Microfluidic-SERS devices for one shot limit-of-detection.

Microfluidic sensing platforms facilitate parallel, low sample volume detection using various optical signal transduction mechanisms. Herein, we introduce a simple mixing microfluidic device, enabling serial dilution of introduced analyte solution that terminates in five discrete sensing elements. We demonstrate the utility of this device with on-chip fluorescence and surface-enhanced Raman scattering (SERS) detection of analytes, and we demonstrate device use both when combined with a traditional inflexible SERS substrate and with SERS-active nanoparticles that are directly incorporated into microfluidic channels to create a flexible SERS platform. The results indicate, with varying sensitivities, that either flexible or inflexible devices can be easily used to create a calibration curve and perform a limit of detection study with a single experiment.

Using well-defined Ag nanocubes as substrates to quantify the spatial resolution and penetration depth of surface-enhanced Raman scattering imaging.

The multiplexing capability and high sensitivity of surface-enhanced Raman scattering (SERS) make this new imaging modality particularly attractive for rapid diagnosis. With 100 nm Ag nanocubes serving as the substrate, this work quantitatively evaluated, for the first time, some of the fundamental parameters of SERS imaging such as blur, spatial resolution and penetration depth. Our results imply that SERS is a high-resolution imaging technique with a blur value of 0.5 µm that is lower than many traditional modalities such as mammography. The spatial resolution was measured to be 1.1 µm, suggesting that SERS images could be collected effectively by adjusting the imaging step size to the same length scale, or no more than 2 µm. The major drawback of SERS imaging is its penetration depth, which is limited by the scattering and absorption of tissues. We demonstrated that enhancement of signal caused by aggregation of multiple nanoparticles could help overcome this potential road-block to in vivo imaging.

Chemically isolating hot spots on concave nanocubes.

We report a simple and general strategy for selectively exposing and functionalizing the sharp corners of concave nanocubes, which are the SERS hot spots for such structures. This strategy takes advantage of the unique shape of the concave cubes by coating the particles with silica and then etching it away to expose only the corner regions, while maintaining the silica coating in the concave faces. These corner regions can then be selectively modified for improved enhancement and signal response with SERS.

Dispersible gold nanorod dimers with sub-5 nm gaps as local amplifiers for surface-enhanced Raman scattering.

We report the synthesis of solution-dispersible, 35 nm diameter gold nanorod dimers with gaps as small as ∼2 nm for surface-enhanced Raman scattering (SERS). Using on-wire lithography (OWL), we prepared tailorable dimers in high yield and high monodispersity (∼96% dimers) that produce both large and reproducible SERS signals with enhancement factors of (6.8 ± 0.7) × 10(8) for single dimers in air and 1.2 × 10(6) for ensemble-averaged solution measurements. Furthermore, we show that these structures, which are the smallest ever made by OWL, can be used to detect molecules on flat surfaces and in aqueous solutions. When combined, these attributes with respect to sensitivity, reproducibility, and tailorability lead to a novel and powerful local amplification system for SERS applications.

Synthesis of Ag nanobars in the presence of single-crystal seeds and a bromide compound, and their surface-enhanced Raman scattering (SERS) properties.

This Article describes the synthesis of Ag nanobars with different aspect ratios using a seed-mediated method and evaluation of their use for surface-enhanced Raman scattering (SERS). The formation of Ag nanobars was found to critically depend on the introduction of a bromide compound into the reaction system, with ionic salts being more effective than covalent molecules. We examined single-crystal seeds with both spherical and cubic shapes and found that Ag nanobars grown from spherical seeds had much higher aspect ratios than those grown from cubic seeds. The typical product of a synthesis contained nanocrystals with three different morphologies: nanocubes, nanobars with a square cross section, and nanobars with a rectangular cross section. Their formation can be attributed to the difference in growth rates along the three orthogonal <100> directions. The SERS enhancement factor of the Ag nanobar was found to depend on its aspect ratio, its orientation relative to the laser polarization, and the wavelength of excitation.

Synthesis of Pd-Au bimetallic nanocrystals via controlled overgrowth.

This paper describes the synthesis of Pd-Au bimetallic nanocrystals with controlled morphologies via a one-step seeded-growth method. Two different reducing agents, namely, L-ascorbic acid and citric acid, were utilized for the reduction of HAuCl(4) in an aqueous solution to control the overgrowth of Au on cubic Pd seeds. When L-ascorbic acid was used as the reducing agent, conformal overgrowth of Au on the Pd nanocubes led to the formation of Pd-Au nanocrystals with a core-shell structure. On the contrary, localized overgrowth of Au was observed when citric acid was used as the reducing agent, producing Pd-Au bimetallic dimers. Through this morphological control, we were able to tune the localized surface plasmon resonance peaks of Pd-Au bimetallic nanostructures in the visible region.

Controlling the shapes of silver nanocrystals with different capping agents.

This paper provides direct evidence to support the role of a capping agent in controlling the evolution of Ag seeds into nanocrystals with different shapes. Starting with single-crystal seeds (spherical or cubic in shape), we could selectively obtain Ag octahedrons enclosed by {111} facets and nanocubes/nanobars enclosed by {100} facets by adding sodium citrate (Na(3)CA) and poly(vinyl pyrrolidone) (PVP), respectively, as a capping agent while all other parameters were kept the same. This research not only offers new insights into the role played by a capping agent in shape-controlled synthesis but also provides, for the first time, Ag octahedrons as small as 40 nm in edge length for optical and spectroscopic studies.

Gold nanocages covered by smart polymers for controlled release with near-infrared light.

