Surface plasmon resonance imaging measurements of ultrathin organic films

Biochemical assays of immobilized oligonucleotides with mass spectrometry

This paper reports the use of mass spectrometry to characterize oligonucleotides immobilized to the surfaces of biochips. Biotinylated oligonucleotides were immobilized to self-assembled monolayers that present a streptavidin layer and then treated with a complementary strand to present short duplexes. Treatment of the surface with 5-methoxysalicylic acid and ammonium citrate matrix allows the individual oligonucleotides to be observed by matrix-assisted laser desorption/iozation and time-of-flight mass spectrometry (MALDI-TOF MS). Examples are shown wherein this method is applied to assays of hybridization, of cleavage by a deoxyribozyme, of a dephosphorylation reaction, and of the adducts formed on treatment of DNA with cis-platin. This work provides an early example of the application of mass spectrometry to DNA biochips and may substantially expand the applications of the now common oligonucleotide arrays.

Quantitative surface plasmon resonance imaging: a simple approach to automated angle scanning

Here we present an automated angle-scanning surface plasmon resonance imaging (SPRi) instrument which provides multiplexed, quantitative reflectance data over a wide angular range. Angle-dependent artifacts, which arise from the simple optical setup, are corrected using software. This enables monitoring of significantly different surface coatings in many solvents, which would be outside the dynamic range of typical fixed-angle instruments. Operation in the visible to near-infrared range without the need for reconfiguration extends the instrument capabilities to increase sensitivity or to investigate the optical properties of surface films. This instrument provides maximum flexibility to study a wide range of systems with full exploitation of the quantitative capabilities of SPRi achieved by fitting data to the Fresnel model.

Ultra-high vacuum surface analysis study of rhodopsin incorporation into supported lipid bilayers

Planar supported lipid bilayers that are stable under ambient atmospheric and ultra-high-vacuum conditions were prepared by cross-linking polymerization of bis-sorbylphosphatidylcholine (bis-SorbPC). X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were employed to investigate bilayers that were cross-linked using either redox-initiated radical polymerization or ultraviolet photopolymerization. The redox method yields a more structurally intact bilayer; however, the UV method is more compatible with incorporation of transmembrane proteins. UV polymerization was therefore used to prepare cross-linked bilayers with incorporated bovine rhodopsin, a light-activated, G-protein-coupled receptor (GPCR). A previous study (Subramaniam, V.; Alves, I. D.; Salgado, G. F. J.; Lau, P. W.; Wysocki, R. J.; Salamon, Z.; Tollin, G.; Hruby, V. J.; Brown, M. F.; Saavedra, S. S. J. Am. Chem. Soc. 2005, 127, 5320-5321) showed that rhodopsin retains photoactivity after incorporation into UV-polymerized bis-SorbPC, but did not address how the protein is associated with the bilayer. In this study, we show that rhodopsin is retained in supported bilayers of poly(bis-SorbPC) under ultra-high-vacuum conditions, on the basis of the increase in the XPS nitrogen concentration and the presence of characteristic amino acid peaks in the ToF-SIMS data. Angle-resolved XPS data show that the protein is inserted into the bilayer, rather than adsorbed on the bilayer surface. This is the first study to demonstrate the use of ultra-high-vacuum techniques for structural studies of supported proteolipid bilayers.

Expanding the specificity of DNA targeting by harnessing cooperative assembly

The precise control of developmental and regulatory processes in the cell requires accurate recognition of specific DNA sites. For genomes as large as that of humans, single-molecule-DNA binders have difficulties accurately and specifically recognizing the intended targets. Natural transcription factors overcome these difficulties by forming non-covalent complexes on the DNA with other transcription factors. These cooperative complexes overcome the difficulties of single-molecule transcription factors, allowing specific, combinatorial control of a range of transcriptional targets. Artificial transcription factors have been designed to take advantage of this technique of cooperative assembly, facilitating future studies in whole genome targeting. In contrast to a simple model of component independence, cooperative complexes as a whole often display slightly altered DNA specificity from what would be expected from the analysis of their separate components. The true sequence specificity of cooperative complexes, and thus their presumed in vivo targets, have to be experimentally probed. A number of techniques, such as the cognate site identity array, now allow for rapid, high-throughput determination of the specificity of cooperative complexes.

