Ultrabright fluorescent nanocomposite structures for enhanced fluorescent bioassays

Abstract

Described herein is a fluorescent nanocomposite. The fluorescent nanocomposite structure may include a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having an excitation maximum wavelength (λEX), and at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC). The fluorescent nanocomposite structure has a fluorescence intensity at least 500 times greater than that of the at least one fluorescent agent alone.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Patent Application No. 62 / 968,314, filed January 31, 2020, the entire contents of which are incorporated herein by reference.

[0002] The present disclosure relates to ultrabright fluorescent nanocomposite structures for enhanced fluorescent bioassays. [Background technology]

[0003] The detection and quantification of various biomolecules in biological fluids and tissues is fundamentally important in biomedical research and clinical diagnostics, as it is impossible to fully characterize complex nonlinear biochemical systems without accurately and quantitatively examining their component molecules. This problem is ubiquitous across all areas of biomedical research and poses a major obstacle to fully understanding health, aging, and disease. This problem is particularly challenging for proteins and peptides, which lack amplification schemes like PCR for nucleic acids, as the relevant concentrations of molecules associated with diseases such as cancer, heart disease, and neurodegeneration can span many orders of magnitude, from femtoseconds to milligrams per milliliter. The abundance of the same molecule can vary by orders of magnitude depending on the physiological state (e.g., healthy vs. diseased) or sample environment (e.g., blood vs. cerebrospinal fluid). Finally, of particular importance to research laboratories, samples are extremely precious and sometimes extremely limited in availability. Fluorescent probes and fluorescence measurement approaches are used in biomedical research not only as imaging tools to visualize the location and dynamics of cells and various subcellular species and molecular interactions in cells and tissues, but also as labels / reporters in fluorescent immunoassays for the detection and quantification of molecular biomarkers. Fluorescence-based techniques have fundamentally transformed biology and life sciences by elucidating the genomic, transcriptomic, and proteomic signatures of disease onset, progression, and response to treatment. However, weak signals have been a persistent and recurring problem in a range of detection and imaging techniques that rely on fluorescence. The detection sensitivity of all fluorescence-based bioanalytical techniques is ultimately limited by the amount of light that can be collected from the individual fluorescent species that function as reporters during the investigation period. Generally, the weak fluorescent signals from individual reporter fluorophores and the associated poor signal-to-noise ratio currently limit the ultimate sensitivity of fluorescence-based assays.

[0004] One approach to address this issue is to improve the detection instrumentation by using more sensitive detectors coupled to optical systems with higher numerical apertures. The drawbacks of this approach are: 1) the significant expense of the detection instrumentation and optical systems; and 2) the high numerical aperture significantly limits the field of view and can result in very long assay readout times. Furthermore, typical fluorophores used in bioassays have a limited usable lifetime during which they can emit photons before photobleaching.

[0005] While fluorescence offers multiple advantages over assay detection schemes such as colorimetric ELISA or chemiluminescence, including multiplexing, a high dynamic range, and broad platform applicability (i.e., it can be used intracellularly, on cells, in tissues, on plates, on beads, in solution, etc.), fluorescence is fundamentally limited by its insufficient signal. To achieve improved fluorescence detection sensitivity, plate-based assays employ complex schemes such as poly-HRP, PCR-ELISA, avidin-biotin complex (ABC) ELISA, and tyramide signal amplification (TSA). All of these are more complex, more expensive, and generally have a poorer dynamic range than the assay versions they replace. To achieve very high detection sensitivity, complex techniques such as digital ELISA (Quanterix Simoa System) or electrochemiluminescence (Meso Scale Discovery) are required, each of which requires specialized substrates, equipment, and workflows.

[0006] In spectrally multiplexed fluorescence assays, different species are labeled with spectrally distinct fluorescent probes, and the more unique fluorophores available, the more highly multiplexed the assay can be. In particular, it has become important to have unique combinations of excitation and emission spectra. Summary of the Invention [Means for solving the problem]

[0007] In one aspect, disclosed herein is a fluorescent nanocomposite structure comprising a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having an excitation maximum wavelength (λEX), and at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC). The fluorescent nanocomposite structure has a fluorescence intensity at least 500 times greater than that of the at least one fluorescent agent alone.

