The SPR Sensor Detecting Cytosine−Cytosine Mismatches

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Abstract
We have synthesized the first surface plasmon resonance (SPR) sensor that detects cytosine−cytosine (C−C) mismatches in duplex DNA by immobilizing aminonaphthyridine dimer 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 dimer could bind strongly to the C−C mismatches having 10 possible flanking sequences with association constants in the order of 106 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.