High-quality surface-enhanced Raman spectra (SERS) of calf thymus DNA, apple single-stranded DNA, and rice single-stranded DNA are obtained by using rough silver electrodes modified with silver nanoparticles as the substrate. The appearance of fruitful Raman-active modes enables to identify the fine vibrational modes of DNA molecules of which the normal Raman spectra are not easy to be measured. It is concluded that the silver electrode modified by silver nanoparticles is a highly sensitive SERS substrate for DNA analysis, due to the uniformly aligned silver nanoparticles in combination with additional contributions of electrode potentials. Furthermore, the SERS spectra of these DNA molecules at varying potential conditions also provide information on the adsorption behavior of these DNA molecules on the silver. It is anticipated that the DNA molecules may tend to lie flat on the nanosilver surface; with increasing negative potentials, the spectra exhibit dramatic fluctuation, which could be associated with interface oxidation and changes of the adsorption behaviors in view of the different hydrophobicity/hydrophilic nature and electrostatic interactions of the phosphate base and the electrode surface.