Classification and recognition of noncanonical DNA secondary structures by surface-enhanced Raman spectroscopy and...

The investigation of DNA secondary structures is of significance for understanding the function and regulation of nucleic acids. However, traditional techniques still face challenges in high-throughput, label-free analysis of DNA secondary structure diversity. Herein, principal component analysis (PCA) was used to optimize the substrate in surface-enhanced Raman spectroscopy (SERS) for the classification and recognition of noncanonical DNA secondary structures. In this assay, 3 kind of anions (Cl^-, Br^-, and I^-) were used to modify the surface of sliver nanoparticles and gold nanoparticles, and 12 kinds of cations were optimized as the aggregation regent. On the basis of the featured peaks corresponding to DNA secondary structures, I^- ions modified AgNPs with Ba²⁺ ions as aggregating agent (Ag IMNPs-Ba²⁺), and Br^- ions modified AuNPs with Ba²⁺ ions as aggregating agent (Au BrMNPs-Ba²⁺) were selected as optimal substrates. With these two optimal substrates, the parallel, hybrid, and antiparallel G4 structures with different numbers of G-quartets, iM with different numbers of C:CH⁺ base pairs, and antiparallel and parallel double-strand DNA, were unambiguously classified. In addition, the complex DNA secondary structures in a mixed solution were accurately identified. This study provides a universal platform for DNA secondary structure analysis, and is implicated for further large-scale screening of SERS substrates.