Spectroscopy on the wing: Naturally inspired SERS substrates for biochemical analysis

We show that naturally occurring chitinous nanostructures found on the wings of the Graphium butterfly can be used as substrates for surface‐enhanced Raman scattering when coated with a thin film of gold or silver. The substrates were found to exhibit excellent biocompatibility and sensitivity, making them ideal for protein assaying. An assay using avidin/biotin binding showed that the substrates could be used to quantify protein binding directly from changes in the surface‐enhanced Raman scattering (SERS) spectra and were sensitive over a concentration range comparable with a typical enzyme‐linked immunosorbent assays (ELISA) assay. A biomimetic version of the wing nanostructures produced using a highly reproducible, large‐scale fabrication process, yielded comparable enhancement factors and biocompatibility. The excellent biocompatibility of the wings and biomimetic substrates is unparalleled by other lithographically produced substrates, and this could pave the way for widespread application of ultrasensitive SERS‐based bioassays. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Hollow Palladium‐Gold Nanochains with Periodic Concave Structures as Superior ORR Electrocatalysts and Highly Efficient SERS Substrates

Unique palladium‐gold hollow nanochains (PdAu HCs) with 1D architecture and an ultrathin Pd‐rich skin exhibit fantastic oxygen reduction reaction (ORR) enhancements due to their high conductivity, structural stability, and maximized atomic utilization. More importantly, such PdAu HCs possess periodic concave structures that boost ORR performance. These structures readily form high‐density high‐index facets, and fewer arc edges. Concave structures can deliver strong strain effects and surface charge accumulation is revealed by off‐axis electron holography. In addition, periodic concave structures can provide strong localized surface–plasmon coupling, which means that PdAu HCs have great potential as efficient surface‐enhanced Raman scattering (SERS) substrates. This study offers a novel and general approach for the design of complex noble metal‐based nanostructures as efficient ORR catalysts and SERS substrates.     

Multiplex single‐cell quantification of rare RNA transcripts from protoplasts in a model plant system

Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface‐enhanced Raman spectroscopy (SERS) and gold nanoprobes at single‐cell resolution. We show the applicability of nanoparticle‐based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold‐nanoparticles decorated with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by transmission electron microscopy, inductively‐coupled plasma‐mass spectrometry and fluorescence imaging. Second, we show the utility of a SERS platform to monitor individual alternatively spliced (AS) variants and miRNA copies within single cells. Finally, the distinctive spectral features of Raman‐active dyes were exploited for multiplex analysis of AtPTB2, AtDCL2, miR156a and miR172a. Furthermore, single‐cell studies were validated by in vitro quantification and evaluation of nanotoxicity of gold probes. Raman tag functionalized gold nanosensors yielded an approach for the tracking of rare RNAs within the protoplasts. The SERS‐based approach for quantification of RNAs has the capability to be a highly sensitive, accurate and discerning method for single‐cell studies including AS variants quantification and rare miRNA detection in specific plant species.     

Fabrication of biosensing surfaces using adhesive polydopamine

Dopamine can be induced to polymerize on a variety of substrates, providing a robust and bioinspired surface coating that can be used to tune substrate surface properties and to sequester other species at the interface. We first exploit the facile nature of this surface modification procedure to generate an array of polydopamine that, in conjunction with fluorescent tags, provides the ability to detect multiple protein targets simultaneously and with great specificity. We then demonstrate the use of polydopamine as a matrix to confine gold nanoparticles at the surface of glass and graphene substrates. The nanoparticles (NPs) are used to template further gold nanoparticle growth in situ at the interface; subsequent calcination to remove the polydopamine matrix and sinter the NPs generates a highly active surface enhanced Raman scattering surface that allows for sensitive molecular detection. These varied uses in surface modification/biosensing demonstrate the utility of polydopamine as a functional surface modification for control of physical and electronic properties at the interface. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:299–306, 2015     

Feature‐based recognition of Surface‐enhanced Raman spectra for biological targets