[0008] In some embodiments, the nanoconstruct may include a silver-coated gold nanorod (AuNR@Ag) plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR) greater than 350 nm, at least one spacer coating, at least one fluorescent agent having a maximally excited wavelength (λEX), and at least one biorecognition element. The gold nanorods (AuNR) used to form the AuNR@Ag have at least one localized surface plasmon resonance wavelength greater than 650 nm before being coated with silver. The fluorescent nanoconstruct has a fluorescence intensity at least 500 times greater than that of the at least one fluorescent agent alone under similar illumination and detection conditions.

[0009] In one aspect, disclosed herein is a method for making a fluorescent nanoconstruct. The method generally includes providing an AuNR@Ag plasmonic nanostructure, where the gold nanorods (AuNR) used to form the AuNR@Ag have at least one localized surface plasmon resonance wavelength greater than 650 nm, coating the AuNR@Ag plasmonic nanostructure with at least one spacer coating, conjugating at least one fluorescent agent to the spacer coating, coating the spacer layer with a functional layer, and conjugating a biorecognition element to one of the at least one spacer coating or the functional layer.

[0010] Further disclosed herein in one aspect is a fluorescent nanocomposite structure including a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having a first maximum excitation wavelength (λEX1) and a first maximum emission wavelength (λEM1), and at least one fluorescent agent having a second maximum excitation wavelength (λEX2) and a second maximum emission wavelength (λEM2). The fluorescent nanocomposite structure can be excited with light at λEX1 and emit light at λEM2, where the emission intensity of λEM2 is greater than the emission intensity of λEM1.

[0011] In one embodiment, a fluorescent nanoconstruct with a long Stokes shift is disclosed herein. The nanoconstruct generally includes a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, and at least one fluorescent agent functioning as a Förster resonance energy transfer (FRET) donor having a maximal excitation wavelength (λEX_D) and at least one fluorescent agent functioning as a FRET acceptor having a maximal emission wavelength (λEM_A), wherein the fluorescent agent functioning as the FRET donor has a λEX_D within 50 nm of at least one of the λLSPRs of the plasmonic nanostructure, and the fluorescent nanoconstruct can be excited at λEX_D and emit light at λEM_A.

[0012] In one aspect, disclosed herein are fluorescent nanoconstructs functionalized with multiple peptide-MHC (pMHC) molecules and capable of recognizing T cell antigen receptors (TCRs) specific for peptides bound to the MHC. The pMHC-functionalized fluorescent constructs enable much higher detection sensitivity than pMHC bound to fluorescently labeled streptavidin, the current standard fluorescent reagent. This is due to the fact that, unlike fluorescent streptavidin, the fluorescent nanoconstructs disclosed herein allow for the conjugation of more than four MHC molecules per complex and are significantly brighter than streptavidin labeled with spectrally equivalent fluorophores. The pMHC-modified fluorescent nanoconstructs disclosed herein can attach to multiple TCRs, even when multiple TCRs are present at low cell surface density.

[0013] In another aspect, disclosed herein is a method for identifying T cells having a specific T cell receptor, which may include providing a sample containing T cells, contacting the sample containing T cells with a fluorescent nanocomposite structure comprising at least one major histocompatibility complex (MHC) molecule loaded with a peptide (pMHC) capable of specifically binding to T cells containing a receptor specific for the peptide, spatially separating the T cells, exciting the fluorescent nanocomposite structure with a wavelength of light that induces fluorescence emission, and detecting the fluorescent nanocomposite structure-labeled T cells.

[0014] Additional embodiments and features are set forth in part in the description that follows, and will become apparent to those skilled in the art upon examination of the specification or may be learned by practice of the disclosed subject matter. A further understanding of the nature and advantages of the present disclosure may be realized by reference to the remaining portions of the specification and drawings that form a part of this disclosure.

