery.