A novel vase-shaped molecular basket 1^3-, consisting of a deep nonpolar pocket of three napthalimide molecules fused to a bicyclic base, with polar glycine residues at the top was synthesized. Biocompatibility of the synthesized molecular basket was examined in vitro. The possible in vitro DNA protective potential of the newly synthesized deep-cavity basket 1^3- at several concentrations (25, 50, 100, 200, and 400 μg/mL) was investigated against hydroxyl and peroxyl radicals-induced DNA damage. Basket at lower concentrations (25, 50, 100 μg/mL) almost completely protected DNA against hydroxyl and peroxyl radicals induced DNA damage. It can be concluded that the newly synthesized molecular basket in the range of concentrations tested showed a significant DNA-protective potential against oxidative modifications of DNA caused by the harmful effects of free radicals.