We propose and compare multiple approaches to automatically process data measured through surface‐enhanced Raman scattering (SERS), in the context of intracellular molecule probing. It relies on locally detecting the most relevant spectra to retrieve all data independently through indexing, thus avoiding any pre‐filtering which occurs with standard processing methods. We first assess our approach on simulated data of the spectrum of Rhodamine 6G, and then validate high‐performing methods on experimental measurements of this compound. The optimized method is then utilized to extract and classify the complex SERS response behavior of gold nanoparticles taken in live cells. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

A simple gold nanoplasmonic SERS method for trace Hg2+ based on aptamer‐regulating graphene oxide catalysis

The as‐prepared graphene oxide (GO) exhibited a strong catalytic effect on reduction of HAuCl₄ by trisodium citrate to form gold nanoplasmons (AuNPs) with a strong surface‐enhanced Raman scattering (SERS) effect at 1615 cm^?1 in the presence of molecular probe Victoria blue 4R (VB4r). SERS intensity increased with nanocatalyst GO concentration due to the formation of more AuNP substrates. The aptamer (Apt) of Hg²⁺ can bind to GO to form Apt–GO complexes, which can strongly inhibit nanocatalysis. When target Hg²⁺ is present, the formed stable Hg²⁺–Apt complexes are separated from the GO surface, which leads to GO catalysis recovery. The enhanced SERS signal was linear to Hg²⁺ concentration in the range 0.25–10 nmol/L, with a detection limit of 0.08 nmol/L Hg²⁺. Thus, a new gold nanoplasmon molecular spectral analysis platform was established for detecting Hg²⁺, based on Apt regulation of GO nanocatalysis.     

Surface interactions of a homologous series of alpha,omega-amino acids on colloidal silver and gold

Surface enhanced Raman spectroscopy (SERS) was used to characterize a homologous series of alpha,omega-amino acids on colloidal gold and silver. Raman and SER spectra of the alpha,omega-amino acids, NH2(CH2)nCOOH (n = 3-7), are presented and analyzed, revealing the probable conformations of the molecules on the metal surfaces. The alpha,omega-amino acids interact with silver and gold through both the amine and carboxylate end groups, and modify the conformation of the molecular backbone in order to maximize these interactions. An odd-even effect is observed for backbone conformations of molecules adsorbed to the silver substrate. The anomolous SER spectrum of 5-aminopentanoic acid on gold suggests the possibility of condensation polymerization at the gold surface.     

Surface‐enhanced Raman spectroscopy for on‐site analysis: A review of recent developments

On‐site identification and quantification of chemicals is critical for promoting food safety, human health, homeland security risk assessment, and disease diagnosis. Surface‐enhanced Raman spectroscopy (SERS) has been widely considered as a promising method for on‐site analysis due to the advantages of nondestructive, abundant molecular information, and outstanding sensitivity. However, SERS for on‐site application has been restricted not only by the cost, performance, and portability of portable Raman instruments, but also by the sampling ability and signal enhancing performance of the SERS substrates. In recent years, the performance of SERS for on‐site analysis has been improved through portable Raman instruments, SERS substrates, and other combined technologies. In this review, popular commercial portable Raman spectrometers and the related technologies for on‐site analysis are compared. In addition, different types of SERS substrates for on‐site application are summarized. SERS combined with other technologies, such as electrochemical and microfluidics are also presented. The future perspective of SERS for on‐site analysis is also discussed.     

