Fluorescence spectral properties of cyanine dye labeled DNA near metallic silver particles

The role of Rayleigh anomalies in the coupling process of plasmonic gratings and the control of the emission properties of organic molecules

We report the investigation of the influence of periodic metallic arrays on the emission properties of organic emitters. Beforehand, the study of the coupling process between nanoparticles through the analysis of the extinction spectra related to Rayleigh anomalies indicate the crucial role of those latter in defining the nature of the excited grating modes. The obtained results emphasis that Rayleigh Anomalies can be considered as the intermediate between individual plasmonic and collective photonic responses. Thereafter, the experimental and numerical studies of the lattice modes and their associated effects on the lifetime and emission directivity of nearby emitters indicate that tuning the geometrical grating parameters offers a possibility to select a particular coupling process from a localized effect to a far field response. Depending on the coupling strength, the emission can be strongly altered by increasing the density of states or providing diffractive orders. Eventually, this study reports that the Rayleigh Anomalies play the role of an excitation source which drives the nanoparticles to act as a set of diffractive objects for shaping the emission to be highly directive.

Fluorescence Enhancement Using Bimetal Surface Plasmon-Coupled Emission from 5-Carboxyfluorescein (FAM)

We demonstrate the enhancement of fluorescence emission from a dye, 5-carboxyfluorescein (FAM), which couples with surface plasmons at the spectral channels of excitation and emission. Experiments and calculations revealed that bimetallic (gold-silver) plasmon, as compared to the monometallic ones, allowed such coupling to be enhanced, at both the spectral channels. We achieved the maximum fluorescence enhancement level of 46.5-fold, with markedly high reproducibility (coefficient of variation ~ 0.5%) at a FAM concentration of 10 nM. We also found that higher fluorescence enhancement was more likely to be reproducible. This encourages the use of this technology for practical applications in fluorescence-based biochemical assays. Moreover, we investigated a FAM concentration-dependent enhancement of fluorescence. It was found that fluorescence enhancement decreased and saturated at above 10 nM concentration possibly due to partial photo-bleaching of FAM molecules.

Gene expression analysis: teaching students to do 30,000 experiments at once with microarray

Genome scale experiments routinely produce large data sets that require computational analysis, yet there are few student-based labs that illustrate the design and execution of these experiments. In order for students to understand and participate in the genomic world, teaching labs must be available where students generate and analyze large data sets. We present a microarray-based gene expression analysis experiment that is tailored for undergraduate students. The methods in this article describe an expression analysis experiment that can also be applied to CGH and SNP experiments. Factors such as technical difficulty, duration, cost, and availability of materials and equipments are considered in the lab design. The microarray teaching lab is performed in two sessions. The first is an introductory wet bench exercise that allows students to master the basic technical skills. The second builds on the concepts and skills with students acquiring and analyzing the microarray data. This lab exercise familiarizes students with large-scale data experiments and introduces them to the initial analysis steps.

Metal nanoparticle plasmon-enhanced light-harvesting in a photosystem I thin film

Silver metal nanoparticle (NP) enhanced fluorescence is investigated in thin films of cyanobacterial Photosystem I trimer complexes (PSI) by correlating confocal laser scanning microscopy, dark-field imaging, and fluorescence lifetime measurements. PSI represents an interesting light-harvesting complex with a 20 nm diameter that is not uniformly contained within the surface-localized plasmon field of the NPs. With weak far-field illumination, 5- to 20-fold fluorescence enhancement is observed for PSI complexes adjacent to NPs, arising from efficient nanoparticle light collection and subsequent localized, surface plasmon excitation of PSI. Enhanced PSI fluorescence is detected most prominently near "rafts" of aggregated NPs that more completely fill the confocal field of view. These results demonstrate opportunities to probe energy transfer within photosynthetic complexes using plasmonic excitation and to design nanostructures for optimizing artificial light-harvesting systems.

Fluorescence Quenching/Enhancement Surface Assays: Signal Manipulation Using Silver-coated Gold Nanoparticles

Gold nanoparticles covalently attached to the indium tin oxide coated glass slide drastically quench fluorescence of a surface immunoassay (approximately 5-fold). Silver electrochemically deposited over the gold particles leads to fluorescence amplification: signal increases approximately 7-8 times if compared to the signal on gold particles not covered with silver. This phenomenon allows enhancing of the surface immunoassays utilizing both types of nanoparticles.

Probing DNA hybridization in homogeneous solution and at interfaces via measurement of the intrinsic fluorescence decay time of a single label

The hybridization of DNA oligomers including molecular beacons can be detected by measurement of either the decay time or the intensity of a single fluorescent label attached to the end of the respective oligonucleotide. The method works both in solution and solid phase and can distinguish between fully complementary and mismatch sequences as demonstrated for a 15-mer oligonucleotide and a 25-mer molecular beacon. The fluorescence lifetime method is advantageous in (a) requiring a single label (and therefore a single labeling step) only; and (b), being based on measurement of a self-referenced magnitude that is hardly affected by parameters such as fluctuations in light intensity that make measurement of intensity more prone to interferences.

