Multi-wavelength immunoassays using surface plasmon-coupled emission

We describe a new method for multi-wavelength immunoassays using surface plasmon-coupled emission (SPCE). This phenomenon is coupling of excited fluorophores with a nearby thin metal film, in our case silver, resulting in strongly directional emission into the underlying glass substrate. The angle at which the radiation propagate through the prism depends on the surface plasmon angle for the relevant wavelength. These angles depend on emission wavelength, allowing measurement of multiple analytes using multiple emission wavelengths. We demonstrated this possibility using antibodies labeled with either Rhodamine Red-X or AlexaFluor 647. These antibodies were directed against an antigen protein bound to the silver surface. The emission from each labeled antibody occurred at a different angle on the glass prism, allowing independent measurement of surface binding of each antibody. This method of SPCE immunoassays can be readily extended to 4 or more wavelengths.     

Optical Response of Plasmonic Nanohole Arrays: Comparison of Square and Hexagonal Lattices

Nanohole arrays in metal films allow extraordinary optical transmission (EOT); the phenomenon is highly advantageous for biosensing applications. In this article, we theoretically investigate the performance of refractive index sensors, utilizing square and hexagonal arrays of nanoholes, that can monitor the spectral position of EOT signals. We present near- and far-field characteristics of the aperture arrays and investigate the influence of geometrical device parameters in detail. We numerically compare the refractive index sensitivities of the two lattice geometries and show that the hexagonal array supports larger figure-of-merit values due to its sharper EOT response. Furthermore, the presence of a thin dielectric film that covers the gold surface and mimics a biomolecular layer causes larger spectral shifts within the EOT resonance for the hexagonal array. We also investigate the dependence of the transmission responses on hole radius and demonstrate that hexagonal lattice is highly promising for applications demanding strong light transmission.     

Engineering the Optical Response of the Novel Plasmonic Binary Nanohole Array

The phenomenon of extraordinary optical transmission (EOT) due to its advantages has been considered by researchers in various applications, and in recent years, many efforts have been made to engineer these structures to get the best possible response for desired applications. In this work, the optical properties of novel binary gold nanohole arrays are investigated theoretically. We engineered the optical response of the system by adjusting the ratio of contribution of surface plasmon polariton (SPP) to localized surface plasmon resonance (LSPR) through the manipulation of the geometrical properties. The changes in the topology of this nanohole array affected the intensity and the wavelength of transmission peaks. The sensitivity of the optical response to the refractive index was also investigated. The designed structure is a good candidate for use as a polarization-independent optical label-free sensor.

     

Extraordinary Transmission Characteristics of Subwavelength Nanoholes with Rectangular Lattice

We investigate the extraordinary optical transmission (EOT) properties of nanohole arrays with a rectangular lattice for label-free refractive index sensing applications. We show that the deviation within the periodicities along the two axes at the nanohole plane leads to more advantageous spectral quality of EOT signal compared to the conventional square lattice geometries. We introduce a way to further improve the sensitivity of the aperture system by carefully choosing the periodicities. We introduce nanohole arrays with a rectangular lattice supporting EOT signals with larger figure-of-merit values as well as enabling much stronger light transmission. We also model a nanohole system covered with a thin dielectric layer, mimicking biomolecules captured on the gold surface, in order to show its biosensing capability. We also show that certain deviation amounts between periodicities create spectral splitting within the EOT signal leading to larger spectral shifts in the presence of a thin dielectric film.     

Shape-Controlled Synthesis of Silver Nanoparticles for Plasmonic and Sensing Applications

The localized surface plasmon resonance of a silver nanoparticle is responsible for its ability to strongly absorb and scatter light at specific wavelengths. The absorption and scattering spectra (i.e., plots of cross sections as a function of wavelength) of a particle can be predicted using Mie theory (for a spherical particle) or the discrete dipole approximation method (for particles in arbitrary shapes). In this review, we briefly discuss the calculated spectra for silver nanoparticles with different shapes and the synthetic methods available to produce these nanoparticles. As validated in recent studies, there is good agreement between the theoretically calculated and the experimentally measured spectra. We conclude with a discussion of new plasmonic and sensing applications enabled by the shape-controlled nanoparticles.     

Microring Switching Control Using Plasmonic Ring Resonator Circuits for Super-Channel Use

The multi-wavelength selection and switching system using the hybrid plasmonic add-drop ring resonator (HPARR) for optical communication is proposed for multi-carrier super-channel-based designed. The plasmonic polariton technique applied in the ring resonator mode to the alternate waveguide interferometer switches the multi-wavelength laser emission in the various ranges. The combination of curvature-coupled plasmon ring and substances with different refractive index allows switching the multi-wavelength emission to shorter the free spectrum range (FSR) and specific wavelengths, without an applied pump signal or adjusted the ring size. It is suitable for the super-channel of wavelength division multiplex (WDM) in the future optical network.

     

Synthesis and Optical Properties of Highly Stabilized Peptide-Coated Silver Nanoparticles

The interaction between peptide and silver nanoparticle surfaces has been increasingly of interest for bionanotechnology applications. To fully understand how to control such interactions, we have studied the optical properties of peptide-modified silver nanoparticles. However, the impacts of peptide binding motif upon the surface characteristics and physicochemical properties of nanoparticles remain not yet fully understood. Here, we have prepared sodium citrate-stabilized silver nanoparticles and coated with peptide IVD (ID₃). These nanomaterials were characterized by UV-visible, transmission electron microscopy (TEM), and z-potential measurement. The results indicate that silver nanoparticles (AgNP)-peptide interface is generated using ID₃ peptide and suggested that the reactivity of peptide is governed by the conformation of the bound peptide on the nanoparticle surface. The peptide-nanoparticle interactions could potentially be used to make specific functionality into the peptide capped nanomaterials and antibacterial applications.     

Tunable Extraordinary Optical Transmission in a Metal Film Perforated with Two-Level Subwavelength Cylindrical Holes

We propose a novel plasmonic metal structure composed of a silver film perforated with a two-dimensional square array of two-level cylindrical holes on a silica substrate. The transmission properties of this structure are theoretically calculated by the finite-difference time-domain (FDTD) method. Double-enhanced transmission peaks are achieved in the visible and infrared regions, which mainly originate from the excitation of localized surface plasmon resonances (LSPRs), the hybridization of plasmon modes, and the optical cavity mode formed in the holes. The enhanced transmission behaviors can be effectively tailored by changing the geometrical parameters and dielectric materials filled in the holes. These findings indicate that our proposed structure has potential applications in highly integrated optoelectronic devices.     

光谱和光强度对西花蓟马雌虫趋光行为的影响

利用行为学方法研究了光谱、光强对西花蓟马Frankliniella occidentalis (Pergande)雌成虫的趋、避光行为的影响。结果显示：（1）在340~605nm波谱内14个波长其光谱趋光行为反应为多峰型,峰间主次较明显。趋光行为反应中,蓝绿区498~524nm有一较宽峰,趋光率20.31%;其它各峰依大小次序分别位于紫光380nm、蓝光440nm;（２）避光行为反应中,蓝光440nm处略高,避光率17.19%;紫外340nm处亦有一峰,避光率15.63%;（３）随光强增强其趋光反应率增大,白光、380nm和524nm刺激时其光强趋光行为反应呈一倒“L”型式样,498nm为峰型,440nm时为一较缓的平直线型;光强最弱时仍均有一定趋光率 ,最强时均未出现高端平台;（４）随光强增强其避光反应率增大,440nm为较平缓直线;340nm刺激时为较缓波动线。结果表明：光谱对其趋光行为有很大影响,光强度的影响较大且影响大小与波长因素有关。     

Comparisons of Surface Plasmon Sensitivities in Periodic Gold Nanostructures

The wavelength sensitivities of three kinds of nanostructures (nanoslits, nanoholes, and concentric circles) with various aperture sizes were compared in water environment. These nanostructures were made on a 110-nm-thick gold film with a period of 600 nm. Surface plasmon resonances in these nanostructures produce transmission dips near the phase-matching conditions while peaks at longer wavelengths. The wavelength sensitivities measured at dips are close to theoretical predictions and about 1.5 times larger than those measured at peaks. Such sensitivity difference is attributed to various surface plasmon distributions, as illustrated by the finite-difference time-domain calculations. In addition, the sensitivity decreases with the increase of aperture size. The nanoslit array and concentric circles have better sensitivities than the nanohole array due to the no cut-off transmission.     

