Femtomolar sensitivity using a channel-etched thin film waveguide fluoroimmunosensor

Extraordinary light transmission through opaque thin metal film with subwavelength holes blocked by metal disks

We observed that when subwavelength-sized holes in an optically opaque metal film are completely covered by opaque metal disks larger than the holes, the light transmission through the holes is not reduced, but rather enhanced. Particularly we report (i) the observation of light transmission through the holes blocked by the metal disks up to 70% larger than the unblocked holes; (ii) the observation of tuning the light transmission by varying the coupling strength between the blocking disks and the hole array, or by changing the size of the disks and holes; (iii) the observation and simulation that the metal disk blocker can improve light coupling from free space to a subwavelength hole; and (iv) the simulation that shows the light transmission through subwavelength holes can be enhanced, even though the gap between the disk and the metal film is partially connected with a metal. We believe these finding should have broad and significant impacts and applications to optical systems in many fields.

Planar silicon nitride waveguides for biosensing

The principles of attenuation of the light intensity due to multiple reflections are realised in a planar silicon oxide (SiO(2))silicon nitride (Si(3)N(4)) waveguiding structure for the purpose of developing optical biosensors with improved sensitivity. The analysis of the experimental data shows that the large difference in refractive indices of core and cladding layers gives rise to an increase in sensitivity by a factor of 3 over previously reported structures. Composite polyelectrolyte self-assembled thin films containing cyclo-tetra-chromotropylene as an indicator and enzymes glucose oxidase or urease were employed in the superstrate as a sensing membrane. Individual enzyme reactions as well as their inhibition by pesticides were studied by monitoring the intensity of light output from the planar waveguide. The results were compatible with those obtained by conventional ultraviolet-visible absorption spectroscopy. The instrument detection limit for Imidacloprid pesticide was found to be as low as 10 ppb in concentration.

Microarray temperature optimization using hybridization kinetics

In any microarray hybridization experiment, there are contributions at each probe spot due to the match and numerous mismatch target species (i.e., cross-hybridizations). One goal of temperature optimization is to minimize the contribution of mismatch species; however, achieving this goal may come at the expense of obtaining equilibrium reaction conditions. We employ two-component thermodynamic and kinetic models to study the trade-offs involved in temperature optimization. These models show that the maximum selectivity is achieved at equilibrium, but that the mismatch species controls the time to equilibrium via the competitive displacement mechanism. Also, selectivity is improved at lower temperatures. However, the time to equilibrium is also extended, so that greater selectivity cannot be achieved in practice. We also employ a two-color real-time microarray reader to experimentally demonstrate these effects by independently monitoring the match and mismatch species during multiplex hybridization. The only universal criterion that can be employed is to optimize temperature based upon attaining equilibrium reaction conditions. This temperature varies from one probe to another, but can be determined empirically using standard microarray experimentation methods.

Nonlinear immunofluorescent assay for androgenic hormones based on resonant structures

We report for the first time the use of two photon fluorescence as detection method of affinity binding reactions. We use a resonant grating waveguide structure as platform enhancement for detecting the interaction between fluorescent labeled Boldenone, a non-natural androgenic hormone, and a specific anti-anabolic antibody. We were able to detect a surface coverage of approximately 0.7 ng/mm(2).

Impact of protein shedding on detection of Mycobacterium avium subsp. paratuberculosis by a whole-cell immunoassay incorporating surface-enhanced Raman scattering

The etiological agent of Johne's disease is Mycobacterium avium subsp. paratuberculosis. Controlling the spread of this disease is hindered by the lack of sensitive, selective, and rapid detection methods for M. avium subsp. paratuberculosis. By using a recently optimized sandwich immunoassay (B. J. Yakes, R. J. Lipert, J. P. Bannantine, and M. D. Porter, Clin. Vaccine Immunol. 15:227-234, 2008), which incorporates a new monoclonal antibody for the selective capture and labeling of M. avium subsp. paratuberculosis and surface-enhanced Raman scattering for sensitive readout, detection limits of approximately 630 and approximately 740 M. avium subsp. paratuberculosis cells/ml are achieved in phosphate-buffered saline and whole milk samples, respectively, after spiking with heat-treated M. avium subsp. paratuberculosis. Surprisingly, these detection limits are 3 orders of magnitude lower than expected based on theoretical predictions. Experiments designed to determine the origin of the improvement revealed that the major membrane protein targeted by the monoclonal antibody was present in the sample suspensions as shed protein. This finding indicates that the capture and labeling of shed protein function as a facile amplification strategy for lowering the limit of detection for M. avium subsp. paratuberculosis that may also be applicable to the design of a wide range of highly sensitive assays for other cells and viruses.

