The SPR Sensor Detecting Cytosine−Cytosine Mismatches

Abstract

We have synthesized the first surface plasmon resonance (SPR) sensor that detects cytosine-cytosine (C[bond]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[bond]C mismatches regardless of the flanking sequences. The fully matched duplexes were not stabilized at all under the same conditions. The C[bond]T, C[bond]A, and T[bond]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[bond]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[bond]C mismatch at the concentration of 10 nM. SPR responses are proportional to the concentration of the C[bond]C mismatch in a range up to 200 nM. Aminonaphthyridine dimer could bind strongly to the C[bond]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[bond]C mismatch.

Recognition of Mismatched Base Pairs in DNA

“…Accordingly, we have used 8-azaquinolone as the recognition element for the adenine, 19,20 and protonated form of 2-amino-1,8-naphthyridine as the recognition element for the cytosine. 21 The mismatch binding ligands (MBLs) we have so far discovered are shown in Figure 5. In this article, we describe the inside story of MBLs about the discovery, identifying the function, and the application in genomic science.…”

“…After many trials for recognition elements, we eventually found that N-alkyl-2-amino-1,8-naphthyridine strongly and selectively bound to the cytosinecytosine mismatch. 21 The ligand we have developed for the recognition of the CC mismatch was the dimeric form of aminonaphthyridine (amND).…”

“…3437 Later, we realized that hairpin structures of trinucleotide repeat sequences (TRS) consisted of a number of mismatched base pairs, and play in fact important roles in the expansion and contraction of TRS eventually leading to the onset of neurological disorders. 21,29 Ligands selectively binding to the particular repeat sequence would be useful as a molecular tool for the deeper understanding of the biological function and may eventually led to therapeutics for diseases related to the repeats. Table 4.…”

“…The MBL we have developed is a key molecular element in developing innovative tools and devices for the detection of single nucleotide polymorphisms (SNPs) 13,19,21,33,59 and for the determination of the length of repeat sequences. 20,27 SNP is the single nucleotide difference of two DNA sequence and the origin of individual difference in phenotype.…”

Plasmonic circular resonators for refractive index sensors and filters

“…Due to the susceptibility of SPs to surrounding dielectric, SPs and surface plasmon resonance (SPR) exhibit excellent properties for sensing applications [11][12][13]. In past decades, various plasmonic sensors based on SPs and SPR have been proposed and investigated [14][15][16][17][18][19][20][21][22][23][24], especially prism-coupled SPR sensors [14][15][16][17] and fiber-coupled SPR sensors [20][21][22][23][24]. Generally, dimensions of prism-coupled SPR sensors are huge for integration of sensors on chips and their sensitivities are not high compared to fiber-coupled SPR sensor.…”