Use of surface plasmon resonance imaging to study viral RNA:protein interactions

Surface plasmon resonance imaging (SPRi) is an emerging microarray technology that is label-free, rapid and extremely flexible. Here the capabilities of SPRi are demonstrated in results of proof-of-concept experiments detailing a method for studying viral genomic RNA:protein interactions in array format. The principal RNA is the well-characterized origin of assembly (OAS) containing region of Tobacco mosaic virus (TMV) RNA, whereas the principal protein is the primary subunit for TMV virion assembly, the 20S capsid protein aggregate. DNA probes complementary to TMV and non-TMV RNA fragments were covalently attached to a thin gold layer deposited on glass. These DNA probes were used to discreetly capture in vitro transcribed TMV and Red clover necrotic mosaic virus (RCNMV) RNA2 (used as a negative control for the subsequent protein binding). The 4S TMV capsid protein monomers were isolated from TMV particles purified from infected plants of Nicotiana tabacum L. and were induced to form 20S stacked disc aggregates. These 20S stacked disc aggregates were then injected onto the array containing the RNA fragments captured by the DNA probes immobilized on the microarray surface. The discrete and preferential binding of the 20S stacked disc aggregates to the array locations containing the TMV OAS RNA sequence was observed. The results demonstrate that SPRi can be used to monitor binding of large RNA molecules to immobilized DNA capture probes which can then be used to monitor the subsequent binding of complex protein structures to the RNA molecules in a single real-time, label-free microarray experiment. The results further demonstrate that SPRi can distinguish between RNA species that have or do not have an origin of assembly sequence specific for a particular viral capsid protein or protein complex. The broader implications of these results in virology research are found in other systems where the research goals include characterizing the specificity and kinetics of viral or host protein or protein complex interactions with viral nucleic acids.

Relating material surface heterogeneity to protein adsorption: the effect of annealing of micro-contact-printed OTS patterns

We have investigated the influence of micrometer- and sub-micrometer-scale surface heterogeneities in patterned octadecyltrichlorosilane (OTS) films on human serum albumin (HSA) adsorption and its spatial distribution. 5-μm-wide OTS patterns were created on glass substrates by micro-contact printing and in some instances subsequent annealing was used to alter OTS molecule distribution within the patterns. Scanning force microscopy (SFM), advancing water contact angles and water vapor condensation figures were used to characterize the OTS films and to assess the nature of the heterogeneities within the various surface areas. High-resolution fluorescence microscopy was used to record images of fluorescently labeled albumin on OTS patterned films and fluorescence intensity was quantified and converted into the adsorbed amount. Adsorbed albumin was also characterized through SFM measurements. Combined SFM topography and lateral force microscopy (LFM) imaging revealed that micro-contact printing of OTS onto glass both replicated the stamp pattern and created small islands within the non-stamped regions between the patterns. The OTS coverage within stamped regions was not fully continuous but improved with subsequent annealing. Annealing also resulted in OTS island growth within the non-stamped regions and decreased average wettability on both the stamped and non-stamped areas. The extent of albumin adsorption was not proportional to OTS coverage, but correlated with the sub-μm distribution of OTS chains. We inferred that the surface distribution of ligands such as OTS on a sub-μm length scale determines the nature of albumin adsorption and its kinetics.

Polymeric optical microscreen for high-resolution surface plasmon resonance microarray imaging

In this study, we demonstrate a simple method to fabricate surface plasmon resonance (SPR) imaging microarrays using polymer micropatterns. The use of a micrometer-scale polymeric optical screen (microPOS) passivates the region deposited with polymer by completely removing SPR signals or by saturating the SPR signal far beyond the detection range of SPR imaging. Two schemes were suggested to create a surface microPOS by either micropatterning a thick insulating layer before deposition of a metal layer (complete removal of SPR) or after deposition of a metal layer (saturation of SPR signal). The two schemes were successfully applied for the imaging of biological adsorption with a high imaging resolution of approximately 100 microm/pattern and 10 microm separation. The validity of the system was verified with a biotin-streptavidin system as a model for the systematic binding of biomolecules. Further, binding of prostate-specific antigen (PSA) onto the anti-PSA SPR microarray was demonstrated as a useful method for detecting a cancer marker.

Label-Free Sensing of Binding to Microarrays Using Brewster Angle Straddle Interferometry

We report an interferometric method to detect chemical binding at an interface. The interference layer consists of the thin native oxide on silicon, and we utilize nearly opposite phase shifts of light at the oxide/water and oxide/silicon interfaces to achieve near-complete destructive interference. We measure selective binding of thrombin in solution to DNA aptamers covalently bound to the oxide. The technique can be used to detect and quantify surface binding of less than 1 A of material, sensitivity similar to that of surface plasmon resonance imaging or arrayed imaging reflectometry. Results are in quantitative agreement with what is predicted theoretically. The method is very convenient to implement since it utilizes unmodified silicon wafers as substrates and is extremely insensitive to both probe light bandwidth and collimation.

Ultrafast studies of gold, nickel, and palladium nanorods

Steady state and ultrafast transient absorption studies have been carried out for gold, nickel, and palladium high aspect ratio nanorods. For each metal, nanorods were fabricated by electrochemical deposition into approximately 6 microm thick polycarbonate templates. Two nominal pore diameters(10 and 30 nm, resulting in nanorod diameters of about 40 and 60 nm, respectively) were used, yielding nanorods with high aspect ratios (>25). Static spectra of nanorods of all three metals reveal both a longitudinal surface plasmon resonance (SPR(L)) band in the mid-infrared as well as a transverse band in the visible for the gold and larger diameter nickel and palladium nanorods. The appearance of SPR(L) bands in the infrared for high aspect ratio metal nanorods and the trends in their maxima for the different aspect ratios and metals are consistent with calculations based on the Gans theory. For the gold and nickel samples, time resolved studies were performed with a subpicosecond resolution using 400 nm excitation and a wide range of probe wavelengths from the visible to the mid-IR as well as for infrared excitation (near 2000 cm(-1)) probed at 800 nm. The dynamics observed for nanorods of both metals and both diameters include transients due to electron-phonon coupling and impulsively excited coherent acoustic breathing mode oscillations, which are similar to those previously reported for spherical and smaller rod-shaped gold nanoparticles. The dynamics we observe are the same within the experimental uncertainty for 400 nm and infrared (5 microm) excitation probed at 800 nm. The transient absorption using 400 nm excitation and 800 nm probe pulses of the palladium nanorods also reveal coherent acoustic oscillations. The results demonstrate that the dynamics for high aspect ratio metal nanorods are similar to those for smaller nanoparticles.

Evanescent wave excited luminescence from levitated quantum dot modified colloids

Evanescent wave excited luminescence of quantum dot modified polystyrene (QDPS) colloids is investigated to measure potential energy profiles of QDPS colloids electrostatically levitated above a planar glass surface. Luminescence is characterized for three different-sized PS colloids modified with three different-sized QDs using confocal microscopy, emission spectra, flow cytometry, and temporal measurements of levitated and deposited colloids. Colloid-surface potential energy profiles constructed from scattering and luminescence intensity data display excellent agreement with each other, theoretical predictions, and independently measured parameters. QDPS luminescence intensity is indirectly confirmed to have an exponential dependence on height similar to conventional colloidal evanescent wave scattering. Our findings indicate that evanescent wave excited QDPS luminescence could enable total internal reflection microscopy measurements of index-matched hard spheres, multiple specific biomolecular interactions via spectral multiplexing, enhanced morphology-dependent resonance modes, and integrated evanescent wave-video-confocal microscopy experiments not possible with scattering.

Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips

We report on the use of PDMS multichannels for affinity studies of DNA aptamer-human Immunoglobulin E (IgE) interactions by surface plasmon resonance imaging (SPRi). The sensing surface was prepared with thiol-terminated aptamers through a self-assembling process in the PDMS channels defined on a gold substrate. Cysteamine was codeposited with the thiol aptamers to promote proper spatial arrangement of the aptamers and thus maintain their optimal binding efficiencies. Four aptamers with different nucleic acid sequences were studied to test their interaction affinity toward IgE, and the results confirmed that aptamer I (5'-SH-GGG GCA CGT TTA TCC GTC CCT CCT AGT GGC GTG CCC C-3') has the strongest binding affinity. Control experiments were conducted with a PEG-functionalized surface and IgG was used to replace IgE in order to verify the selective binding of aptamer I to the IgE molecules. A linear concentration-dependent relationship between IgE and aptamer I was obtained, and a 2-nM detection limit was achieved. SPRi data were further analyzed by global fitting, and the dissociation constant of aptamer I-IgE complex was found to be 2.7 x 10(-7) M, which agrees relatively well with the values reported in the literature. Aptamer affinity screening by SPR imaging demonstrates marked advantages over competing methods because it does not require labeling, can be used in real-time, and is potentially high-throughput. The ability to provide both qualitative and quantitative results on a multichannel chip further establishes SPRi as a powerful tool for the study of biological interactions in a multiplexed format.

Generation of infrared surface plasmon resonances with high refractive index sensitivity utilizing tilted fiber Bragg gratings

We demonstrate the use of tilted fiber gratings to assist the generation of localized infrared surface plasmons with short propagation lengths and a sensitivity of dlambda/dn = 3,365 nm in the aqueous index regime. It was also found that the resonances could be spectrally tuned over 1,000 nm at the same spatial region with high coupling efficiency (in excess of 25 dB) by altering the polarization of the light illuminating the device.

Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays

Cell surface carbohydrates play important roles in a wide variety of biological processes including cell adhesion, fertilization, differentiation, development, and tumor cell metastasis. Lectins are proteins of nonimmune origin which recognize and bind to specific carbohydrate structural epitopes. We have recently described the development and use of lectin arrays as tools for the elucidation of the carbohydrate structures expressed on cell surfaces. In the present work this technology is employed for the characterization of differences in carbohydrate expression patterns on normal and tumorigenic human breast cell lines, as well as on sublines differing in their tendency to "home" to different tissues during metastasis. Significant differences were observed, including changes that correlate with metastatic potential as well as with tissue-specific homing of metastatic cells.

Dissipation-enhanced quartz crystal microbalance studies on the experimental parameters controlling the formation of supported lipid bilayers

We report on the investigations of the transformation of spherically closed lipid bilayers to supported lipid bilayers in aqueous media in contact with SiO(2) surfaces. The adsorption kinetics of small unilamellar vesicles composed of dimyristoyl- (DMPC) and dipalmitoylphosphatidylcholine (DPPC) mixtures on SiO(2) surfaces were investigated using a dissipation-enhanced quartz crystal microbalance (QCM-D) as a function of buffer (composition and pH), lipid concentration (0.01-1.0 mg/mL), temperature (15-37 degrees C), and lipid composition (DMPC and DMPC/DPPC mixtures). The lipid mixtures used here possess a phase transition temperature (T(m)) of 24-33 degrees C, which is close to the ambient temperature or above and thus considerably higher than most other systems studied by QCM-D. With HEPES or Tris.HCl containing sodium chloride (150 mM) and/or calcium chloride (2 mM), intact vesicles adsorb on the surface until a critical density ((c)) is reached. At close vesicle contact the transformation from vesicles to supported phospholipid bilayers (SPBs) occurs. In absence of CaCl(2), the kinetics of the SPB formation process are slowed, but the passage through (c) is still observed. The latter disappears when buffers with low ionic strength were used. SPB formation was studied in a pH range of 3-10, yet the passage through (c) is obtained only for pH values above to the physiological pH (7.4-10). With an increasing vesicle concentration, (c) is reached after shorter exposure times. At a vesicle concentration of 0.01-1 mg/mL, vesicle fusion on SiO(2) proceeds with the same pathway and accelerates roughly proportionally. In contrast, the pathway of vesicle fusion is strongly influenced by the temperature in the vicinity of T(m). Above and around the T(m), transformation of vesicles to SPB proceeds smoothly, while below, a large number of nonruptured vesicles coexist with SPB. As expected, the physical state of the membrane controls the interaction with both surface and neighboring vesicles.

Real-time and full-field detection of near-wall salinity using surface plasmon resonance reflectance

An idea of real-time and full-field detection of near-wall salinity is presented to use the surface plasmon resonance (SPR) reflectance that changes with refractive index variations of the tested saline fluid. The laboratory-designed SPR system, based on the Kretschmann's configuration, uses a 47.5 nm thick gold layer as the SPR resonator, coated on a BK7 prism (n=1.515), and requires a one-time system calibration to establish a correlation of the specified saline mass concentration levels to the corresponding CCD (charge-coupled device) pixel gray levels. As a gravity-falling saline drop in water reaches the bottom and diffuses thereafter, the SPR system quantitatively maps the evolution of the salinity distributions in the near-wall region (less than 1 microm). An elaborate uncertainty analysis shows that the overall measurement uncertainties critically depend on the uniformity of the metal film thickness and the accuracy of its dielectric constant.

Multichannel biosensing platform of surface-immobilized gold nanospheres for linear and nonlinear optical imaging

What we believe to be a new label-free multichannel biosensing platform is proposed. It is composed of surface-immobilized gold nanospheres (SIGNs) above a gold surface with a nanogap supported by a merocyanine self-assembled monolayer. The circular SIGN spots with a diameter of 120 microm were arrayed for multichannel biosensing on a glass slide. Two kinds of sensing methods were examined: One is a reflectivity measurement of a blue ray and the other is a second-harmonic generation measurement. It was found that the SIGN system can be used as a promising platform for multichannel biosensing in both sensing methods.

Multicolor Surface Plasmon Resonance Imaging of Ink Jet-Printed Protein Microarrays

We report a technique that utilizes surface plasmon resonance dispersion as a mechanism to provide multicolor contrast for imaging thin molecular films. Illumination of gold surfaces with p-polarized white light in the Kretschmann configuration produces distinct reflected colors due to excitation of surface plasmons and the resulting absorption of specific wavelengths from the source light. In addition, these colors transform in response to the formation of thin molecular films. This process represents a simple detection method for distinguishing between films of varying thickness in sensor applications. As an example, we interrogated a protein microarray formed by a commercial drop-on-demand chemical ink jet printer. Submonolayer films of a test protein (bovine serum albumin) were readily detected by this method. Analysis of the dispersion relations and absorbance sensitivities illustrate the performance and characteristics of this system. Higher detection sensitivity was achieved at angles where red wavelengths coupled to surface plasmons. However, improved contrast and spatial resolution occurred when the angle of incidence was such that shorter wavelengths coupled to the surface plasmons. Simplified optics combined with the robust microarray printing platform are used to demonstrate the applicability of this technique as a rapid and versatile, high-throughput tool for label-free detection of adsorbed films and macromolecules.

