Capture single-stranded DNA with an attached alkanethiol linking moiety (capture HS-ssDNA) and 6-mercaptohexan-1-ol were chemisorbed on nanostructured GaN covered with sputtered layers of plasmonic metals (like silver and gold). The structure of the formed layer was determined by surface-enhanced Raman scattering (SERS) measurements. Hybridization with the target ssDNA, complementary to the chains of immobilized capture HS-ssDNA, induced changes in the conformation of the chains of chemisorbed ω-substituted alkanetiols (6-mercaptohexan-1-ol and the alkanethiol linking moiety of HS-ssDNA). Such changes are significantly larger in the case of experiments on silver than on gold and gold/silver SERS substrates. This means that silver substrates are significantly more promising for the SERS observation of such hybridization-induced rearrangements than the gold substrates previously used. Although the sputtered metal films have a nanograin structure, the nanostructuring of the GaN substrates plays an important role in the SERS-activity of this nanomaterial.