A label-free optical sensor based on nanoporous gold arrays for the detection of oligodeoxynucleotides

Interest in using nanoporous materials for sensing applications has increased. The present study reports a method of preparing well-ordered nanoporous gold arrays using a porous silicon (PSi) template. Gold nanolayer could be electrodeposited on the surface of the PSi template at low electrolysis currents in low concentration of chloroauric acid (HAuCl₄) solution. Surface morphology characterizations and optical measurements revealed that a PSi-templated nanoporous gold (Au–PSi) array well replicated the nanoporous structure and retained the optical properties of PSi. Fourier transform reflectometric interference spectra showed that a characteristic blue-shifted effective optical thickness (EOT) was observed due to the low refractive index of the gold film. An optical DNA biosensor was then fabricated via the self-assembly of single-stranded DNA (ssDNA) with a specific sequence on the surface of Au–PSi. The attachment of ssDNA and its hybridization with target oligonucleotides (ODNs) persistently caused the blue shift of the EOT. Consequently, a relationship between the EOT shift and the ODN concentration was established. The mechanism of the optical response caused by DNA hybridization on the Au–PSi surface was qualitatively explained by the electromagnetic theory and electrochemical impedance spectroscopy (EIS). The lowest detection limit for target ODNs was estimated at around 10⁻¹⁴ mol L⁻¹, when the baseline noise, a variation in the value of EOT is around 5 nm. The fabricated Au–PSi based optical biosensor has potential use in the discovery of new ODN drugs because it will be able to detect the binding event between ODNs and the target DNA.     

Extremely High Transmittance at Visible Wavelength Induced by Magnetic Resonance

A new quasi-3D structure composed of stacked double-layer subwavelength metal gratings is designed for magnetic resonance in the visible region. The coupling of two-layer gratings induces a type of magnetic plasmon propagation mode characterized by extraordinary optical transmission (EOT) with extremely high transmittance of up to 0.94 for transverse magnetic polarization. The results show that magnetic resonance is an effective method to enhance the transmittance and avoid much energy loss, one of the barriers for application in the visible region. The magnetic resonance or EOT is strongly dependent on the wavelength which can simply be tuned by the period of gratings. This work paves a way to designing metallic metamaterials that are magnetically active in the visible spectral ranges. In addition, the proposed structure can be easily constructed using nanofabrication.     

Decay-associated emission spectra and other spectral evidence for the physical intercalation of 7,8-dihydroxy-7,8-dihydrobenzo[a]pyrene into DNA

A benzo[a]pyrene derivative, 7,8-dihydroxy-7,8-dihydrobenzo[a]pyrene, forms physical complexes with DNA. The measured absorption spectrum of the hydrocarbon in the complex is shifted approximately 10 nm to the red and the fluorescence emission spectrum is red-shifted approximately 6 nm, characteristic of a physical intercalation complex. The decay-associated emission spectra of the hydrocarbon in the presence of DNA have been measured, thus providing a new technique to obtain information about the DNA binding sites. The decay-associated emission spectra of the free and bound hydrocarbons were obtained by deconvoluting the time-dependent emission at several wavelengths. Stern-Volmer plots with iodide and silver ions as quenchers suggest that at least one set of binding sites for the formation of a physical intercalation complex between the benzo[a]pyrene derivative and DNA is at guanine sites in the biopolymer.     

