A DNA walker-driven SERS-fluorescent dual-mode aptasensor based on optimized aptamers to detect Shigella flexneri

In this study, a dual-mode SERS-fluorescent aptasensor based on a DNA walker was developed for Shigella flexneri (S. flexneri). Fe@SiO2@QDs were connected with H1 and the walking chain (hybrid strands of aptamer and cDNA) to fabricate fluorescent probes, and AgR6G@SiO2 were connected with H2 to fabricate SERS tags. Aptamer (Kd = 42.6 ± 3.16 nM) selective binding of S. flexneri, left the walking chain. The Zn2+-specific DNAzyme in the cDNA was exposed thus driving the DNA walker. The sequence on H1 containing BHQ3 was cleaved from fluorescent probes to restore the fluorescence. The remaining H1 sequence could bind to the H2 to generate Raman signals. The detection limit of the fluorescence signal was 11 CFU/mL, and the Raman signal was 3 CFU/mL. In addition, the aptasensor was successfully applied to the detection of actual samples with recovery ranges of 98.35–107.27% and 97.57–105.91% for the fluorescence and SERS methods, respectively.