UV Resonance Raman Spectroscopic Marker Bands of Base Pair Formation During Nucleic Acids Assembly

The controlled assembly of nucleic acids (NAs) underpins the function of DNA and RNA structures. Here, we demonstrate the use of UV resonance Raman (UVRR) spectroscopy as a chemically selective and label-free tool to inform one about the structural details of the molecular assembly of NAs and their underlying interactions with a particular focus on H-bonding between base pairs. Using experimental H/D exchange and hybrid DFT-based computational Raman spectra, we identify UVRR marker bands that involve vibrations of C=O, NH, and NH2 groups, which are relevant to H-bonding interactions in guanine-cytosine (G-C) and adenine-thymidine (A-T) Watson-Crick base pairs. Analyzing peak shifts and changes in relative intensities of these marker bands that are consistent with computational spectra, we successfully follow the conformational assembly of oligonucleotide strands by recording their UVRR spectra during thermal hybridization to double helices. Variations in obtained thermal sigmoidal transitions can inform one on mechanistic details in complex DNA and RNA architectures.