  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 intra-molecular
interaction between DNA bases. Furthermore, we experimentally demonstrate that
the effect holds under more general conditions when the molecules don't
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.
