Detection of Respiratory Syncytial Virus DNA with Gold Nanorod Surface Enhanced Raman Spectroscopy Active Substrates

Abstract

Surface enhanced Raman scattering (SERS) is a powerful spectroscopic tool that can be used to identify and characterize compounds at low concentrations. Recent literature reports suggest that SERS may be applicable for the detection and identification of viruses present in biofluids. In this investigation, gold nanorod arrays were evaluated as SERS substrates with the specific purpose of probing spectral differences between single stranded (ssDNA) and hybridized, or double stranded (dsDNA) DNA. This was deemed as the first step in developing a SERS-based hybridization assay for viral identification. Hybridization was carried out both off and on the substrate surface to determine whether there are observable spectral differences from the two different methods of hybridization. Studies were also carried out to determine if it was possible to detect mismatched DNA pairs after hybridization had been attempted. Gold SERS active substrates were utilized instead of silver giving the advantage that these substrate do not oxidize under ambient conditions. It has also been found that ozone cleaning gold substrates before sample application increases the hydrophilicity of the gold, making the use of smaller sample volumes possible. Ozone cleaning the gold substrate after ample binding time has passed increases the SERS signal as well. It is believed that this cleaning immediately prior to SERS acquisition cleans the gold surface to a point where the plasmon being formed is more likely to move up the sample which increases the intensity of the SERS signal. In addition to examining the possibility of using gold instead of silver for the SERS substrates, a method allowing for 36 separate DNA assays to be run at one time was investigated. This is accomplished by creating wells with polymer. Up to 36 wells fit on one glass microscope slide meaning that anywhere from 1 to 36 DNA probes can be attached within individual wells. This allows for either 36 different biological assays for the same virus or 1 biological sample to be tested for 36 different viruses or virus strains.