A DNA configuration switch was designed to fabricate a reversible and regenerable Raman-active substrate. The substrate is composed of an Au film and hairpin-shaped DNA strand (hot spot generation probes, HSGPs) labeled with dye-functionalized silver nanoparticle (AgNP). Another ssDNA that recognizes a specific trigger was used as an antenna. The HSGPs are immobilized on the Au film to draw the dye-functionalized AgNPs close to the Au surface and create an intense electromagnetic field. Hybridization of HSGP with the two arm segments of the antenna forms a triplex-stem structure to separate the dye-functionalized AgNP from the Au surface and cause a quenching of the Raman signal. Interaction with its trigger leads to release of the antenna from the triplex-stem structure, and the hairpin structure of the HSGP is restored, thereby creating an effective “off” to “on” state of the Raman signal. Nucleic acid sequence associated with the HIV-1 U5 long terminal repeat sequences and ATP are used as the triggers. The substrate shows excellent reversibility, reproducibility and controllability of SERS effects, which are significant requirements for practical SERS sensor applications.

Combining the specific recognization of MutS protein for mismatched DNA sequences with the target-driven molecular switch that acts as both the template and primer of the polymerization reaction, a new label-free and sensitive fluorescent assay strategy for specific single-stranded DNA sequences or SNPs is proposed.