We have synthesized the first surface plasmon resonance (SPIR) sensor that detects cytosine-cytosine (C-C) mismatches in duplex DNA by immobilizing aminonaphthyridine dinner on the gold surface. The ligand consisting of two 2-aminonaphthyridine chromophores and an alkyl linker connecting them strongly stabilized the C-C mismatches regardless of the flanking sequences. The fully matched duplexes were not stabilized at all under the same conditions. The C-T, C-A, and T-T mismatches were also stabilized with a reduced efficiency. SPR analyses of mismatch-containing 27-mer duplexes were performed with the sensor surface on which the aminonaphthyridine dimer was immobilized. The response for the C-C mismatch in 5'-GCC-3/3'-CCG-5' was about 83 times stronger than that obtained for the fully matched duplex. The sensor successfully detects the C-C mismatch at the concentration of 10 nM. SPR responses are proportional to the concentration of the C-C mismatch in a range up to 200 nM. Aminonaphthyridine dinner could bind strongly to the C-C mismatches having 10 possible flanking sequences with association constants in the order of 10(6) M-1. The facile protonation of 2-aminonaphthyridine chromophore at pH 7 producing the hydrogen-bonding surface complementary to that of cytosine was most likely due to the remarkably high selectivity of 1 to the C-C mismatch.