Engineering Noble-Metal Nanoparticles for Sensing and Imaging with Surface-Enhanced Raman Scattering

This research investigated the surface-enhanced Raman scattering: SERS) from Ag and Au nanoparticles with an aim to better understand the SERS mechanism and to implement this technique for single-molecule detection and imaging. In addition, SERS was used as a sensitive probe to study molecules confined to a nanoparticle\u27s surface. The first part of this work focused on measuring the SERS from different Ag and Au nanoparticles and determining how their structural and physical properties affect SERS. The effects of shape, size, and Au-Ag composition on SERS are determined using Ag nanocubes, Ag nanospheres, and Au-based nanocages. I also demonstrate several techniques used to study the SERS of single nanoparticles, one at a time, which has provided significant insight into the SERS effect. I then discuss the development of a new and simple way to create large SERS enhancements by taking advantage of the supporting substrate of a nanoparticle. In this technique, simply depositing a single Ag nanocube on a metal substrate can increase its SERS enhancements to levels capable of single-molecule detection. In the second part of this work I used SERS as a molecular probe to understand how glucose molecules interact at a nanocube\u27s surface, and as an optical thermometer to quantify the temperature change at the surface of a Au-based nanocage during the photothermal effect. The nanoparticles were coated with highly ordered self-assembled monolayers: SAMs), and then SERS was used to determine the structural and conformational changes in the SAMs as a result of perturbations from the environment. This allowed me to use SERS to directly probe the molecules on the nanoparticle\u27s surface. In the final part of this work, I used nanocubes and nanospheres in SERS imaging. The resolution, sensitivity, and penetration depth are determined for our Raman microprobe system. In addition, phantoms are used to generate SERS images of three-dimensional microstructures

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Staphylococcus aureus</it>. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for <it>S. aureus</it>, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (<it>Escherichia coli</it>, <it>Helicobacter pylori</it>, and <it>Lactococcus lactis</it>). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis.</p> <p>Conclusion</p> <p>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.</p

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

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

Chemically isolating hot spots on concave nanocubes

The article of record as published may be found at http://dx.doi.org/10.1021/nl3032235We 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 SERSFunded by Naval Postgraduate School.AFOSRNational Science FoundationNERC (DOE)Awards No. N00244-09-1-0012 and N00244-09-1-0071 (NPS)Award no. FA9550-09-1-0294 (AFOSR)DMR-0520513 and DMR-01121262 (NSF)Award no. DE-SC0000989 (NERC

Successive Deposition of Silver on Silver Nanoplates: Lateral versus Vertical Growth

NSF [DMR-0804088, ECS-0335765]; Washington University in St. Louis; Ministry of Education, Science and Technology [R32-20031]; China Scholarship Counci

Replacement of Poly(vinyl pyrrolidone) by Thiols: A Systematic Study of Ag Nanocube Functionalization by Surface-Enhanced Raman Scattering

In this work, we used surface-enhanced Raman scattering to monitor the replacement of poly(vinyl pyrrolidone) (PVP) on Ag nanocubes by cysteamine, thiol-terminated poly(ethylene glycol), and benzenedithiol. PVP is widely used as a colloidal stabilizer and capping agent to control the shape of Ag (as well as many other noble metals) nanocrystals during synthesis and to stabilize the final colloidal suspension. However, the surface chemistry of Ag nanocrystals often needs to be tailored for specific applications, so the PVP coating must be removed and/or replaced by other ligands. By monitoring the signature peak from the carbonyl groups of PVP, we show, for the first time, that the PVP adsorbed on the surface of Ag nanocubes was completely replaced by the thiol molecules at room temperature over the course of a few hours. We observed the same trend no matter if the Ag nanocubes were suspended in an aqueous solution of the thiol or supported on a silicon substrate and then immersed in the thiol solution

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