Optical Absorption in Overcoats of Nanoparticle Arrays on a Metallic Substrate

Surface plasma oscillations in metallic particles as well as in thin metallic films have been studied extensively in the past decades. New features regarding surface plasma excitations are, however, constantly discovered, leading, for example, to surface-enhanced Raman scattering studies and enhanced optical transmission though metal films with nanohole arrays. In the present work, the role of a metallic substrate is examined in two cases, one involving an overcoat of dielectric nanoparticles and the other an overcoat of metallic nanoparticles. Theoretical results are obtained by modeling the nanoparticles as forming a two-dimensional, hexagonal lattice of spheres. The scattered electromagnetic field is then calculated using a variant of the Green function method. Comparison with experimental results is made for nanoparticles of tungsten oxide and tin oxide deposited on either gold or silver substrates, giving qualitative agreement on the extra absorption observed when the dielectric nanoparticles are added to the metallic surfaces. Such absorption would be attributed to the mirror image effects between the particles and the substrate. On the other hand, calculations of the optical properties of silver or gold nanoparticle arrays on a gold or a silver substrate demonstrate very interesting features in the spectral region from 400 to 1,000 nm. Interactions between the nanoparticle arrays surface plasmons and their images in the metallic substrate would be responsible for the red shift observed in the absorption resonance. Moreover, effects of particle size and ambient index of refraction are studied, showing a great potential for applications in biosensing with structures consisting of metallic nanoparticle arrays on metallic substrates.     

Plasmonic Heating-Assisted Transformation of SiO2/Au Core/Shell Nanospheres (Au Nanoshells): Caveats and Opportunities for SERS and Direct Laser Writing

The selective modification of silica/gold nanospheres (gold nanoshells) driven by plasmonic heating is demonstrated. Direct laser writing and reshaping of nanoshell assemblies can be easily controlled and exploited for nanofabrication purposes. The modified nanoshells exhibit improved surface enhanced Raman scattering, allowing to settle most of the issues related to nanoshell stability under working conditions.

SERS and integrative imaging upon internalization of quantum dots into human oral epithelial cells

CdTe quantum dots (QDs) are widely used in bio‐applications due to their size and highly efficient optical properties. However internalization mechanisms thereof for the variety of freshly extracted, not cultivated human cells and their specific molecular interactions remains an open topic for discussion. In this study, we assess the internalization mechanism of CdTe quantum dots (3.3 nm) capped with thioglycolic acid using non cultivated oral epithelial cells obtained from healthy donors. Naked gold nanoparticles (40 nm) were successfully used as nanosensors for surface‐enhanced Raman spectroscopy to efficiently identify characteristic Raman peaks, providing new evidence indicating that the first interactions of these QDs with epithelial cells occurred preferentially with aromatic rings and amine groups of amino acid residues and glycans from trans‐membrane proteins and cytoskeleton. Using an integrative combination of advanced imaging techniques, including ultra‐high resolution SEM, high resolution STEM coupled with EDX spectroscopy together with the results obtained by Raman spectroscopy, it was determined that thioglycolic acid capped CdTe QDs are efficiently internalized into freshly extracted oral epithelial cells only by facilitated diffusion, distributed into cytoplasm and even within the cell nucleus in three minutes.

     

Gold Micro-Flowers: One-Step Fabrication of Efficient, Highly Reproducible Surface-Enhanced Raman Spectroscopy Platform

We present a new method enabling simultaneous synthesis and deposition of gold micro-flowers (AuMFs) on solid substrates in a one-pot process that uses two reagents, auric acid and hydroxylamine hydrochloride, in aqueous reaction mixture. The AuMFs deposited onto the substrate form mechanically stable gold layer of expanded nanostructured surface. The morphology of the AuMFs depends on and can be controlled by the composition of the reaction solution as well as by the reaction time. The nanostructured metallic layers obtained with our method are employed as efficient platforms for chemical and biological sensing based on surface-enhanced Raman spectroscopy (SERS). SERS spectra recorded by such platforms for p-mercaptobenzoic acid and phage lambda exhibit enhancement factors above 10⁶ and excellent reproducibility.     