Metal particle-enhanced fluorescent immunoassays on metal mirrors

We present fluoroimmunoassays on plain metal-coated surfaces (metal mirrors) enhanced by metal nanoparticles (silver island films [SIFs]). Metal mirrors (aluminum, gold, or silver protected with a thin silica layer) were coated with SIFs, and an immunoassay (model assay for rabbit immunoglobulin G or myoglobin immunoassay) was performed on this surface using fluorescently labeled antibodies. Our results showed that SIFs alone (on glass surface not coated with metal) enhance the immunoassay signal approximately 3- to 10-fold. Using a metal mirror instead of glass as support for SIFs results in up to 50-fold signal enhancement.

Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles

The effects of metal-enhanced fluorescence (MEF) have been measured for two dyes commonly used in DNA microarrays, Cy3 and Cy5. Silver island films (SIFs) grown on glass microscope slides were used as substrates for MEF DNA arrays. We examined MEF by spotting biotinylated, singly-labeled 23 bp DNAs onto avidin-coated SIF substrates. The fluorescence enhancement was found to be dependent on the DNA spotting concentration: below approximately 12.5 muM, MEF increased linearly, and at higher concentrations MEF remained at a constant maximum of 28-fold for Cy5 and 4-fold for Cy3, compared to avidin-coated glass substrates. Hybridization of singly-labeled oligonucleotides to arrayed single-stranded probes showed lower maximal MEF factors of 10-fold for Cy5 and 2.5-fold for Cy3, because of the smaller amount of immobilized fluorophores as a result of reduced surface hybridization efficiencies. We discuss how MEF can be used to increase the sensitivity of DNA arrays, especially for far red emitting fluorophores like Cy5, without significantly altering current microarray protocols.

Distance-dependent emission from dye-labeled oligonucleotides on striped Au/Ag nanowires: effect of secondary structure and hybridization efficiency

When fluorescently tagged oligonucleotides are located near metal surfaces, their emission intensity is impacted by both electromagnetic effects (i.e., quenching and/or enhancement of emission) and the structure of the nucleic acids (e.g., random coil, hairpin, or duplex). We present experiments exploring the effect of label position and secondary structure in oligonucleotide probes as a function of hybridization buffer, which impacts the percentage of double-stranded probes on the surface after exposure to complementary DNA. Nanowires containing identifiable patterns of Au and Ag segments were used as the metal substrates in this work, which enabled us to directly compare different dye positions in a single multiplexed experiment and differences in emission for probes attached to the two metals. The observed metal-dye separation dependence for unstructured surface-bound oligonucleotides is highly sensitive to hybridization efficiency, due to substantial changes in DNA extension from the surface upon hybridization. In contrast, fluorophore labeled oligonucleotides designed to form hairpin secondary structures analogous to solution-phase molecular beacon probes are relatively insensitive to hybridization efficiency, since the folded form is quenched and therefore does not appreciably impact the observed distance-dependence of the response. Differences in fluorescence patterning on Au and Ag were noted as a function of not only chromophore identity but also metal-dye separation. For example, emission intensity for TAMRA-labeled oligonucleotides changed from brighter on Ag for 24-base probes to brighter on Au for 48-base probes. We also observed fluorescence enhancement at the ends of nanowires and at surface defects where heightened electromagnetic fields affect the fluorescence.

Radiative decay engineering 5: metal-enhanced fluorescence and plasmon emission

Metallic particles and surfaces display diverse and complex optical properties. Examples include the intense colors of noble metal colloids, surface plasmon resonance absorption by thin metal films, and quenching of excited fluorophores near the metal surfaces. Recently, the interactions of fluorophores with metallic particles and surfaces (metals) have been used to obtain increased fluorescence intensities, to develop assays based on fluorescence quenching by gold colloids, and to obtain directional radiation from fluorophores near thin metal films. For metal-enhanced fluorescence it is difficult to predict whether a particular metal structure, such as a colloid, fractal, or continuous surface, will quench or enhance fluorescence. In the present report we suggest how the effects of metals on fluorescence can be explained using a simple concept, based on radiating plasmons (RPs). The underlying physics may be complex but the concept is simple to understand. According to the RP model, the emission or quenching of a fluorophore near the metal can be predicted from the optical properties of the metal structures as calculated from electrodynamics, Mie theory, and/or Maxwell's equations. For example, according to Mie theory and the size and shape of the particle, the extinction of metal colloids can be due to either absorption or scattering. Incident energy is dissipated by absorption. Far-field radiation is created by scattering. Based on our model small colloids are expected to quench fluorescence because absorption is dominant over scattering. Larger colloids are expected to enhance fluorescence because the scattering component is dominant over absorption. The ability of a metal's surface to absorb or reflect light is due to wavenumber matching requirements at the metal-sample interface. Wavenumber matching considerations can also be used to predict whether fluorophores at a given distance from a continuous planar surface will be emitted or quenched. These considerations suggest that the so called "lossy surface waves" which quench fluorescence are due to induced electron oscillations which cannot radiate to the far-field because wavevector matching is not possible. We suggest that the energy from the fluorophores thought to be lost by lossy surface waves can be recovered as emission by adjustment of the sample to allow wavevector matching. The RP model provides a rational approach for designing fluorophore-metal configurations with the desired emissive properties and a basis for nanophotonic fluorophore technology.