[0015] The present specification will be more fully understood with reference to the following figures and data graphs, which are presented as various embodiments of the present disclosure and should not be construed as a complete description of the scope of the present disclosure. [Brief explanation of the drawings]

[0016] [Figure 1] 1 is an exemplary embodiment of a schematic for generating unique plasmonic core nanoparticles used to generate plasmonic fluorophores. In this schematic, core AuNRs with λ LSPRs greater than 810 nm can be coated with silver to generate AuNR@Ag with a dominant λ LSPR between 650 nm and 800 nm, or core AuNRs with λ LSPRs greater than 660 nm and less than 800 nm can be used to generate AuNR@Ag with a dominant λ LSPR between 450 nm and 650 nm. [Figure 2] Figure 1 shows the extinction spectrum, normalized to 1 at its maximum, for an exemplary embodiment of AuNR@Ag plasmonic particles suitable for enhancing fluorescent agents that can be excited by 460-500 nm light, such as Cy2, FITC, and AlexaFluor488. [Figure 3] Figure 1 shows the extinction spectrum, normalized to 1 at its maximum, for an exemplary embodiment of AuNR@Ag plasmonic particles suitable for enhancing fluorescent agents that can be excited by 480-540 nm light, such as TRITC, Cy3, MB543, and AlexaFluor532. [Figure 4] Figure 10 is an extinction spectrum, normalized to 1 at its maximum, for an exemplary embodiment of AuNR@Ag plasmonic particles suitable for enhancing fluorescent agents that can be excited by 620-650 nm light, such as Cy5, AlexaFluor633, and IR Dye650. [Figure 5] Figure 10 is an extinction spectrum, normalized to 1 at its maximum, for an exemplary embodiment of AuNR@Ag plasmonic particles suitable for enhancing fluorescent agents that can be excited by 650-680 nm light, such as Cy5.5, IR Dye680LT, and AlexaFluor680. [Figure 6]Figure 1 shows the extinction spectrum, normalized to 1 at its maximum, for an exemplary embodiment of AuNR@Ag plasmonic particles suitable for enhancing fluorophores that can be excited by 750-790 nm light, such as Cy7.5, IRDye800CW, and AlexaFluor790. [Figure 7] Figure 1 shows exemplary embodiments of plasmonic fluorophores exhibiting long Stokes shifts. Two examples are shown here: one containing a single FRET pair (donor and acceptor fluorophores), and the other containing a FRET triple in which an intermediate fluorophore (donor 2 / acceptor 1) serves as a bridge between the first donor fluorophore (donor 1) and the last acceptor fluorophore (acceptor 2). In both cases, the resulting plasmonic fluorophores can be excited at wavelengths that excite the shortest wavelength donor fluorophore (λEX_D) and emit at the maximum emission wavelength of the longest wavelength acceptor fluorophore (λEM_A). [Figure 8] Figure 1 shows a plot of the emission spectra of two exemplary embodiments of long Stokes-shift plasmonic fluorophores excited by 470 nm light, one coated with the FRET pair FITC-Cy3 and the other coated with the FRET triple FITC-Cy3-Cy5. In both cases, significant fluorescence is observed from the longest wavelength acceptor molecule (Cy3 in the FITC-Cy3 pair and Cy5 in the FITC-Cy3-Cy5 triple), while the fluorescence of the donor molecule is suppressed, indicating efficient FRET. [Figure 9]

