The effect of DNA bases permutation on surface-enhanced Raman scattering spectrum

Abstract

Surface-enhanced Raman scattering (SERS) process results in a tremendous increase of Raman scattering cross section of molecules adsorbed to plasmonic metals and influenced by numerous physico-chemical factors such as geometry and optical properties of the metal surface, orientation of chemisorbed molecules and chemical environment. While SERS holds promise for single molecule sensitivity and optical sensing of DNA sequences, more detailed understanding of the rich physico-chemical interplay between various factors is needed to enhance predictive power of existing and future SERS-based DNA sensing platforms. In this work, we report on experimental results indicating that SERS spectra of adsorbed single-stranded DNA (ssDNA) isomers depend on the order on which individual bases appear in the 3-base long ssDNA due to intramolecular interaction between DNA bases. Furthermore, we experimentally demonstrate that the effect holds under more general conditions when the molecules do not experience chemical enhancement due to resonant charge transfer effect and also under standard Raman scattering without electromagnetic or chemical enhancements. Our numerical simulations qualitatively support the experimental findings and indicate that base permutation results in modification of both Raman and chemically enhanced Raman spectra.

Raman spectroscopy and artificial intelligence open up accurate detection of pathogens from DNA‐based sub‐species level classification

“…[ 42 ] The chemical enhancement mechanism for both SERS and TERS to increase the specificity is crucial for DNA sequencing studies. Rubin et al [ 43 ] have experimentally and theoretically demonstrated the effect of spatial arrangements of DNA bases in ssDNA 3‐mers on SERS and Raman spectra. Their results indicated a difference between the acquired SERS and Raman spectra of sequences for permutation of the DNA bases.…”

Label-Free Detection of DNA Base Mutation and Hybridized DNA by an Electrostatically Modified 3D Plasmonic Array

“…However, the signal from adenine often dominates the spectrum due to alterations in the base sequence permutation. 22 Indirect detection methods have been proposed, utilizing SERS-labeling molecules to specifically recognize target DNA. For example, Eva Green, a nucleic acid dye, binds to the DNA double helix grooves during the PCR reaction, and the amount of bound DNA is indirectly measured by the SERS intensity of the dye.…”

“…To solve this problem, strategies have been developed to anchor DNA to SERS substrates by modification with thiol groups. However, the signal from adenine often dominates the spectrum due to alterations in the base sequence permutation . Indirect detection methods have been proposed, utilizing SERS-labeling molecules to specifically recognize target DNA.…”