Radiative decay engineering. 2. Effects of Silver Island films on fluorescence intensity, lifetimes, and resonance energy transfer

Metallic surfaces can have unusual effects on fluorophores such as increasing or decreasing the rates of radiative decay and the rates of resonance energy transfer (RET). In the present article we describe the effects of metallic silver island films on the emission spectra, lifetimes, and energy transfer for several fluorophores. The fluorophores are not covalently coupled to the silver islands so that there are a range of fluorophore-to-metal distances. We show that proximity of fluorophores to the silver islands results in increased fluorescence intensity, with the largest enhancement for the lowest-quantum-yield fluorophores. Importantly, the metal-induced increases in intensity are accompanied by decreased lifetimes and increased photostability. These effects demonstrate that the silver islands have increased the radiative decay rates of the fluorophore. For solvent-sensitive fluorophores the emission spectra shifted to shorted wavelengths in the presence of the silver islands, which is consistent with a decrease of the apparent lifetime for fluorophores near the metal islands. We also observed an increased intensity and blue spectral shift for the protein human glyoxalase, which displays a low quantum yield for its intrinsic tryptophan emission. In this case the blue shift is thought to be due to increased emission from a buried low-quantum-yield tryptophan residue. Increased intensities were also observed for the intrinsic emission of the nucleic acid bases adenine and thymine and for single-stranded 15-mers poly(T) and poly(C). And finally, we observed increased RET for donors and acceptors in solution and when bound to double-helical DNA. These results demonstrate that metallic particles can be used to modify the emission from intrinsic and extrinsic fluorophores in biochemical systems.     

Extraordinary Optical Transmission Property of X-Shaped Plasmonic Nanohole Arrays

Optical transmission properties of periodic X-shaped plasmonic nanohole arrays in a silver film are investigated by performing the finite element method. Obvious peaks appear in the transmission spectra due to surface plasmon polaritons (SPPs) on the top surface of the silver film, to the Fabry–Ferot resonance effect of SPPs in the nanohole, and to the localized surface plasmon resonance of the nanohole. Besides the topologic shape parameters of the X-shaped nanohole, transmission properties strongly depend on incident polarization. The results of this study not only present a tunable plasmonic filter, but also aid in the understanding of the mechanisms of the extraordinary optical transmission phenomenon.     

Anomalous X-ray diffraction with soft X-ray synchrotron radiation.

Anomalous diffraction with soft X-ray synchrotron radiation opens new possibilities in protein crystallography and materials science. Low-Z elements like silicon, phosphorus, sulfur and chlorine become accessible as new labels in structural studies. Some of the heavy elements like uranium exhibit an unusually strong dispersion at their M(V) absorption edge (lambdaMV = 3.497 A, E(MV) = 3545 eV) and so does thorium. Two different test experiments are reported here showing the feasibility of anomalous X-ray diffraction at long wavelengths with a protein containing uranium and with a salt containing chlorine atoms. With 110 electrons the anomalous scattering amplitude of uranium exceeds by a factor of 4 the resonance scattering of other strong anomalous scatterers like that of the lanthanides at their L(III) edge. The resulting exceptional phasing power of uranium is most attractive in protein crystallography using the multi-wavelength anomalous diffraction (MAD) method. The anomalous dispersion of an uranium derivative of asparaginyl-tRNA synthetase (hexagonal unit cell; a = 123.4 A, c = 124.4 A) has been measured for the first time at 4 wavelengths near the M(V) edge using the beamline ID1 of ESRF (Grenoble, France). The present set up allowed to measure only 30% of the possible reflections at a resolution of 4 A, mainly because of the low sensitivity of the CCD detector. In the second experiment, the dispersion of the intensity of 5 X-ray diffraction peaks from pentakismethylammonium undecachlorodibismuthate (PMACB, orthorhombic unit cell; a = 13.003 A, b = 14.038 A, c = 15.450 A) has been measured at 30 wavelengths near the K absorption edge of chlorine (lambdaK = 4.397 A, EK= 2819.6 eV). All reflections within the resolution range from 6.4 A to 3.4 A expected in the 20 degree scan were observed. The chemical state varies between different chlorine atoms of PMACB, and so does the dispersion of different Bragg peaks near the K-edge of chlorine. The results reflect the performance of the beamline ID1 of ESRF at wavelengths beyond 3 A at the end of 1998. A gain by a factor 100 for diffraction experiments with 4.4 A photons was achieved in Autumn 1999 when two focusing mirrors had been added to the X-ray optics. Further progress is expected from area detectors more sensitive to soft X-rays. Both CCD detectors and image plates would provide a gain of two orders of measured intensity. Image plates would have the additional advantage that they can be bent cylindrically and thus cover a larger solid angle in reciprocal space. In many cases, samples need to be cooled: closed and open systems are presented. A comparison with the state of art of soft X-ray diffraction, as it had been reached at HASYLAB (Hamburg, Germany), and as it is developing at the Brookhaven National Laboratory (USA), is given.     