[0033] Figure 1 shows an exemplary embodiment of constructing a plasmonic fluorophore using AuNR@Ag plasmonic core particles. The AuNR@Ag plasmonic core particles are coated with a spacer layer, and then fluorescent dye molecules are conjugated to the spacer layer. This dye-spacer layer is then coated with a functional layer (in this example, a combination of biotinylated bovine serum albumin (BSA) and free BSA). Optionally, this biotinylated plasmonic fluorophore can be further modified by binding streptavidin, and then, optionally, modified with a biotinylated antibody. [Figure 10] In this exemplary embodiment, a plasmonic fluorophore is constructed using AuNR@Ag plasmonic core particles. The AuNR@Ag plasmonic core particles are coated with a spacer layer, to which fluorescent dye molecules are then conjugated. This dye-spacer layer is then coated with a functional layer, in this example a combination of trans-cyclooctene (TCO), BSA, and free BSA. Optionally, this TCO-conjugated plasmonic fluorophore can be further reacted with a tetrazine (TZ)-conjugated antibody. TCO and TZ are just one example of a "click" chemistry pair, but any click pair will work. [Figure 11] 1 is an exemplary embodiment of a pMHC-modified plasmonic fluorophore and a method for making the same. Streptavidin-conjugated plasmonic fluorophores can be used to make pMHC-modified plasmonic fluorophores by adding the streptavidin-conjugated plasmonic fluorophore to a solution containing an excess of biotinylated pMHC. DETAILED DESCRIPTION OF THE INVENTION

[0017] The present disclosure can be understood by reference to the following detailed description in conjunction with the drawings described below. It should be noted that for clarity of illustration, certain elements in the various drawings may not be drawn to scale. Several variations of devices are presented herein. Various components, parts, and features of different variations may be combined together and / or substituted for one another, and it should be understood that all of them are within the scope of the present application, even if not all variations and specific variations are shown in the drawings. Mixing and matching of features, elements, and / or functions between various variations is expressly contemplated herein, and therefore, those skilled in the art should also understand from this disclosure that features, elements, and / or functions of one variation may be appropriately incorporated into another variation, unless otherwise specified.

[0018] Here are some definitions that apply throughout this disclosure: As used herein, "about" refers to a numerical value, including whole numbers, fractions, percentages, etc., whether explicitly stated or not. The term "about" generally refers to a range of numerical values, such as ±0.5-1%, ±1-5%, or ±5-10% of the recited value, that are considered equivalent to the recited value, for example, having the same function or result.

[0019] The term "comprising" means "including, but not necessarily limited to," and specifically indicates open-ended inclusion or membership in such listed combinations, groups, series, etc. As used herein, the terms "comprising" and "including" are inclusive and / or open-ended and do not exclude additional, unrecited elements or method steps. The term "consisting essentially of" is more restrictive than "comprising," but less restrictive than "consisting of." Specifically, the term "consisting essentially of" limits membership to the specified materials or steps and those that do not materially affect the essential characteristics of the claimed invention.

[0020] As used herein, the term "plasmonic fluorophore" or "fluorescent nanoconstruct" refers to a composite structure having at least a plasmonic nanostructure at its core, a spacer layer coating the plasmonic nanostructure, and at least one fluorescent agent conjugated to its surface. In some variations, the "plasmonic fluorophore" or "fluorescent nanoconstruct" may further include a scaffold layer and / or a biorecognition element (e.g., MHC, pMHC, streptavidin, etc.).

[0021] As used herein, the term "fluorescent agent" means a dye, fluorescent probe, or fluorophore that is capable of producing fluorescent emission upon excitation.

[0022] Provided herein are ultrabright fluorescent nanoconstructs, plasmonic fluorophores (PFs), based on novel silver-containing plasmonic nanostructures. Additionally, disclosed herein are novel plasmonic fluorophores that exhibit a large Stokes shift, the difference between the maximum position of the fluorophore's excitation spectrum and the maximum position of its emission spectrum. Plasmonic fluorophores can be conjugated to one or more biorecognition elements and used to enhance existing biological assays. Furthermore, these plasmonic fluorophores may enable novel biological assays due to their superior brightness. The plasmonic fluorophore technology disclosed herein can reduce instrumentation requirements because they are significantly brighter (i.e., they emit more photons in a given period) than typical organic fluorophores.

[0023] Plasmonic fluorophores exhibit long Stokes shifts that allow significant separation between excitation and emission and are ultrabright. This may enable simpler and less expensive fluorescence detection systems by using broadband excitation sources (e.g., LEDs) with longer wavelength detection. Furthermore, it may be possible to excite many different fluorophores with the same excitation source and specifically detect each one using different bandpass filters or even monochromators. This is particularly important in highly multiplexed fluorescence assays such as flow cytometry and immunohistochemistry / immunocytochemistry, where some fluorophores are used to specifically identify cell populations and others are used to provide information about the proteins expressed within these populations.

