Limitations of Surface Enhanced Raman Scattering in Sensing DNA Hybridization Demonstrated by Label-Free DNA Oligos as Molecular Rulers of Distance-Dependent Enhancement

This article presents a critical evaluation of silver nanorod arrays as substrates for assaying nucleic acid hybridization by surface enhanced Raman scattering (SERS). SERS spectra acquired on complementary oligos, alone or in combination, contain the known spectral signatures of the nucleotides that comprise the oligo; however, no signature bands characteristic of the hybrid were observed. Spectra acquired on an oligo with a 5'- or 3'-thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting a degree of control over the orientation of the oligo on the nanorod surface. A set of oligos consisting of adenine tracts in a polycytosine chain served as molecular rulers to probe the distance dependence of the SERS enhancement. Using these, we have identified the point at which the characteristic bands for the nucleotides that comprise the oligo disappear from the spectrum. These findings suggest that the applicability of SERS for label-free detection of nucleic acid hybridization is limited to short oligos of less than nine nucleotides.