Figure 2.

Detection and identification of single base pairs and mismatches in short synthetic DNA sequences. A four-component DNA microarray consisting of DNA probes (P_A, P_C, P_G and P_N) was used. The upper right inset depicts the array pattern. The ligation reaction was first performed in the presence of 10 pM target DNA (T) for 2 h at room temperature. The surface was then denatured with 8 M urea and rinsed with hybridization buffer. (a) An SPR difference image was obtained by subtracting images taken before and after the exposure of the ligated array to L^C-modified gold nanoparticles. SPR signal increase due to hybridization adsorption of the nanoparticles was observed only at the P_G array elements, where the probe sequence is perfectly matched to T. Non-specific adsorption was not observed either on the other probe array elements or on the PEG background. (b) A line profile taken from the SPR difference image in (a) for 10 pM target DNA. (c) A line profile taken from an SPR difference image obtained from a separate experiment using 1 pM T. The percent reflectivity scale is the same for both (b) and (c). The ligation reaction with 1 pM DNA was performed at a temperature of 45 °C.