Probing Non-Canonical A*C Base Pairs in DNA using SERS

ABSTRACT

Raman spectroscopy probes the vibrational modes of a molecule. In recent years, surface-enhanced Raman spectra (SERS) of oligonucleotides on gold or silver nanoparticles have yielded significantly stronger signals. Raman spectra of DNA are high throughput, quantitative, and label-free and show distinct features created by vibrational modes such as ring deformation, backbone bending, and hydrogen bond stretching. Here we are using gold nanoparticles to probe various structural changes in a short helical DNA designed to mimic SL1 of coronavirus and SL of U6 snRNA. Phosphate buffers containing 1 M KCl or 10 mM magnesium chloride were utilized at two different pH (5.5 and 7). Differences in peak intensity are being observed between canonically paired helical DNA and DNA of similar composition with modifications containing non-canonical A*C base pair. We are comparing ion binding, pH-related, and temperature-variable conditions to observe changes in DNA structures.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.