Unveiling DNA Hybridization Dynamics via High-Sensitivity SERS Detection: Insights into Conformational Changes and Oligonucleotide Length Effects

This study demonstrates the highly sensitive detection of DNA hybridization using commercially available Surface-Enhanced Raman Spectroscopy (SERS) substrates. We functionalized the gold nanostructures with thiolated single-stranded adenine (polyA) DNA of various lengths (5–20 bases) and investigated their hybridization with complementary thymine (polyT) strands across different concentrations. DNA hybridization was confirmed by significant spectral changes in the adenine ring breathing mode at 735 cm^–1, highlighting its potential as a key marker for hybridization detection. Finite-difference time-domain (FDTD) simulations were used to visualize the distribution of the electromagnetic field at the gold surface. In parallel, principal component analysis (PCA) successfully identified spectral changes resulting from DNA hybridization. By combining experimental SERS measurements with computational modeling, we present a highly sensitive and specific method for monitoring DNA hybridization. These results support the development of advanced nucleic acid detection techniques and offer a reliable platform for investigating biomolecular interactions.