Revealing the effect of intramolecular interactions on DNA SERS detection: SERS capability for structural analysis

Abstract

Intramolecular interactions are key factors for constructing the secondary conformations of biomolecules and they are also vital for biomolecular functions. Their effect on the surface-enhanced Raman spectroscopy (SERS) spectra is also important for reliable label-free detection. The current work focuses on three GCGC-quadruplexes as model molecules for SERS studies, which contain both the G-quartet and the GCGC-quartet. Their spectra are compared with the ones of the G-quadruplex and the duplex. The present work presents the specific effect of intramolecular interactions, including various Watson–Crick and Hoogsteen hydrogen bonds as well as base stacking, on the SERS signals of closely-related secondary conformations. The overall results indicated a significant influence on the direct label-free detection of DNA molecules and the SERS capability for secondary structural analysis.