Optically responsive nanoparticle layers for the label-free analysis of biospecific interactions in array formats

A novel nanocomposite surface is prepared by coating surface-adsorbed dielectric colloidal particles with a contiguous layer of gold nanoparticles. The resulting surface shows pronounced optical extinction in reflection with the extinction peaks located in the UV-Vis and NIR region of the electromagnetic spectrum. The peak positions of these maxima change very sensitively with the adsorption of organic molecules onto the surface. For the adsorption of a monolayer of octadecanethiol, we observe a peak shift of 55 nm on average, which is about five times that of established label-free sensing methods based on propagating and localized surface plasmons. In a first proof-of-principle experiment, the interaction of peptides with specific antibodies has been detected without labeling by means of a fiber-optical set-up with microscopic lateral resolution. To avoid crosstalk in high-density arrays, the optically responsive surface areas can be locally separated on a micro- or even nanometer scale. Accordingly, the newly developed optically responsive surfaces are well suited for integration into high-density peptide or DNA arrays as demanded in genomics, proteomics, and biomedical research in general.

Localized Surface Plasmon Resonance Spectroscopy and Sensing

Localized surface plasmon resonance (LSPR) spectroscopy of metallic nanoparticles is a powerful technique for chemical and biological sensing experiments. Moreover, the LSPR is responsible for the electromagnetic-field enhancement that leads to surface-enhanced Raman scattering (SERS) and other surface-enhanced spectroscopic processes. This review describes recent fundamental spectroscopic studies that reveal key relationships governing the LSPR spectral location and its sensitivity to the local environment, including nanoparticle shape and size. We also describe studies on the distance dependence of the enhanced electromagnetic field and the relationship between the plasmon resonance and the Raman excitation energy. Lastly, we introduce a new form of LSPR spectroscopy, involving the coupling between nanoparticle plasmon resonances and adsorbate molecular resonances. The results from these fundamental studies guide the design of new sensing experiments, illustrated through applications in which researchers use both LSPR wavelength-shift sensing and SERS to detect molecules of chemical and biological relevance.

Integrated Label-Free Protein Detection and Separation in Real Time Using Confined Surface Plasmon Resonance Imaging

We demonstrate a label-free protein detection and separation technology for real-time monitoring of proteins in micro/nanofluidic channels, confined surface plasmon resonance imaging (confined-SPRi). This was achieved by fabricating ultrathin fluidic channels (500 nm high, 500 microm wide) directly on top of a specialized SPRi sensor surface. In this way, SPRi is uniquely used to detect proteins deep into the fluidic channel while maintaining high lateral accuracy of separated products. The channel fluid and proteins were driven electrokinetically under an external electric field. For this to occur, the metallic SPR sensor (46 nm of Au on 2 nm of Cr) was segmented into an array of squares (each 200 microm x 200 microm in size and spaced 8 microm apart) and coated with 30 nm of CYTOP polymer. In this work, we track label-free protein separation in real time through a simple cross-junction fluidic device with an 8-mm separation channel length under 30 V/cm electric field strength.

Specific Immobilization of Streptavidin on Mixed Self-Assembled Monolayers as Mixing Ratio

We report on the distribution of mixed self-assembled monolayers (SAMs) composed of biotinylated and diluent alkylthiolates for streptavidin immobilization. Two thiol derivatives, 11-mercapto-1-undecanol (MUOH) and 11-mercaptoundecanoic-(8-biotinylamido-3,6-dioxaoctyl) amide (MBDA), were employed for mixed SAM. These thiols formed self-assembled monolayer without local domain, and streptavidins were immobilized onto biotinylated gold surface without nonspecific binding. In order to find the optimized condition of immobilization of streptavidin, we controlled the mixing ratio of two kind thiols by colorimetric detection assay, and the immobilization was characterized by atomic force microscopy (AFM), scanning tunneling microscopy (STM), and ellipsometer.

