Surface enhanced raman scattering for discovering and scoring single base differences in DNA

Information about DNA sequence variation is increasingly being recognized as an important tool in the analysis of many diseases and in the development of diagnostic, therapeutic, and preventive strategies. Surface enhanced Raman scattering (SERS) is suggested as a new, potentially powerful method for detection and identification of single base differences in double stranded DNA fragments. Enhanced Raman signal is originated from nucleotides that are in direct contact with SERS active metal surface. Aromatic rings in double stranded perfectly matched DNA are hydrogen bonded and do not interact with the metal. In the case of an insertion, deletion or base mismatch, hydrogen bonding is disrupted and an open region is formed. Raman scattering from base pairs in this region undergoes an enhancement resulting in SERS spectrum. Model experiments were performed with 209 base pairs DNA fragment containing one mismatch and adsorbed on electrochemically roughened silver surface. A fragment of the same length but without mismatch was used as a control. No spectra were obtained from the control adsorbed on the SERS substrate, whereas the sample with one mismatch yielded a distinct SERS spectrum. It is believed that all bands in the spectrum correspond to the mismatched base pair and bases from the closest environment around the mismatch.