Detection of single nucleotide polymorphisms by the specific interaction between transition metal ions and mismatched base pairs in duplex DNA

Single nucleotide polymorphisms (SNPs) are base differences in the human genome. These differences are favorable markers for genetic factors including those associated with risks of complex diseases and individual responses to drugs. When two duplex DNAs with different types of SNPs are mixed and reannealed, the two novel heteroduplexes containing mismatched base pairs are formed in addition to the two initial perfectly matched homoduplexes. Heteroduplex analysis recognizing the newly formed mismatched base pairs is useful for SNP detection. Various strategies to detect the mismatched base pairs were devised due to the potential applications of SNPs. However, they were not always convenient and accurate. Here, we propose a novel strategy to detect the mismatched base pairs by the specific interaction between the Hg2+ ion and a T:T mismatched base pair and that between the Ag+ ion and a C:C mismatched base pair. UV melting indicated that the melting temperature of only the heteroduplexes with the T:T and C:C mismatched base pair specifically increased on adding the Hg2+ and Ag+ ion, respectively. Fluorescence resonance energy transfer analyses indicated that the intensity of fluorophore emission of only the fluorophore and quencher-labeled heteroduplexes with the T:T and C:C mismatched base pair specifically decreased on adding the Hg2+ and Ag+ ion, respectively. We propose that the addition of the metal ion could be a convenient and accurate strategy to detect the mismatched base pair in the heteroduplex. This novel strategy might make the heteroduplex analysis easy and eventually lead to better SNP detection.