Effects of fill fraction on the capture efficiency of nanoscale molecular transducers

We study the effects of nanotransducer fill fraction on the molecular capture efficiency contribution to overall sensor response. Contrary to expectation, we show that the relative capture efficiency can exceed the fill fraction in the transient regime. However, at thermodynamic equilibrium, the relative efficiency equals the fill fraction in the probe-limited case. When the number of target molecules in solution is the limiting factor in capture, then gains in capture efficiency can be obtained even at thermodynamic equilibrium. The important implication of these results is that significant intrinsic nanotransducer enhancement is necessary in order to provide net gain in sensor response, but that nanotransducer enhancement does not need to exceed the inverse fill fraction. In addition, net gain in overall sensor response is more readily achievable at low target concentrations.

Cross-Correlation of Optical Microcavity Biosensor Response with Immobilized Enzyme Activity. Insights into Biosensor Sensitivity

Porous silicon multilayer structures have remarkable optical and morphological properties that can be exploited for biosensing. In particular, a high internal surface area (>100 m(2)/cm(3)) and a linear response profile to changes in the dielectric environment enable fabrication of sensitive devices and a straightforward quantitation of the optical response. These essential operating characteristics are illustrated for p+ mesoporous silicon (pore diameter 15-20 nm) optical microcavities. A series of devices were prepared to permit the immobilization of glutathione-S-transferase ( approximately 50 kDa) within the porous matrix. Enzyme activity was exploited as an indirect means to quantitate the amount of protein immobilized. Activity was positively correlated with the optical sensor response. However, at high enzyme load the activity becomes nonlinear while the microcavity response remains linear. These data were used to determine the transduction limit (minimum amount of protein required to transduce an optical response), which is reported as areal mass sensitivity ranging between 50 and 250 pg/mm(2). This value is considered in context with the dynamic range of the bulk sensitivity, defined as the magnitude of the wavelength shift per refractive index unit, which was measured as a function of microcavity design parameters. This work has uncovered key parameters that can be tuned to improve the detection limit of this sensor modality. Because of the ever increasing number of emerging new biosensor technologies, defining sensor detection limits has become an ambiguous topic and a need exists to standardize measurements and sensitivity units. For chip-based devices, it seems appropriate to report sensitivity in terms of the minimum number of grams of bound target per surface area.

Single-chain polymorphism analysis in long QT syndrome using planar waveguide fluorescent biosensors

Rapid detection of single nucleotide polymorphisms (SNPs) has potential applications in both genetic screening and pharmacogenomics. Planar waveguide fluorescent biosensor technology was employed to detect SNPs using a simple hybridization assay with the complementary strand ("capture oligo") immobilized on the waveguide. This technology allows real-time measurements of DNA hybridization kinetics. Under normal conditions, both the wild-type sequence and the SNP-containing sequence will hybridize with the capture oligo, but with different reaction kinetics and equilibrium duplex concentrations. A "design of experiments" approach was used to maximize the differences in the kinetics profiles of the two. Nearly perfect discrimination can be achieved at short times (2 min) with temperatures that destabilize or melt the heteroduplex while maintaining the stability of the homoduplex. The counter ion content of the solvent was shown to have significant effect not only on the melting point of the heteroduplex and the homoduplex but also on the hybridization rate. Changes in both the stability and the difference between the hybridization rates of the hetero- and homoduplex were observed with varying concentrations of three different cations (Na(+), K(+), Mg(2+)). With the difference in hybridization rates maximized, discrimination between the hetero- and the homoduplex can be obtained at lower, less rigorous temperatures at hybridization times of 7.5 min or longer.

Integrated optical microcavities for enhanced evanescent-wave spectroscopy

The use of integrated optical microcavities (MCs) for enhanced optical spectroscopy and sensing is investigated. The MC sustains high- Q whispering-gallery modes, in which the energy of the optical field can be efficiently stored. The resulting enhanced field can be used to probe fluorescent molecules in the cladding of the MC. Enhanced fluorescence excitation with an integrated optical MC is demonstrated experimentally for what is believed to be the first time. A comparison between a MC and a straight waveguide shows that the MC may give an increase of 40 times in fluorescence excitation. Because of the ultrasmall size of the MC (15 microm in radius), the fluorescence signal may be observed from only 20 molecules in the cladding.

Molecular Recognition of Avidin on Biotin-Functionalized Gold Surfaces Detected by FT-IRRAS and Use of Metal Carbonyl Probes

Fourier transform infrared reflection-absorption spectroscopy (FT-IRRAS) was successively used to monitor the covalent immobilization of biotin molecules onto a planar gold substrate covered with a self-assembled monolayer of cystamine and to transduce the molecular recognition of avidin and biotin. This detection was greatly facilitated and made selective by the labeling of avidin and of biotin with various transition metal carbonyl probes. The binding of avidin to the surface was optimized by blocking the nonspecific binding sites by adsorption of an unrelated protein, bovine serum albumin. This work exemplifies the feasibility of detecting biomolecular associations involving molecules of any size at a liquid/solid interface by using a simple and accessible surface analysis technique.

