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G-quadruplex DNAs (G4 DNAs) are emerging as promising anticancer drug targets due to their presence in the promoter regions of different oncogenes. Utilizing different spectroscopic techniques like UV–Vis absorption titration, thermal denaturation, spectrofluorimetric titration, fluorescence displacement assay, Job plot analysis, circular dichroism spectroscopy and also, molecular docking studies, the interaction of a synthetic nitro-flavone, 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO), with various G4 DNA structures (c-KIT1, c-KIT2, c-MYC, h-TELO and VEGF) was elucidated. We also investigated the effect of 4NCO on different cancer cell lines. Effect on cell morphology, DNA damage, cell cycle arrest, viability and mode of cell death were evaluated in A375 melanoma cells. Our findings indicated that 4NCO showed preferential binding towards c-MYC promoter G4 to stabilize it with a binding constant (Kb) value of the order of ~105 M−1 and binding stoichiometry of ~1:1. It also showed a unique dual binding mode when bound to c-MYC with a lower binding free energy having multiple strong interactions when compared to the other G4s. In cells, it induced DNA damage resulting in cell cycle arrest at G1/S phase until 24 h, after which, cells strictly underwent apoptosis. It also showed a preferential cytotoxicity towards the A375 melanoma cells. The ability of 4NCO to stabilize the c-MYC G4 to possibly suppress the over-expression of MYC was responsible for inhibition of proliferation of these cells. Hence, these results present a novel finding on the effectiveness of the nitro-flavone derivative 4NCO as a potent ligand for c-MYC G4 DNA thereby, providing possibilities of its use in cancer therapy for regulating the oncogene expression in cancer cells.