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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.