This paper describes a novel method for the fabrication of nanodot arrays with 30nm period which will be used as a platform for the highly sensitive and specific Surface enhanced Raman spectroscopy (SERS) detection of the polymerase chain reaction (PCR). The usual detection methods for PCR involve time consuming methods of DNA labelling, using labels that are capable of altering original DNA properties. We present a detection method which has the advantages of being label free, requiring small analyte volumes and achieving high sensitivity due to SERS enhancement. The required reproducible SERS environment is achieved by the nanofabrication of gold pillars on glass with the use of an electron-beam writer.
Noble metal nanoparticles interact strongly with visible light due to resonant excitation of conduction electron oscillations, an interaction referred to as a local surface plasmon resonance (LSPR) interaction. This LSPR interaction results in an enhancement of the electromagnetic field surrounding the nanoparticle, with a concomitant enhancement of optical signals. Recent interest in SER spectroscopy (SERS) has been rekindled by the observation of single molecule SERS. Nanofabrication provides a method for producing metal substrates for SERS with well-defined size and shape characteristics. Gold nanopillar structures are fabricated for this work by electron beam lithography. Rabbit skeletal-myosin-II HMM and actin can be produced in gram quantities and provide the basis for a highly reproducible <i>in-vitro</i> motility assay system. Using this well established assay linked with SERS we can look at how the heads of myosin interact with filaments of actin to produce steps in greater detail. This technique will provide information of subtle mechanistic interactions between components of a molecular motor, with the future possibility of providing a model system for measuring the “proximity effect” in ligand binding (e.g. protein-protein and DNA-DNA interactions) and LSPR-analyte interactions.