Evaluation of fluorescence- and mass spectrometry-based CYP inhibition assays for use in drug discovery

The potential for metabolism-related drug-drug interactions by new chemical entities is assessed by monitoring the impact of these compounds on cytochrome P450 (CYP) activity using well-characterized CYP substrates. The conventional gold standard approach for in vitro evaluation of CYP inhibitory potential uses pooled human liver microsomes (HLM) in conjunction with prototypical drug substrates, often quantified by LC-MS/MS. However, fluorescent CYP inhibition assays, which use recombinantly expressed CYPs and fluorogenic probe substrates, have been employed in early drug discovery to provide low-cost, high-throughput assessment of new chemical entities. Despite its greatly enhanced throughput, this approach has been met with mixed success in predicting the data obtained with the conventional gold standard approach (HLM+LC-MS). The authors find that the predictivity of fluorogenic assays for the major CYP isoforms 3A4 and 2D6 may depend on the quality of the test compounds. Although the structurally more optimized marketed drugs yielded acceptable correlations between the fluorogenic and HLM+LC-MS/MS assays for CYPs 3A4, 2D6, and 2C9 (r2 = 0.5-0.7; p < 0.005), preoptimization, early discovery compounds yielded poorer correlations (r2 < or = 0.2) for 2 of these major isoforms, CYPs 3A4 and 2D6. Potential reasons for the observed differences are discussed.     

Early diagnosis of oral cancer based on the surface plasmon resonance of gold nanoparticles

The high mortality rate in cancer such as oral squamous cell carcinoma is commonly attributed to the difficulties in detecting the disease at an early treatable stage. In this study, we exploited the ability of gold nanoparticles to undergo coupled surface plasmon resonance and set up strong electric fields when closely-spaced to improve the molecular contrast signal in reflectance-based imaging and also to enhance the Raman signal of bioanalytes in cancer. Colloidal gold nanoparticles were synthesized and conjugated to anti-epidermal growth factor receptor (EGFR) for imaging. A self-assembled surface enhanced Raman scattering (SERS)-active gold nanoparticle monolayer film was also developed as a biosensing surface using a simple drop-dry approach. We have shown that gold nanoparticles could elicit an optical contrast to discriminate between cancerous and normal cells and their conjugation with antibodies allowed them to map the expression of relevant biomarkers for molecular imaging under confocal reflectance microscopy. We have also shown that the SERS spectra of saliva from the closely-packed gold nanoparticles films was differentiable between those acquired from normal individuals and oral cancer patients, thus showing promise of a simple SERS-based saliva assay for early diagnosis of oral cancer.     

Surface enhanced Raman scattering for narcotic detection and applications to chemical biology

Raman spectroscopy is rapidly finding favour for applications in the life science because of the ease with which it can be used to extract significant data from tissue and cells. However, the Raman effect is an inherently weak effect, which hinders the analysis of low concentration analytes. Raman sensitivity can be improved via the surface enhanced Raman scattering (SERS) effect. In SERS, Raman spectra are dramatically amplified when a molecule is adsorbed onto nano-roughened noble metal surfaces such as silver and gold. The degree of enhancement enables single-molecule detection, which offers the potential for the unambiguous identification of analytes at concentrations that are useful in both a forensic and a chemical biology context. Here we discuss some of the practical applications of SERS to both low-level narcotic detection, and how this can be applied to chemical biology.     

Nanostructure shape effects on response of plasmonic aptamer sensors

A localized surface plasmon resonance (LSPR) sensor surface was fabricated by the deposition of gold nanorods on a glass substrate and subsequent immobilization of the DNA aptamer, which specifically bind to thrombin. This LSPR aptamer sensor showed a response of 6‐nm λ_max shift for protein binding with the detection limit of at least 10 pM, indicating one of the highest sensitivities achieved for thrombin detection by optical extinction LSPR. We also tested the LSPR sensor fabricated using gold bipyramid, which showed higher refractive index sensitivity than the gold nanorods, but the overall response of gold bipyramid sensor appears to be 25% less than that of the gold nanorod substrate, despite the approximately twofold higher refractive index sensitivity. XPS analysis showed that this is due to the low surface density of aptamers on the gold bipyramid compared with gold nanorods. The low surface density of the aptamers on the gold bipyramid surface may be due to the effect of shape of the nanostructure on the kinetics of aptamer monolayer formation. The small size of aptamers relative to other bioreceptors is the key to achieving high sensitivity by biosensors on the basis of LSPR, demonstrated here for protein binding. The generality of aptamer sensors for protein detection using gold nanorod and gold nanobipyramid substrates is anticipated to have a large impact in the important development of sensors toward biomarkers, environmental toxins, and warfare agents. Copyright © 2013 John Wiley & Sons, Ltd.     

