Base-Pair Contents and Sequences of DNA Double Helices Differentiated by Surface-Enhanced Raman Spectroscopy

Direct, label-free sequence analysis of DNA hybridization has been achieved by surface-enhanced Raman spectroscopy. In this work, aluminum-ion-aggregated and iodide-modified silver nanoparticles were used as substrates to obtain Raman spectra of the DNA strands with the same base composition but different sequences, which form random coils or various hairpin conformations. Upon DNA hybridization, reproducibly enhanced bands were easily observed, corresponding well to the formation of Watson–Crick hydrogen bonds, base ring breathing vibrations, and hairpin loops. These characteristic bands can be used to unambiguously distinguish the hairpins from the random DNA conformation. Moreover, by using the deoxyribose band (959 cm^–1) as an internal standard to normalize the characteristic bands at 1703 cm^–1 corresponding to the dG ν_C=O H bond, the guanine–cytosine base-pair contents and sequence in DNA hairpins can be accurately measured. Applying this method, a single base mutation in a functional double helix was confidently identified.