Single-pad scheme for integrated optical fluorescence sensing

A new scheme for integrated optical fluorescence sensing is presented. The principle is based on a planar waveguide containing multiple sensing units, each consisting of a single-pad grating coupler structure. Single-pad means that all the following functions are incorporated in one single pad: laser light input, excitation of the labeled analyte molecules, efficient collection of the emitted fluorescent light into the waveguide, background suppression, and coupling the guided wave out to the detector. The results demonstrate a high efficiency of the fluorescence light excitation and collection, as well as a good suppression of the volume background.

Resonant-enhanced evanescent-wave fluorescence biosensing with cylindrical optical cavities

We show that the artificial resonances of dielectric optical cavities can be used to enhance the detection sensitivity of evanescent-wave optical fluorescence biosensors to the binding of a labeled analyte with a biospecific monolayer. Resonant coupling of power into the optical cavity allows for efficient use of the long photon lifetimes (or equivalently, the high internal power) of the high-Q whispering gallery modes to increase the probability of photon absorption into the fluorophore, thereby enhancing fluorescence emission. A method to compare the intrinsic sensitivity between resonant cavity and waveguide formats is also developed. Using realistic estimates for dielectric cylindrical cavities in both bulk and integrated configurations, we can expect sensitivity enhancement by at least an order of magnitude over standard waveguide evanescent sensors of equivalent sensing geometries. In addition, the required sample volume can be reduced significantly. The cylindrical cavity format is compatible with a large variety of sensing modalities such as immunoassay and molecular diagnostic assay.

Multiple-analyte fluoroimmunoassay using an integrated optical waveguide sensor

A silicon oxynitride integrated optical waveguide was used to evanescently excite fluorescence from a multianalyte sensor surface in a rapid, sandwich immunoassay format. Multiple analyte immunoassay (MAIA) results for two sets of three different analytes, one employing polyclonal and the other monoclonal capture antibodies, were compared with results for identical analytes performed in a single-analyte immunoassay (SAIA) format. The MAIA protocol was applied in both phosphate-buffered saline and simulated serum solutions. Point-to-point correlation values between the MAIA and SAIA results varied widely for the polyclonal antibodies (R2 = 0.42-0.98) and were acceptable for the monoclonal antibodies (R2 = 0.93-0.99). Differences in calculated receptor affinities were also evident with polyclonal antibodies, but not so with monoclonal antibodies. Polyclonal antibody capture layers tended to demonstrate departure from ideal receptor-ligand binding while monoclonal antibodies generally displayed monovalent binding. A third set of three antibodies, specific for three cardiac proteins routinely used to categorize myocardial infarction, were also evaluated with the two assay protocols. MAIA responses, over clinically significant ranges for creatin kinase MB, cardiac troponin I, and myoglobin agreed well with responses generated with SAIA protocols (R2 = 0.97-0.99).

Screening ligands for membrane protein receptors by total internal reflection fluorescence: the 5-HT3 serotonin receptor

The screening of ligands for membrane receptor proteins is central to the discovery of new pharmaceutical drugs. We present a general method to reversibly attach receptor proteins via an affinity tag to a quartz surface and subsequently detect with high sensitivity the real-time binding of ligands by total internal reflection fluorescence. A serotonin-gated ion channel protein was immobilized, and the binding of a fluorescent ligand was investigated. The affinity and the kinetic parameters of binding were measured, and the effect of unlabeled compounds was determined by competition. The pharmacology of the immobilized receptor was identical to that of the native receptor. The affinity of unlabeled ligands was rapidly and effectively determined. The method described here is generally applicable for membrane proteins and opens new ways for the discovery of pharmacologically active compounds.

Regenerable biosensor platform: a total internal reflection fluorescence cell with electrochemical control

A new biosensor platform that provides simultaneous fluorescence detection and electrochemical control of biospecific binding has been developed and investigated using antibody-antigen and streptavidin-biotin interactions. Specifically, biotin was covalently bound to a transparent indium-tin oxide (ITO) working electrode, which also served as an integral part of a total internal reflection fluorescence (TIRF) flow cell. TIRF was used to monitor biospecific interactions, while electrochemical polarization was employed to control interactions between biotin and streptavidin or between biotin and anti-biotin antibodies. Both streptavidin and polyclonal anti-biotin antibodies bound kinetically irreversibly to the biotinylated surface. In the absence of electrochemical control, the assay exhibited an extremely slow release of the bound analytes, causing poor regeneration ability of the biosensor surface. However, electrochemical polarization was found to stimulate dissociation of kinetically irreversibly bound biotin-streptavidin and antibody-antigen complexes. A "square wave" polarization function stimulated dissociation more effectively than a "saw tooth" function over the same voltage range. Application of the square wave polarization resulted in regeneration of an active biotinylated surface. Electrochemical polarization also modified affinity and kinetics of protein adsorption, which could likely be used to promote biospecific interactions and/or to suppress nonspecific adsorption.