Nonfouling surfaces: a review of principles and applications for microarray capture assay designs

Microarray technology, like many other surface-capture diagnostic methods, relies on fidelity of affinity interactions between a surface-bound probe (e.g., nucleic acid or antibody) and its target in the sample milieu to produce an assay signal specific to analyte. These interfacial interactions produce the assay result with the associated assay requirements for sensitivity, specificity, reproducibility, and ease-of-use. For surface-capture assays, surface properties play a critical role in this performance. Microarray surfaces are routinely immersed into aqueous target solutions of varying complexity, from simple saline or buffer solutions to serum, tissue, food, or microbiological lysates involving thousands of different solutes. The surface chemistry must not only be capable of immobilizing probes at high density in microscale patterned spots, retaining probe affinity for target within these spots, reducing target capture outside of these spots, but also be efficient at eliminating nontarget capture anywhere else on the surface. Historically, the development of surface chemistry with these specific "nonfouling" properties has been an intense interest for bioassays, with many types of architectures, molecular compositions, and performance capabilities across many different surface-capture assays. The unique environment of the bioassay, including the long-standing problems associated with high concentrations of "nontarget" proteins and other surface-active biomolecules in the assay milieu, has proven to be quite challenging to surface chemistry performance. Microarray technology designs with microspotted patterns must address these problems in these challenging dimensions in order to improve signal:noise ratios for captured target signals on surfaces. This chapter reviews principles of protein-surface interfacial physical chemistry, protein adsorption as a source of assay noise, and various approaches to control this interface in the context of surface-capture assay fabrication and improving assay performance from complex milieu. Practical methods to modify surfaces for biological assay are presented. Polymer substrate coating methods, including "grafting from" and "grafting to" strategies, polymer brushes, and alternative surface modification methods are reviewed. Methods to assess biological "fouling" in the bioassay format are also discussed.

Surface plasmon resonance as a time-resolved probe of structural changes in molecular films: considerations for correlating resonance shifts with adsorbate layer parameters

Surface plasmon resonance (SPR) spectroscopy is an efficient probe of transient structural changes in molecular films. To analyze kinetic SPR data for such systems, generally it is necessary to adapt an adequate theoretical framework that would allow one to express the measured optical quantities (time-dependent shifts of the resonance angle or wavelength) in terms of the structural parameters (layer thickness, mass density, or surface coverage) of the sample molecules. We present here theoretical calculations and illustrative experimental results to address certain essential elements of this type of data analysis for transient SPR systems. The phenomenological framework we consider here is based on multilayer reflectivity calculations, and can be applied to a broad class of systems involving ordered molecular layers on supporting gold films. A typical application of these calculations is demonstrated through the analysis of specific SPR experiments designed to probe the kinetics of pH-induced structural changes in a molecular film of 11-mercaptoundecanoic acid (MUA) on a thin gold film.

Self-Assembled Monolayers with Latent Aldehydes for Protein Immobilization

Aldehyde functions are widely used for immobilization of biomolecules on glass surfaces but have found little attention for biofunctionalization of self-assembled monolayers (SAMs) on gold, due to interference between thiol and aldehyde functions. This problem was recently solved by synthesis of an alkanethiol that carried a vicinal diol group [Jang et al. (2003) Nano Lett. 3, 691-694]. The latter served as a latent aldehyde function that was unmasked by short exposure of the vicinal diol-terminated SAM to aqueous periodate. However, the synthesis of the new vicinal diol-terminated alkane thiol was time-consuming and had an overall yield of approximately 3.5%. In the present study, a general modular strategy was introduced by which SAM components with vicinal diol functions were rapidly synthesized with high yield: this was accomplished by amide bond formation between a SAM-forming carboxylic acid (exemplified by lipoic acid and 16-mercaptohexadecanoic acid) with 3-aminopropane-1,2-diol, using suitable protecting groups. The disulfide or free thiol group afforded SAM formation on gold and, after periodate oxidation of the vicinal diol functions, proteins were covalently bound via their lysine residues. At 1 mg/mL protein concentration, complete surface coverage was reached within minutes. No further protein was bound by nonspecific adsorption, but cognate proteins were specifically bound with high capacity. Pyrogallol-O-hexadecanoic acid and 10-undecenoic acid were also coupled with 3-aminopropane-1,2-diol by amide bond formation, thereby producing latent aldehyde-containing SAM components for metal oxides and hydrogen-terminated silicon, respectively, to show the general usefulness of the new synthetic design.

Production of radially and azimuthally polarized polychromatic beams

We describe a system that efficiently provides radially or azimuthally polarized radiation from a randomly polarized source. It is constructed from two conical reflectors and a cylindrical sheet of polarizing film. Envisaged applications include a microscope illuminator for high-resolution surface plasmon resonance microscopy, illumination for high-resolution microlithography, and efficient coupling of a laser source to hollow optical fibers. The angular coherence function of light polarized by the device was measured to evaluate its usefulness for these applications.

Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging

RNA microarrays were created on chemically modified gold surfaces using a novel surface ligation methodology and employed in a series of surface plasmon resonance imaging (SPRI) measurements of DNA-RNA hybridization and RNA aptamer-protein binding. Various unmodified single-stranded RNA (ssRNA) oligonucleotides were ligated onto identical 5'-phosphate-terminated ssDNA microarray elements with a T4 RNA ligase surface reaction. A combination of ex situ polarization modulation FTIR measurements of the RNA monolayer and in situ SPRI measurements of DNA hybridization adsorption onto the surface were used to determine an ssRNA surface density of 4.0 x 10(12) molecules/cm2 and a surface ligation efficiency of 85 +/- 10%. The surface ligation methodology was then used to create a five-component RNA microarray of potential aptamers for the protein factor IXa (fIXa). The relative surface coverages of the different aptamers were determined through a novel enzymatic method that employed SPRI measurements of a surface RNase H hydrolysis reaction. SPRI measurements were then used to correctly identify the best aptamer to fIXa, which was previously determined from SELEX measurements. A Langmuir adsorption coefficient of 1.6 x 10(7) M(-1) was determined for fIXa adsorption to this aptamer. Single-base variations from this sequence were shown to completely destroy the aptamer-fIXa binding interaction.

Quantitative multispectral biosensing and 1D imaging using quasi-3D plasmonic crystals

We developed a class of quasi-3D plasmonic crystal that consists of multilayered, regular arrays of subwavelength metal nanostructures. The complex, highly sensitive structure of the optical transmission spectra of these crystals makes them especially well suited for sensing applications. Coupled with quantitative electrodynamics modeling of their optical response, they enable full multiwavelength spectroscopic detection of molecular binding events with sensitivities that correspond to small fractions of a monolayer. The high degree of spatial uniformity of the crystals, formed by a soft nanoimprint technique, provides the ability to image binding events over large areas with micrometer spatial resolution. These features, together with compact form factors, low-cost fabrication procedures, simple readout apparatus, and ability for direct integration into microfluidic networks and arrays, suggest promise for these devices in label-free bioanalytical detection systems.

Diffusing colloidal probes of protein and synthetic macromolecule interactions

A new approach is described for measuring kT and nanometer scale protein-protein and protein-synthetic macromolecule interactions. The utility of this method is demonstrated by measuring interactions of bovine serum albumin (BSA) and copolymers with exposed polyethyleneoxide (PEO) moieties adsorbed to hydrophobically modified colloids and surfaces. Total internal reflection and video microscopy are used to track three-dimensional trajectories of many single diffusing colloids that are analyzed to yield interaction potentials, mean-square displacements, and colloid-surface association lifetimes. A criterion is developed to identify colloids as being levitated, associated, or deposited based on energetic, spatial, statistical, and temporal information. Whereas levitation and deposition occur for strongly repulsive or attractive potentials, association is exponentially sensitive to weak interactions influenced by adsorbed layer architectures and surface heterogeneity. Systematic experiments reveal how BSA orientation and PEO molecular weight produce adsorbed layers that either conceal or expose substrate heterogeneities to generate a continuum of colloid-surface association lifetimes. These measurements provide simultaneous access to a broad range of information that consistently indicates purely repulsive BSA and PEO interactions and a role for surface heterogeneity in colloid-surface association. The demonstrated capability to measure nonspecific protein interactions provides a basis for future measurements of specific protein interactions.

Reversible pH-Driven Conformational Switching of Tethered Superoxide Dismutase with Gold Nanoparticle Enhanced Surface Plasmon Resonance Spectroscopy

A new class of surface-immobilized protein nanomachines can be reversibly actuated by cycling the solution pH between 2.5 and 12.3, which induces a conformational change, thereby modulating the thickness of superoxide dismutase (SOD1) tethered to the Au thin film. By placing Au nanoparticles (AuNP) atop the immobilized SOD1 by means of a gold-thiol assembly, the nanoscale motion of SOD1 at the interface produces mechanical work to lift and then lower the AuNP from the Au substrate by a distance of ca. 3 nm and transduces this motion into an easily measurable reflectivity change in the surface plasmon resonance (SPR) spectrum. As-made supported conjugate consisting of SOD1 and AuNP is quite robust and stable, and its operation in response to pH variations, which mirrors the conformational changes of responsive SOD1 at the interface, is found to be highly reversible and reproducible. This is the first demonstration of the development of novel solid-state sensors and/or switching devices based on substrate-bound protein conformational changes and AuNP enhanced SPR spectroscopy.