[0024] Plasmonic fluorophores have a relatively large surface area, allowing them to be functionalized with many biorecognition elements, including, but not limited to, MHC, pMHC, streptavidin, neutravidin, or avidin. This results in structures with higher apparent affinity (or avidity) than isolated biorecognition elements. This is particularly important when targeting complexes with low affinity but multiple targets, such as in major histocompatibility complex (MHC) assays for the identification of antigen-specific T cells. Plasmonic fluorophores functionalized with peptide-loaded MHC (pMHC) molecules represent the most sensitive reagents available for T cell receptor recognition. This is due not only to their incredible brightness but also to their ability to be densely loaded with large amounts of pMHC.

[0025] The present disclosure relates to an ultrabright fluorescent nanocomposite or plasmonic fluorophore. The fluorescent nanocomposite may include a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having an excitation maximum wavelength (λEX), and at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC). The fluorescent nanocomposite structure has a fluorescence intensity at least 500 times greater than that of the at least one fluorescent agent alone.

[0026] In some examples, the plasmonic nanostructure is a silver-coated gold nanorod nanostructure (AuNR@Ag) used as a core particle in an ultrabright fluorescent nanoconstruct. Typically, gold is the metal of choice for nanostructures (e.g., gold nanorods (AuNR)) with a primary LSPR peak above 600 nm, while silver is considered preferred for nanostructures with a primary LSPR peak below 600 nm. For the purpose of creating plasmon-enhanced fluorescent nanoparticles, silver may generally be preferred over gold because it has a stronger plasmon than gold and can support multiple plasmon modes. Herein, we present a plasmonic core particle (AuNR@Ag) with a tunable LSPR peak between approximately 390 nm and approximately 800 nm, which has silver as the metal on the surface and a gold nanorod in the center. Silver has a stronger plasmon than gold, and thus its incorporation into a plasmonic fluorophore can result in high fluorescence. The silver coating on the AuNR blue-shifts the resulting primary LSPR peak relative to the primary LSPR peak of the original AuNR. Generally, AuNRs with a dominant LSPR wavelength 100 nm to 400 nm longer than the target dominant LSPR peak of the resulting AuNR@Ag are selected. Because AuNR@Ag nanostructures possess multiple plasmon modes due to the silver, it is demonstrated herein that even these non-dominant plasmon modes can be used to enhance the fluorescence of conjugated fluorophores.

[0027] As shown in Figure 1, AuNR@Ag core particles can be fabricated from gold nanorods (AuNRs) with a major LSPR peak between 460 nm and 800 nm by coating gold nanorods with higher LSPR wavelengths with silver. For example, to fabricate AuNR@Ag with a major LSPR peak between 750 and 800 nm, one would start with AuNRs with an LSPR between 1050 and 1200 nm. Another example would be to use AuNRs with an LSPR between 850 and 950 nm to fabricate AuNR@Ag with a major LSPR peak between 510 and 680 nm. Another example would be to use AuNRs with a major LSPR peak between 640 and 700 nm to fabricate AuNR@Ag with a major LSPR peak between 460 and 510 nm. In addition to the major LSPR peak, there is a significant minor LSPR peak appearing at wavelengths as low as 395 nm.

[0028] In one embodiment, the difference between at least one λLSPR and λEX is less than 75 nm. In at least one example, the dominant LSPR peak of the AuNR@Ag is within 50 nm of the excitation maximum of the fluorophore being enhanced. Examples of extinction spectra with identified dominant peaks and examples of fluorophores used to create the resulting plasmonic fluorophores are shown in Figures 2-6. In another embodiment, the significant LSPR peak of the AuNR@Ag is within 50 nm of the excitation maximum of the fluorophore being enhanced. For example, AuNR@Ag nanostructures corresponding to the spectra shown in Figures 2-5 can be used to enhance dyes excited by a 405 nm laser, such as Pacific Blue, by taking advantage of the non-dominant LSPR peak of these structures in the 390 nm to 410 nm range.

