Water-soluble Naphthalene diimide (NDI) binds to the DNA duplex via threading intercalation mode. This has provided unique DNA analytical techniques, functional DNA polymers, and supramolecular polymers. Especially the ferrocene-containing NDIs, having electrochemically active sites, has been applied to an electrochemical gene detection system and also utilized in the precision analysis of genes and single nucleotide polymorphisms. Recently, NDI derivatives have been recognizing as potential candidate for anticancer therapeutics and for designing a unique cancer-detection system.