Development of an Ultra-sensitive Detection Method for Genetically Modified Soybeans in Natto, a Traditional Japanese Fermented Food

Abstract

When extracting soybean DNA from natto, a traditional Japanese fermented food, Bacillus subtilis var. natto DNA is commonly present despite fastidious washing of samples. We confirmed that DNA extracted from B. subtilis var. natto inhibited PCR amplification of the soybean endogenous lectin gene (Le1) as well as the recombinant nopaline synthase terminator sequence (Nos-ter), which is used to identify genetically modified soybean (GMS) in natto. To mitigate B. subtilis var. natto DNA contamination, we developed a novel method for the specific extraction of Le1 and Nos-ter genes using DNA probes immobilized on streptavidin-coated magnetic beads with hybridization enhancement blockers, which are capable of enhancing the affinity between the target gene DNA and the probe DNA. By using the proposed extraction method, both Le1 and Nos-ter genes could be detected in samples containing B. subtilis var. natto DNA. DNA extraction from commercial nattos and identification of GMS were also successfully accomplished.