The peaks for a complex of DNA-interacting ligands naphthalene monoimide (NMI), naphthalene diimide (NDI) and ethidium bromide and groove binding ligand Hoechst 33258 with a duplex of oligonucleotide 5 ' -CCCCGGGG-3 ' were observed successfully in MALDI-TOF mass spectroscopy. The appearance of the peak of the complex depended on both the binding mode (classical intercalation, threading intercalation, or groove binding) and the duplex structure (fully matched or mismatched).