Fluorescence enhancement of fluorophores tethered to different sized silver colloids deposited on glass substrate

We studied fluorescence enhancements of fluorescein tethered to silver colloids of different size. Thiolated 23-mer oligonucleotide (ss DNA-SH) was bound selectively to silver colloids deposited on 3-aminopropyltriethoxysilane (APS)-treated quartz slides. Fluorescein-labeled complementary oligonucleotide (ss Fl-DNA) was added in an amount significantly lower than the amount of unlabeled DNA tethered to the colloids. The hybridization kinetics, observed as an increase in fluorescence emission, on small (30-40 nm) and large (> 120 nm) colloids were similar. However, the final fluorescence intensity of the sample with large colloids was about 50% higher than that observed for the sample with small colloids. The reference sample without ss DNA-SH was used to estimate the fluorescence enhancements of fluorescein tethered to the small colloids (E = 2.7) and to the large colloids (E = 4.1) due to its steady fluorescence signal. The proposed method, based on controlled hybridization with minimal amount of fluorophore labeled ss DNA, can be used to reliably estimate the fluorescence enhancements on any silver nanostructures.

Ultrabright fluorescein-labeled antibodies near silver metallic surfaces

Fluorescein-labeled antibodies are widely used in clinical assays and fluorescence microscopy. The fluorescent signal per labeled antibody is limited by fluorescein self-quenching, which occurs when the antibody is heavily labeled with multiple fluoresceins. We examined immunoglobulin G (IgG) when labeled with 0.7 to about 30 fluoresceins per antibody molecule. The extent of self-quenching was decreased, and the signal increased, when the labeled antibody was in close proximity to metallic silver particles. Time-resolved measurements showed that the intensity increase was due in part to a silver-induced increase in the radiative decay rate. These results suggest the use of labeled antibodies conjugated to silver particles as ultrabright probes for imaging or analytical applications.

Metal-Enhanced Fluorescence: A Novel Approach to Ultra-Sensitive Fluorescence Sensing Assay Platforms

We describe the development of a novel generic approach to fluorescence sensing based on metal-enhanced fluorescence (MEF). This work follows our initial reports of radiative decay engineering (RDE), where we experimentally demonstrated dramatic signal enhancements of fluorophores positioned close to surface-bound silver nanostructures. The attractive changes in spectral properties of fluorophores includes increased rates of excitation, increased quantum yields, decreased fluorescence lifetimes with an increased photostability, and drastically increased rates of multi-photon excitation. In this report we present a new class of fluorescent biomarkers which are strongly enhanced by metallic particles. This has afforded the development of a novel generic approach for ultra-sensitive fluorescence assay technology. The assay platform utilizes metal particles deposited on glass/quartz surfaces, covered with sub-nanometer layers of a fluorescent biomarker. As such the fluorescence signal of the composite is strongly enhanced. This readily allows easy, quantitative and inexpensive fluorescence detection of minimal traces of specific antigens. We also explore different sensing geometries, such as using evanescent wave excitation.

Advances in surface-enhanced fluorescence

We report recent achievements in metal-enhanced fluorescence from our laboratory. Several fluorophore systems have been studied on metal particle-coated surfaces and in colloid suspensions. In particular, we describe a distance dependent enhancement on silver island films (SIFs), release of self-quenching of fluorescence near silver particles, and the applications of fluorescence enhancement near metalized surfaces to bioassays. We discuss a number of methods for various shaped silver particle deposition on surfaces.

Effects of metallic silver island films on resonance energy transfer between N,N'-(dipropyl)-tetramethyl- indocarbocyanine (Cy3)- and N,N'-(dipropyl)-tetramethyl- indodicarbocyanine (Cy5)-labeled DNA

Resonance energy transfer (RET) is typically limited to distances below 60 A, which can be too short for some biomedical assays. We examined a new method for increasing the RET distances by placing donor- and acceptor-labeled DNA oligomers between two slides coated with metallic silver particles. A N,N'-(dipropyl)-tetramethylindocarbocyanine donor and a N,N'-(dipropyl)-tetramethylindodicarbocyanine acceptor were covalently bound to opposite 5' ends of complementary 23 base pair DNA oligomers. The transfer efficiency was 25% in the absence of silver particles or if only one slide was silvered, and it increased to an average value near 64% between two silvered slides. The average value of the Forster distance increased from 58 to 77 A. The energy transfer data were analyzed with a model assuming two populations of donor-acceptor pairs: unaffected and affected by silver island films. In an affected fraction of about 28%, the apparent energy transfer efficiency is near 87% and the Forster distance increases to 119 A. These results suggest the use of metallic silver particles to increase the distances over which RET occurs in biomedical and biotechnology assays.