Comparative study of fluorescence and surface-enhanced Raman scattering with magnetic microparticle-based assay for target bacterial DNA detection

Abstract

Magnetic microparticles (MMPs) have been extensively utilized in various assays as protein biomarkers or nucleic acid targets using a magnetic field owing to the diverse surface chemistry and ease of separation. In this study, we designed a simple MMP-based assay for target bacterial DNA with two different optical signals: fluorescence and Raman scattering. The sensitivity and multiplexing capability of both the signals were rigorously compared under optimized assay conditions. The MMP-based assay enabled the detection of multiple target bacterial DNAs with high reliability, sensitivity, and multiplexing capability, as demonstrated by the designed target DNA sequences from Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus. The surface-enhanced Raman scattering (SERS)-based detection of the Escherichia coli genome DNA exhibited better sensitivity (similar to 30 fM) than that of the fluorescence method. Hence, the MMP-based assay in this scheme is a promising method of detecting bacteria. Further, the results of the systematic comparison between fluorescence and surface-enhanced Raman scattering will be beneficial for future designs of assay protocols with optical signals.