(90a) Terminus-Dependent Phenomenon of DNA-Functionalized Nanoparticles for Microchip DNA Sensing

For the detection of DNA single-base substitutions, gold nanoparticles (GNPs) has been attracting considerable interests, because GNP aggregation accompanied by the surface plasmon shift can be clearly recognized with the naked eye. The method is in general a sandwich assay in which a target DNA molecule cross-links two DNA-functionalized GNPs by hybridization. In contrast, we recently discovered that GNPs also aggregate with a non-cross-linking (NCL) manner; formation of fully complementary duplexes on GNP surfaces induces the aggregation at relatively high salt concentration. Interestingly, the NCL aggregation exhibits extraordinary selectivity against terminal mismatches; single-base mismatches at the free ends of the duplexes make very stable dispersions (e.g., no aggregation). Unlike conventional hybridization-based assays, this system can detect the terminal mismatches without precise temperature control. Because of this surprising selectivity for terminal mismatches, rapid and reliable SNPs typing after single-base primer extension is possible without time-consuming analysis such as mass spectrometry. NCL interaction between fully-matched DNA duplex on GNPs (FM-Au) and duplex on a gold substrate was studied using SPR imaging. A significant increase in intensity was observed where the substrate-anchored DNA probe hybridized with its fully-matched target showing a blunt end. In contrast, no change in intensity was observed with the one-base mismatched target. The FM-Au specifically discriminates the terminal base-pairing at the sensor surface.