Two square-planar coordination compounds, namely [Cu(CPYA)Cl(2)] (1) and [Pd(CPYA)Cl(2)] (2), were prepared from the ligand 4-chloro-N-(pyridin-2-ylmethyl)aniline (CPYA) and two chloride salts, and were fully characterized, including by X-ray diffraction. Spectroscopic, electrophoretic and AFM studies revealed that the two isostructural compounds were interacting differently with DNA. In both cases, the initial interaction involves electrostatic contacts of the CPYA ligand in the minor groove (as suggested by molecular docking), but subsequent strong binding occurs with the palladium(II) complex 2, whereas the binding with the copper complex 1 is weaker and concentration dependent. The strong binding of 2 eventually leads to the cleavage of the double strand and the redox activity of 1 allows to oxidatively cleave the biomolecule.