The aim of this study is to develop new recognition molecules for the DNA higher-ordered structure on the basis of new concept of DNA recognition mode. In order to bind two remote binding sites of DNA at the same time, we designed the new bidentate ligands that have two Hoechst 33258 units connected by a spacer. DNA binding affinity of the ligands was evaluated by measuring SPR (surface plasmon resonance). As a result, we have achieved discrimination of the length of two remote binding region of a DNA duplex.