The specific interactions of Cu2+ with self-complementary DNA sequences involving d[G(4)C(4)(GC)(2)G(4)C(4)], d[(GC)(10)], and d[(AT)(10)], as well as the chiral recognition mechanism of ofloxacin enantiomers via the Cu-II-modulated DNAs, were investigated using characterizations of circular dichroism, gel electrophoresis, FT-IR spectroscopy, UV melting measurement, electron paramagnetic resonance, and HPLC. The Cull-coordinated GC-rich DNAs exhibit amplified enantioselectivity toward the S-enantiomer of ofloxacin. Especially in the case of d[G(4)C(4)(GC)(2)G(4)C(4)], ofloxacin enantiomers intercalate into the two adjacent guanine bases through the minor groove mediated by Cu2+, which leads to a more favorable binding between S-ofloxacin and DNA. The highest ee value of ofloxacin enantiomers in the permeate after being adsorbed by the Cu-II-DNA complex is obtained as 49.2% in the R-enantiomer at the [Cu2+]/[base] molar ratio of 0.25, while at the [Cu2+]/[base] molar ratio of 0.05 the highest ee value of ofloxacin enantiomers in the retentate reaches 26.3% in the S-enantiomer. This work illustrates a novel promising route to construct DNA-based chiral selectors toward certain drug enantiomers through the programmable enantioselective recognition on the basis of DNA chirality and the specific binding of transition metal ions.