Sensitive and Label-Free SERS Detection of Single-Stranded DNA Assisted by Silver Nanoparticles and Gold-Coated Magnetic Nanoparticles

An efficient surface-enhanced Raman scattering (SERS) method combined with DNA ligation is demonstrated in this proof-of-concept study for the detection of the single-strand DNA associated with BRAF V600E mutation. Gold-coated magnetic nanoparticles with 6-mercaptopyridine-3-carboxylic acid (MPCA) as internal reference attached on the surface (MNP@SiO2@Au-MPCA) and silver nanoparticles with Raman reporter 4-mercaptobenzonic acid (4-MBA) on the surface (Ag@4-MBA) are used as the SERS substrates. Rationally designed DNA probes are conjugated to these two types of nanoparticles, respectively. The single-stranded DNA containing the BRAF V600E mutation is the target analyte, which would act as the substrate for MNP@SiO2@Au-MPCA and Ag@4-MBA to be linked together through ligation. After multiple cycles of DNA ligation, more Ag@4-MBA are brought to the surface of MNP@SiO2@Au-MPCA. The resulting nanoparticles are easily isolated by a magnet rapidly from the mixture and redispersed in aqueous solution for homogeneous SERS measurement. The detection sensitivity is improved by the enhancement of the SERS peaks of 4-MBA between the plasmonic nanoparticles, and the detection quantification is improved by the use of internal reference, MPCA, for signal normalization. The intensity ratio of 4-MBA/MPCA increases linearly in the 1–100 fmol range of the matched DNA (BRAF mutation). Different ratios of matched DNA in the background of a large number of the single-base mismatched DNA (BRAF normal) are used to mimic real samples, and the intensity ratios of 4-MBA/MPCA are linear in the 0.02–1% range of matched DNA/mismatched DNA. The high sensitivity and specificity of the method demonstrate its potential for clinical use.