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Surface-Enhanced Raman Scattering (SERS) of silicon nanostructures coated with a gold-silver substrate can be used to detect DNA hybridisation for taxonomic, biomedical and medical diagnostics purposes, according to a new study by researchers in Singapore. Cheng Fang, Ajay Agarwala, Kavitha Devi Buddharaju, Narayanan Balasubramanian, and Dim-Lee Kwong of the Institute of Microelectronics, at the Agency for Science, Technology and Research (A*Star), on Jurong Island, Singapore, working with Nizamudin Mohamed Khalid Shaik Mohamed Salim, Effendi Widjaja, and Marc Garland of the Institute of Chemical and Engineering Sciences at A*Star have demonstrated the potency of SERS in detecting DNA hybridization at low concentrations. SERS was first used in 1977 and since the has proven itself as an extremely sensitive analytical technique requiring only small volumes of sample and with wide application. Researchers have suggested that it is so sensitive that it could be used as a new tool in single molecule detection to augment or even displace techniques such as laser-induced fluorescence, frequency-modulated optical absorption at low temperature, and electrochemical detection of redox-active species. Electrochemically roughened metal surfaces, metallic nanoparticle arrays, and nanofabricated substrates have been used in countless SERS experiments to date. However these substrates suffer from imprecise control of their surfaces on the nanoscale. "Controllable nanostructures, however, are crucial for the SERS effect because the strong electromagnetic field on a metal surface, which is the main contributor for enhancement beyond the chemical enhancement," explain Fang and colleagues. Tip-Enhanced Raman Scattering was developed as a way to circumvent this problem, but Fang's team and others have recognised that better control during fabrication of the substrate's surface features held more promise. The A*Star researchers used standard silicon processing methods of the kind used in the microelectronics industry including conventional deep UV photolithography, reactive ion etching, thermal oxidation and physical vapour deposition of silver and gold. They were able to fabricate a SERS substrate with gaps of around 15 nanometres. They were able to create capture sites for hybridised DNA molecules using cysteine-modified Peptide Nucleic Acids (PNA). When a molecule of target DNA melds, or hybridises, with the PNA-modified sites on the substrate, the phosphate groups from its backbone can then bind to another additive, an inorganic linker in the form of zirconium(IV) ions. This produces an assembly comprising substrate+PNA+DNA+Zr. The key to detecting the target DNA on the device is then based on the fact that the PNA has no phosphate groups of its own and so forms no bonds with the linker metal ion unless it is hybridised with the complementary target DNA. The final step is to incubate the SERS device with a Raman label, Rhodamine B (RB), The RB's carboxylic acid groups react with zirconium(IV) so bonding the label only to those points on the device to which target DNA has adhered. The team can then look for Raman peaks corresponding to the presence of RB with a detection limit of 1×10−12 molar. Until now, the direct detection of DNA sequences at low concentration using SERS has eluded scientists. The main problem is that there is too little difference between the Raman spectra of the target DNA and its complementary bases, hence the need for a Raman label. "The present approach can be generalized for the detection of other DNA sequences using appropriate and complementary PNA sequences," explain the researchers. Related links:
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Kwong, helping build SERS substrates to spot DNA hybrids |