Direct evidence for surface plasmon-mediated enhanced light transmission through metallic nanohole arrays

This paper provides direct evidence for the role of surface plasmons in the enhanced optical transmission of light through metallic nanoscale hole arrays. Near-field optical images directly confirmed the presence of surface plasmons on gold nanohole arrays with interhole spacings larger than the surface plasmon wavelength. A simple interference model provides an intuitive explanation of the two types of fringe wavelengths observed in the near-field optical images. Far-field spectroscopy revealed a surface plasmon band that contributed a factor > 8 to the transmission enhancement. Furthermore, silicon nanohole arrays did not exhibit any features in the near-field, which demonstrates that metallic materials are necessary for enhanced light transmission through nanohole arrays.

Surface plasmon resonance imaging on a microchip for detection of DNA-modified gold nanoparticles deposited onto the surface in a non-cross-linking configuration

Recently we reported that gold nanoparticles (GNPs) with fully matched duplexes on their surfaces are selectively deposited onto walls of poly(dimethylsiloxane) (PDMS) microchannels at high salt concentrations. In this study, the surface plasmon resonance (SPR) imaging technique was applied to monitor this phenomenon for improvement of detection sensitivity and elucidation of the phenomenon. The microchip was fabricated by bonding a surface-patterned PDMS plate and a gold thin film-deposited glass substrate. Probe oligonucleotide-modified GNPs were hybridized with target oligonucleotides to make fully matched or single-base-mismatched duplexes. The hybridized GNP solution was mixed with an NaCl solution in a Y-shaped microchannel. The deposition of the GNPs onto the gold sensor surface was detected by SPR imaging. Discrimination of the targets was possible with limit of detection of 32 nM (19 fmol) without temperature control in 5 min. Detailed analysis indicated that a seed layer of GNPs was initially adsorbed onto the sensor surface regardless of the target sequence. Therefore, in combination with a portable SPR device, the proposed method is promising for point-of-care testing of single-nucleotide polymorphsims.

Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies

Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.

Measurement of antibody binding to protein immobilized on gold nanoparticles by localized surface plasmon spectroscopy

Antibody binding to bovine serum albumin (BSA) and human serum albumin (HSA) immobilized onto gold nanoparticles was studied by means of localized surface plasmon resonance (LSPR) spectroscopy. Amine-modified glass was prepared by self-assembly of amine-terminated silane on substrate, and gold (Au) nanoparticles were deposited on the amine-modified glass substrate. Au nanoparticles deposited on the glass surface were functionalized by BSA and HSA. BSA immobilization was confirmed by LSPR spectroscopy in conjunction with surface-enhanced Raman scattering spectroscopy. Then, LSPR response attributable to the binding of anti-BSA and anti-HSA to BSA- and HSA-functionalized Au nanoparticles, respectively, was examined. Anti-HSA at levels larger than approximately 10 nM could be detected by HSA-immobilized chips with LSPR optical response, which was saturated at concentrations greater than approximately 650 nM of anti-HSA.

Charging behavior of single-stranded DNA polyelectrolyte brushes

DNA monolayers are widely used in fundamental and applied genomics and are versatile experimental models for elucidating the behavior of charged polymers at interfaces. The physical behavior of these systems is to a large extent governed by their internal ionic microenvironment, which is investigated here for layers of end-tethered, single-stranded DNA oligonucleotides (DNA brushes). Retention of counterions by the DNA brush manifests as lowered susceptibility of the interfacial capacitance to external salt conditions. A physical model based on concepts adapted from polymer science was used to further elucidate the connection between monolayer organization and its charging behavior. The data indicate a reorganization of the monolayer with changes in ionic strength and strand coverage that is consistent with that expected for a polyelectrolyte brush. A method for electrochemical quantification of strand coverage, based on shift of reduction potential for redox counterions associated with the DNA monolayer, is also described. These results provide guidance for development of label-free electrochemical diagnostics employing DNA monolayers and formulate a description of monolayer behavior within a polymer science framework.

Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films

Aldehyde-terminated self-assembled monolayers (SAMs) on gold surfaces were modified with proteins and employed to capture intact living cells through specific ligand-cell surface receptor interactions. In our model system, the basic fibroblast growth factor (bFGF) binding receptor was targeted on baby hamster kidney (BHK-21) cells. Negative control and target proteins were immobilized on a gold surface by coupling protein primary amines to surface aldehyde groups. Cell-binding was monitored by phase contrast microscopy or surface plasmon resonance (SPR) imaging. The specificity of the receptor-ligand interaction was confirmed by the lack of cell binding to the negative control proteins, cytochrome c and insulin, and by the disruption of cell binding by treatment with heparitinase to destroy heparan sulfate which plays an essential role in the binding of bFGF to FGF receptors. This approach can simultaneously probe a large number of receptor-ligand interactions in cell populations and has potential for targeting and isolating cells from mixtures according to the receptors expressed on their surface.