Development of an aptamer-based Surface-Enhanced Raman Spectroscopy (SERS) sensor for quantitative analysis of fluoride

Abstract

Fluoride ions are critical in water quality management. While trace amounts support dental and skeletal health, excessive intake can cause dental and skeletal fluorosis, and low intake increases the risk of dental decay. Given fluoride’s health and industrial significance, detecting trace levels of fluoride is essential for ensuring both health safety and product quality. Accurate detection of trace levels remains challenging due to limitations, such as low sensitivity and interference from common ions. Therefore, there is an increasing demand for a highly sensitive and selective method for quantifying very low levels of fluoride. This study presents a cell-free aptamer-based biosensor using Surface-Enhanced Raman Spectroscopy (SERS) for quantifying fluoride concentrations in the picomolar to nanomolar range. The sensor utilises a derivative of the fluoride-responsive riboswitch (FRS) aptamer domain from Bacillus cereus as the fluoride recognition element. The FRS aptamer is immobilised on a silver nanoparticle (AgNP), which serves as the SERS substrate, with glutathione acting as a capping agent and methylene blue as the reporter molecule. Mg2+ ions were employed to facilitate structural folding of the aptamer, enabling its specific binding to fluoride. Using carbodiimide chemistry (EDC/NHS), the aptamer was covalently attached to silver nanoparticles (AgNPs), with glutathione (GSH) serving as a capping agent to facilitate stable conjugation. The working model for fluoride detection relies on the conformational changes in the aptamer triggered by anion binding, which brings methylene blue closer to the silver nanoparticle surface. This proximity enhances the SERS signal at the characteristic 1623 cm-1 Raman band. The parameters for the fluoride detection assay were optimised, with methylene blue (3 ppm), glutathione (10-7 M), and aptamer (30nM), ensuring efficient surface coverage without compromising signal amplification. Calibration experiments conducted with fluoride concentrations ranging from 5 × 10-12M to 1×10-9M showed a strong linear relationship (R2 = 0.96) for fluoride. This sensor offers a promising platform for accurate, trace-level fluoride detection, making it suitable for environmental monitoring, industrial, and healthcare applications.