We report a method for obtaining highly reproducible surface-enhanced Raman spectroscopy (SERS) of single and double-stranded thiolated DNA oligomers. Following a protocol that relaxes the DNA into an extended conformation, SERS spectra of DNA oligonucleotides are found to be extremely similar, strongly dominated by the Stokes modes of adenine. A spectral correlation function analysis useful for assessing reproducibility and for quantifying the highly complex changes corresponding to modifications in molecular conformation of the adsorbate molecules is introduced. This approach is used to monitor the interaction of DNA with cisplatin, a chemotherapy agent in widespread use.