Application for the fluorescent detection of single nucleotide difference using cytosine bulge hairpin primers

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PCR primer having a cytosine-bulge site at the end of 5' was designed, and using fluorescence molecule, we investigated a novel method of SNP typing. This fluorescence molecule did not inhibit on the PCR, and the hairpin unit was extended in the PCR. The fluorescence molecule binding specifically to C-bulge unit could bind to the PCR-hairpin- primer, however, after PCR, it could bind to the hairpin primer because of disappearance of C-bulge unit. The measurement of fluorescence intensity showed the PCR products, which showed this novel method could be used for the SNP typing.