Precise Methylation Detection of Tumor Suppressor Gene Promoters by Magnetic Enrichment and Nano Silver Adduct–Promoted Surface‐Enhanced Raman Scattering

Noninvasive liquid biopsies can be used for early tumor diagnosis by identifying the methylation level of the tumor suppressor genes (TSGs)-a reliable index for cancer evaluation. However, identifying trace circulating genes from specimens remains challenging. This work introduces a novel method that combines magnetic isolation and surface-enhanced Raman scattering (SERS) to concentrate and detect the methylated TSG promotors. A superparamagnetic iron oxide nanoparticle modified with streptavidin is prepared as a universal magnetic bead. Biotin-terminated probe single-strand DNA (ssDNA) is immobilized on the magnetic beads through biotin-streptavidin bioconjugation. Artificial target ssDNA fragments with various methylation levels are applied as a promoter gene model. Concentrated double-strand DNA (dsDNA) is produced by a hybridizing probe and target ssDNA on magnetic nanobeads, as well as an additional magnetic isolation process. The well-prepared DNA adduct, which consists of 3 nm cisplatin-modified Ag nanoclusters, can specifically bind with guanine-cytosine base pairs of dsDNA. Ag-nanoparticle-induced localized SERS amplified signals of 5-methylcytosine (5-mC) from the dsDNA in Raman spectra, enabling accurate methylation level measurement in mixtures of 0-1 µm methylated DNA, with a detection limit of 0.05 µm. This method shows promise for enabling the methylation level evaluation of various TSGs and promoters in early cancer liquid biopsies.