Photosensitive caged compounds have enhanced our ability to address the complexity of biological systems by generating effectors with remarkable spatial/temporal resolutions. The caging effect is typically removed by photolysis with ultraviolet light to liberate the bioactive species. Although this technique has been successfully applied to many biological problems, it suffers from a number of intrinsic drawbacks. For example, it requires dedicated efforts to design and synthesize a precursor compound for each effector. The ultraviolet light may cause damage to biological samples and is suitable only for in vitro studies because of its quick attenuation in tissue. Here we address these issues by developing a platform based on the photothermal effect of gold nanocages. Gold nanocages represent a class of nanostructures with hollow interiors and porous walls. They can have strong absorption (for the photothermal effect) in the near-infrared while maintaining a compact size. When the surface of a gold nanocage is covered with a smart polymer, the pre-loaded effector can be released in a controllable fashion using a near-infrared laser. This system works well with various effectors without involving sophisticated syntheses, and is well suited for in vivo studies owing to the high transparency of soft tissue in the near-infrared region.

Measuring the SERS Enhancement Factors of Dimers with Different Structures Constructed from Silver Nanocubes.

We describe a systematic investigation on the SERS enhancement factors of individual dimers (EF(dimer)) constructed from two Ag nanocubes that display a face-to-face, edge-to-face, or edge-to-edge structure. The highest field-enhancements were obtained for the dimers displaying a face-to-face and edge-to-face configuration. In these two systems, EF(dimer) was insensitive the dimer geometry and corresponded to 2.0×10(7) and 1.5×10(7), respectively. However, EF(dimer) was decreased to 5.6×10(6) for the edge-to-edge structure. These variations in the detected field-enhancements could be explained based on the relative orientation of the nanocubes and the number of probe molecules enclosed in the hot-spot region for each dimer configuration.

Measuring the surface-enhanced Raman scattering enhancement factors of hot spots formed between an individual Ag nanowire and a single Ag nanocube.

This paper describes a systematic study of the surface-enhanced Raman scattering (SERS) activity of hot spots formed between a Ag nanowire and a Ag nanocube with sharp corners. We investigated two distinct dimer structures: (i) a nanocube having one side face nearly touching the side face of a nanowire, and (ii) a nanocube having one edge nearly touching the side face of a nanowire. The field enhancements for the dimers displayed a strong dependence on laser polarization, and the strongest SERS intensities were observed for polarization along the hot-spot axis. Moreover, the detected SERS intensities were dependent on the hot-spot structure, i.e., the relative orientation of the Ag nanocube with respect to the nanowire's side face. When the dimer had a face-to-face configuration, the enhancement factor EF(dimer) was 1.4 x 10(7). This corresponds to 22-fold and 24-fold increases compared to those for individual Ag nanowires and nanocubes, respectively. Conversely, when the dimer had an edge-to-face configuration, EF(dimer) was 4.3 x 10(6). These results demonstrated that the number of probe molecules adsorbed at the hot spot played an important role in determining the detected SERS intensities. EF(dimer) was maximized when the dimer configuration allowed for a larger number of probe molecules to be trapped within the hot-spot region.

Surface-enhanced Raman scattering: comparison of three different molecules on single-crystal nanocubes and nanospheres of silver.

We have investigated the surface-enhanced Raman scattering (SERS) of chemically prepared single-crystal nanocubes and nanospheres of Ag with three different molecules to quantitatively understand the effect of sharp features on the SERS enhancement factor. Both experimental measurements and theoretical calculations confirmed a higher SERS activity for the nanocubes as a result of sharp features on their surfaces. We also found major discrepancies between the measured SERS intensities and those predicted from the electromagnetic mechanism. Through analysis of SERS bands, we concluded that sharp features on the Ag nanocubes could greatly increase the contribution of the chemical enhancement to the SERS intensity.

A SERS study of the molecular structure of alkanethiol monolayers on Ag nanocubes in the presence of aqueous glucose.

We report progress towards the surface-enhanced Raman scattering (SERS) characterization of self-assembled monolayers (SAMs) on uniform Ag nanocubes. This study quantifies changes in the SAMs induced by the presence of aqueous glucose. The SAMs were prepared from dodecanethiol and they were representative of highly ordered monolayers as indicated by SERS analysis. We examined the SAMs response to glucose and observed conformational changes in the alkanethiolate SAMs. Analysis of the trans and gauche bands as well as the C-H stretching modes of the SAMs suggest that the analyte-SAM interactions were superficial and there was no penetration for the glucose molecules into the monolayers.

Isolating and probing the hot spot formed between two silver nanocubes.

Out of the frying pan: Hot spots can greatly increase the sensitivity of surface-enhanced Raman scattering, but they remain poorly understood. A new strategy based on plasma etching (see picture) can be used to isolate and exclusively probe the SERS-active molecules adsorbed in the hot-spot region between two silver nanocubes.

Etching and growth: an intertwined pathway to silver nanocrystals with exotic shapes.

Two-faced nanocrystals: Rapid addition of a second aliquot of silver nitrate during a polyol synthesis led to the formation of anisotropically truncated octahedrons as a result of oxidative etching and overgrowth of silver nanocubes. Three adjacent faces of the nanocube grew more rapidly than the three other faces, generating a non-centrosymmetric structure (see picture).

Toward the automated generation of genome-scale metabolic networks in the SEED.

BACKGROUND: Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. RESULTS: We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. CONCLUSION: Our method sets the stage for the automated generation of substantially complete metabolic networks for over 400 complete genome sequences currently in the SEED. With each genome that is processed using our tools, the database of common components grows to cover more of the diversity of metabolic pathways. This increases the likelihood that components of reaction networks for subsequently processed genomes can be retrieved from the database, rather than assembled and verified manually.