Label-Free Detection of Tetramolecular i-Motifs by Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) can probe DNA primary structure; however, the direct analysis of DNA secondary structure is still technically challenging. In this study, we developed a novel method based on introducing aluminum ion as the aggregation agent for silver nanoparticles, affording high-quality SERS signals of tetramolecular DNA. Thus, the formation of tetramolecular i-motifs was precisely analyzed by SERS signals for the first time and structural features involving glycosidic torsion, protonated cytosine, and cytosine rings were investigated. Moreover, the number of intercalated base pairs in i-motifs were quantified based on the relative intensities of the characteristic SERS bands. The proposed approach would have widespread applications in DNA analysis, especially for detecting various DNA secondary structures.