Naphthalene diimide (1) carrying cysteines at the termini of amide substituents were synthesized to act as a molecular staple of double stranded DNA. Since 1 is able to bind to double stranded DNA with threading intercalation, the complex of 1 with double stranded DNA can be topologically immobilized on a gold surface through the SAu linkage as confirmed by cyclic voltammetric experiment. Ferrocenyl-double stranded 23-mertic oligonucleotide, dsFcODN, was immobilized on gold electrode with 1.0×1012 molecules cm−2 when electrode was treated with 2.0 µM dsFcODN and 4.0 µM 1 for 1 h at room temperature. The coverage density was similar to that obtained for the terminal thiol-modified oligonucleotide. Compound 1 was applied to detect the 321-meric PCR product of P. gingivalis, which is important in the diagnosis of periodontal disease. This experiment, coupled with the use of ferrocenylnaphthalene diimide, FND as electrochemical indicator for double stranded DNA, resulted in quantitative detection of PCR product within the range of 10 pg µL−1–10 ng µL−1 (15 nM–15 µM). The 1 and FND established a simple and rapid detection method of double stranded PCR product with a detection limit of 10 pg µL−1 (15 nM).