Plasmonics-enhanced spikey nanorattle-based biosensor for direct SERS detection of mRNA cancer biomarkers

Abstract

We present a plasmonics-enhanced spikey nanorattle-based biosensor for direct surface-enhanced Raman scattering (SERS) detection of mRNA cancer biomarkers. Early detection of cancers such as head and neck squamous cell carcinoma (HNSCC) is critical for improving patient outcomes in regions with limited access to traditional diagnostic methods. Our method targets Keratin 14 (KRT14), a promising diagnostic mRNA biomarker for HNSCC, using a sandwich hybridization approach with magnetic beads and SERS spikey nanorattles (SpNR). We synthesized SpNR with a core-gap-shell structure to enhance SERS signals, achieving a limit of detection of 90 femtomolar. A pilot study using clinical samples demonstrated the efficacy of our biosensor in distinguishing between tissue with positive or negative diagnosis for HNSCC, highlighting its potential for rapid and sensitive cancer diagnostics in low-resource settings. This plasmonic assay offers a promising avenue for portable and high-specificity detection of nucleic acid biomarkers, with implications for early cancer detection and improved patient care, especially in middle and low-resource settings.

Keywords: Biomarker; Biosensor; Nanoparticles; Plasmonics; SERS; mRNA.

Fig. 1

SpNR synthesis workflow (A). Schematic of SpNR DNA plasmonic assay (B). Inset of assay mechanism where SpNR are functionalized with reporter probes and magnetic beads are functionalized with capture probes which hybridize to an mRNA target (C). DNA probe sequences and their melting temperature and delta G when hybridized with the target sequence (D).

Fig. 2

Scanning transmission electron microscopy – X ray diffraction (STEM-XRD) images of the Au@Ag Cages. The scale bar is 100 nm. SEM image (top left), Au only (top right), Ag only (bottom left), and Au/Ag overlay (bottom right).

Fig. 3

Schematic representation of NR and SpNR synthesis and example transmission electron microscopy (TEM) of both (A). UV-vis absorbance spectra of goldcages, NR, and SpNR (B). SERS comparison of NR and SpNR at 1357 cm⁻¹ peak (C).

Fig. 4

Calibration curves using synthetic DNA target for KRT14 after 2-hour incubation (A). Background subtracted spectra with target range blank to 100pM KRT14 (B). Kinetic study of Projected SERS intensity at 1357cm⁻¹ (C) and projected SERS spectra (D) for a range of incubation times 30 minutes to 2 hours. The inset shows and example of raw and background subtracted spectra. SERS spectra in (B, C) were offset for clarity.

Fig. 5

Projected SERS peak intensity from SpNR plasmonic assay for 4 clinical samples (A). Corresponding RT-PCR values for each clinical sample (B). Combined projected SERS peak intensities from all clinical samples, grouped by sample status N=5, 6 with non-paired t-test P value =0.0011 (C). Projected SERS spectra from each clinical sample (D). SERS spectra in (D) were offset for clarity.