Direct Fabrication Route to Plastic-Supported Gold Nanoparticles for Flexible NIR-SERS

Stable gold nanoparticles with surface plasmon resonance tunable from visible (Vis) to near-infrared (NIR) are deposited via a direct sputtering methodology on large area polyethylene terephthalate (PET) to be used as effective, flexible NIR surface-enhanced Raman scattering (SERS) substrates. An O₂ plasma treatment of PET is used to tailor growth dynamics, geometry, and plasmonic properties of nanoparticles. The O₂ plasma treatment of PET results also in effective improvement of nanoparticle anchoring on the plastic substrate, providing more stable, flexible SERS systems. The functionality of fabricated SERS substrates has been tested using benzylthiol, and SERS enhancement factors in the range 10⁴ have been achieved, which are comparable with those reported in literature for gold nanostructures fabricated on silicon substrate. These results attest the great potentiality of this methodology for the production of cost-effective flexible and reusable large-scale SERS substrates.     

An A666G mutation in transmembrane helix 5 of the yeast multidrug transporter Pdr5 increases drug efflux by enhancing cooperativity between transport sites

Resistance to antimicrobial and chemotherapeutic agents is a significant clinical problem. Overexpression of multidrug efflux pumps often creates broad‐spectrum resistance in cancers and pathogens. We describe a mutation, A666G, in the yeast ABC transporter Pdr5 that shows greater resistance to most of the tested compounds than does an isogenic wild‐type strain. This mutant exhibited enhanced resistance without increasing either the amount of protein in the plasma membrane or the ATPase activity. In fluorescence quenching transport assays with rhodamine 6G in purified plasma membrane vesicles, the initial rates of rhodamine 6G fluorescence quenching of both the wild type and mutant showed a strong dependence on the ATP concentration, but were about twice as high in the latter. Plots of the initial rate of fluorescence quenching versus ATP concentration exhibited strong cooperativity that was further enhanced in the A666G mutant. Resistance to imazalil sulfate was about 3–4x as great in the A666G mutant strain as in the wild type. When this transport substrate was used to inhibit the rhodamine 6G transport, the A666G mutant inhibition curves also showed greater cooperativity than the wild‐type strain. Our results suggest a novel and important mechanism: under selection, Pdr5 mutants can increase drug resistance by improving cooperative interactions between drug transport sites.     

The extracellular loop between TM5 and TM6 of P-glycoprotein is required for reactivity with monoclonal antibody UIC2.

P-glycoprotein (P-gp), encoded by the MDR1 gene, is a plasma membrane transporter which confers resistance to many chemotherapeutic drugs. Monoclonal antibodies raised against P-gp have been used as tools to study P-gp topology and activity. Monoclonal antibody UIC2 recognizes a functional conformation of P-gp on the cell surface and blocks P-gp-mediated drug transport. Knowledge about the UIC2 epitope and the mechanism of its inhibitory effects may be helpful for understanding P-gp structure and developing P-gp inhibitors. In the present work, using several chimeras of MDR1 and MDR2, we found that the native sequence of the predicted extracellular loop between transmembrane domains (TM) 5 and 6 of P-gp is necessary, but not sufficient, for UIC2 reactivity. In addition, UIC2 reactivity is also affected by mutations in TM6, a region known to be involved in interactions of P-gp with substrates. These observations suggest that residues in the extracellular loop between TM5 and TM6 are directly involved in the display of the UIC2 epitope. Since TM6 has been shown to be actively involved in drug transport process, the proximity of this region to TM6 may help to explain why UIC2 binding is sensitive to the functional state of P-gp and why binding of UIC2 inhibits P-gp-mediated drug transport.