We have developed a novel and rapid SNP (single nucleotide polymorphism) detection system named SMAP version 2 (SMAP 2). SMAP 2 (SMart Amplification Process) is isothermal and achieved high levels of amplification within 30 minutes when performed with a new DNA polymerase cloned from Alicyclobacillus acidocaldarius (Aac). In SMAP 2, DNA amplification only occurred with a perfect primer match; hence, amplification alone was sufficient to identify the target allele. In establishing SMAP 2, two unique approaches were employed for suppression of exponential background DNA amplification. A mismatch binding protein Thermus aquaticus MutS (Taq MutS), was added to the reaction solution to inhibit background DNA from entering the amplification cycle by specifically binding to mis-primed amplification products. And, an asymmetrical primer design using a combination of turn-back and folding primers was employed to minimize alternative mis-amplification pathways. Furthermore, to assist the scientific community in configuring SMAP assays, we developed a software specific for SMAP primer design. With these new tools, a high precision and rapid DNA amplification technology becomes available for applications in pharmacogenomics and molecular diagnostics.
Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
K.K. Dnaform, 75-1, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, JAPAN
Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
