The design and fabrication of nanopores within three-dimensionally structured gold films with spherical microcavities of 1.2 μm diameter and 0.6 μm deep in hexagonal close-packed arrays, are described. The cavities are fabricated by electroplating gold around self-assembled arrays of polymer spheres. Following removal of the spheres, and `lift-off' of the 3D structured gold film, some of the microcavities were milled with a Helium Ion Microscope to provide nanopores through the centre of the microcavity base right through the film. The geometry of the nanopore within the device is designed using theoretical approaches to provide the optimal electric field intensity in the very centre of the nanopore when excited with light of ~ 600 nm (in water). In this paper we report the theoretical simulations used to evaluate the optimal geometry of the nanopore within the centre/base of the gold microcavity. Although a number of various geometries and sizes of pores were considered the theoretical results provide evidence that a pore of 50nm with rounded corners will provide the greatest electrical field intensity inside the pore and the fabrication results provide a demonstrated practical approach for creation of these nanopores within these 3D gold structured films.

Design and fabrication of three-dimensionally structured, gold membranes containing hexagonally close-packed microcavities with nanopores in the base, are described. Our aim is to create a nanoporous structure with localized enhancement of the fluorescence or Raman scattering at, and in the nanopore when excited with light of approximately 600 nm, with a view to provide sensitive detection of biomolecules. A range of geometries of the nanopore integrated into hexagonally close-packed assemblies of gold micro-cavities was first evaluated theoretically. The optimal size and shape of the nanopore in a single microcavity were then considered to provide the highest localized plasmon enhancement (of fluorescence or Raman scattering) at the very center of the nanopore for a bioanalyte traversing through. The optimized design was established to be a 1200 nm diameter cavity of 600 nm depth with a 50 nm square nanopore with rounded corners in the base. A gold 3D-structured membrane containing these sized microcavities with the integrated nanopore was successfully fabricated and 'proof of concept' Raman scattering experiments are described.

Detection of DNA sequences is pivotal to many modern molecular diagnostic methods, but the ability to directly detect DNA sequences, without the need for signal amplification (such as by applying a polymerase chain reactions) is highly desirable. Here we investigate the potential for gold inverted pyramidal structures (also known as Klarite®) for DNA detection, as these simple chips containing the structured surface on a face could offer an improved format for DNA based diagnostic methods. Our strategy included optimization of the fabrication protocols to achieve flat gold surfaces within the inverted pyramidal surface and then a subsequent assessment of these substrates for direct DNA detection by Raman microscopy. These studies demonstrate for the first time the potential of these gold structured planar substrates for DNA analysis applications.

Colloidal quantum dots (QDs) have received considerable attention as luminescent probes for DNA analysis applications. The underlying photophysical and photochemical properties of these probes need consideration when designing assays for DNA analysis. These properties include intermittent fluorescence often termed 'blinking', photobleaching, photoinduced fluorescence enhancement and, as a result of recent evidence, photo-induced generation of reactive oxygen species leading to DNA damage. Even though the design of assays for DNA analysis using QDs needs care, QDs do provide advantages over fluorophores for many emerging DNA analysis methods where low copy numbers of DNA are present. Many of the more traditional DNA assay methods using fluorophore labeled probes either cannot be translated, or show no benefit in using QDs as the lumophore.

An investigation of the photoinduced fluorescence enhancement (PFE) behavior of CdSe/ZnS core/shell quantum dots deposited at low densities, under anhydrous and controlled water humidity, under oxygen or argon, is presented. The photoluminescence properties of CdSe/ZnS QDs are highly dependent upon the local gaseous environment. Under anhydrous conditions, under either oxygen or argon, there was no observed PFE, even though there were remarkable differences in the photoluminescence spectra. Under argon, (i) the initial photoluminescence properties are independent of humidity level; however, (ii) the PFE effect observed is highly dependent on the environmental humidity levels. Under oxygen, (i) the initial photoluminescence properties (spectra and yield) are dependent on humidity levels and (ii) the PFE effect observed is highly dependent on the humidity levels. Comparing D2O versus H2O humidity level effects on the photoluminescence properties of CdSe/ZnS QDs provides evidence for a water-molecule-stabilized state that facilitates luminescence processes. The products of CdSe/ZnS QDs exposed under a humid oxygen environment were evaluated by X-ray photoelectron spectroscopy. Oxidation of both the CdSe core and the ZnS shell was established. Oxidation of the ZnS shell is suggested to be a result of reaction with peroxide products resulting from the oxygen radical anion. These results highlight the important sensitivity of QDs to water and prove the existence of competing electronic and chemical effects on different time scales.

Serrated-edge droplets: The wetting of metallic microstructures with nanoscale features, used as substrates for surface-enhanced Raman scattering, can result in sharp bending of the droplet edges. Tethering of the liquid/air/substrate contact line induces flows of analyte to particular locations as the droplet recedes during evaporation (see SEM image). Molecules are preferentially deposited in the pyramidal pits on these structures.