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

Having multiple peaks within fitness landscapes critically affects the course of evolution, but whether their presence imposes specific requirements at the level of genetic interactions remains unestablished. Here we show that to exhibit multiple fitness peaks, a biological system must contain reciprocal sign epistatic interactions, which are defined as genetic changes that are separately unfavorable but jointly advantageous. Using Morse theory, we argue that it is impossible to formulate a sufficient condition for multiple peaks in terms of local genetic interactions. These findings indicate that systems incapable of reciprocal sign epistasis will always possess a single fitness peak. However, reciprocal sign epistasis should be pervasive in nature as it is a logical consequence of specificity in molecular interactions. The results thus predict that specific molecular interactions may yield multiple fitness peaks, which can be tested experimentally.     

Mechanisms Responsible for Extraordinary Optical Transmission Through One-Dimensional Periodic Arrays of Infinite Sub-wavelength Slits: the Origin of Previous EOT Position Prediction Misinterpretations

We have studied theoretically and numerically the effect of extraordinary optical transmission of light propagating through the one-dimensional periodic arrays of infinite slits with sub-wavelength dimensions. In our study, we have concentrated on mechanisms which are responsible for this effect. Within our analysis, we have attempted to draw the attention towards the origin and reasons of earlier misinterpretations concerning the spectral position of EOT prediction and the related role of surface plasmon polaritons in manifestation of the effect. Using the sequence of suitable parameter two-dimensional spaces (in terms of structure period-filling factor; thickness-wavelength; wavelength-angle), we were able to look into subtle physical mechanisms operating in the background of this extraordinary optical transmission effect. To study these effects associated with the extraordinary optical transmission, we have applied our efficient two-dimensional numerical technique based on the rigorous coupled-wave analysis. Within the thickness-wavelength parameter space, we have been able to identify and describe three distinct interaction regions, with specific behaviour. Finally, we have proposed and discussed the supporting mechanism explaining the interaction, based on the interference of resonant and non-resonant contributions at the slit openings.     

Circular dichroic spectrum of poly-L-tyrosine in aqueous solution

The UV and CD spectra of poly-L-tyrosine were investigated at pH 10.6 and pH 11.2. At pH 10.6 (μ=0.1), the CD spectrum exhibits a medium positive band at 230mμ, an extremely small negative band at 217mμ, and a large positive band at 200mμ. At pH 11.2 (μ=0.1), a new positive CD band appears at 277mμ while the bands at 230mμ and 217mμ are shifted to longer wavelengths by 15 and 10mμ respectively. These results, together with UV spectral data and a specific rotation- pH profile, suggest that at pH 10.6, poly-L-tyrosine exists in the helical conformation with only a small fraction of its side chains ionized; at pH 11.2, the polypeptide retains its helical structure but with a considerable increase in ionization.     

Fluorescence in situ hybridisation coupled to ultra small immunogold detection to identify prokaryotic cells using transmission and scanning electron microscopy

We describe a method based on fluorescence in situ hybridisation (FISH) that allows the identification of individual cells by electron microscopy. We hybridised universal and specific fluorescein-labelled oligonucleotide probes to the ribosomal RNA of prokaryotic microorganisms in heterogeneous cell mixtures. We then used antibodies against fluorescein coupled to sub-nanometer gold particles to label the hybridised probes in the ribosome. After increasing the diameter of the metal particles by silver enhancement, the specific gold-silver signal was visualised by optical microscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). It is the first time that SEM is applied to the detection of gold nanoparticles hybridised to an intracellular target, such as the ribosome. The possibility to couple phylogenetic identification by FISH to cell surface and ultrastructure observation at electron microscopy resolution has promising potential applications in microbial ecology.