[0029] The synthesis of AuNR@Ag nanostructures, whose UV-VIS spectra are shown in Figures 2-6, is achieved by adjusting the ratio of silver nitrate to gold nanorods in the silver overgrowth step. As an example procedure for synthesizing AuNR@Ag with a dominant (major) peak between 750 and 800 nm, as shown in Figure 6, begins with 380 mL of AuNR solution in 10 mM cetyltrimethylammonium chloride (CTAC), which has an absorbance of 0.228 for AuNR with an LSPR of 1050 nm. Add 15.2 mL of 10 mM silver nitrate. Heat this mixture to 60 °C, add 3.8 mL of 100 mM ascorbic acid, mix rapidly, and incubate at 60 °C for at least 6 hours. To fabricate AuNR@Ag nanoparticles with different LSPR peaks, simply follow the procedure described above, starting with AuNR nanoparticles with a primary LSPR wavelength 100 nm to 400 nm longer than the target primary LSPR peak of the resulting AuNR@Ag nanoparticles, but modifying the ratio of the chemical components (gold nanorods, CTAC, silver nitrate, and ascorbic acid). Figures 2–6 show the spectra of AuNR@Ag nanoparticles with LSPR peaks ranging from approximately 390 nm to approximately 800 nm, fabricated using the silver overgrowth procedure. Nanoparticles containing silver on their surfaces are typically susceptible to oxidation in aqueous solutions, potentially degrading their plasmonic properties. The AuNR@Ag nanoparticles used to fabricate fluorescent nanostructures (plasmonic phosphors) can be prepared within a week, and coating them with a spacer layer can protect the AuNR@Ag nanoparticles from oxidation. These particles were stored in aqueous solutions for over six months without significant oxidation or changes in their plasmonic properties.

[0030] The advantages of using AuNR@Ag as the core plasmonic microparticle in plasmonic fluorophores are its ease of synthesis, its strong plasmon, and the tunability of its LSPR wavelength in the range of commonly used fluorescent dyes; however, it should be noted that plasmonic fluorophores can also be fabricated using some other structures that can support plasmonic resonance at the appropriate wavelength, including, but not limited to, gold nanorods, silver nanocubes, silver or gold nanospheres, bimetallic nanostructures, gold-core-silver-shell nanocuboids, gold or silver nanotubes, gold nanorods, silver nanocubes, silver nanospheres, nanostructures with sharp tips, nanostars, hollow nanostructures, nanocages, nanorattle, nanobipyramids, nanoplates, and nanoraspberries.

[0031] In one embodiment, the AuNR@Ag nanostructure serves as the central core for the plasmonic phosphor. The AuNR@Ag nanostructure can then be coated with at least one spacer coating or spacer layer. For example, the AuNR@Ag nanostructure can be coated with a spacer layer, as shown in Figures 9 and 10. This spacer layer can be any dielectric material that can be coated onto the AuNR@Ag structure and has a precisely controllable thickness. In some embodiments, the spacer coating has a thickness of about 0.5 nm to about 20 nm, about 1 nm to about 10 nm, or about 2 nm to about 5 nm.

[0032] Ideally, the spacer layer should have reactive groups that allow for conjugation of fluorescent dye molecules and remain stable in solution after coating. An exemplary spacer layer consists of an initiation layer using (3-mercaptopropyl)trimethoxysilane (MPTMS), which bonds to the silver surface and allows for the growth of additional silane layers, and a growth layer containing a mixture of trimethoxy(propyl)silane (TMPS) and (3-aminopropyl)trimethoxysilane (APTMS). The ratio of TMPS to APTMS can be varied to adjust the zeta potential of the coated nanostructures and the density of reactive groups on the surface. To coat AuNR@Ag particles with the optimal spacer thickness corresponding to the spectrum shown in Figure 6, for example, first add 400 microliters of MPTMS to a 400 mL solution of AuNR@Ag in 1 mM CTAC. Here, AuNR@Ag has a major LSPR peak at approximately 760 nm and an absorbance of 6–10 nm. This mixture can be incubated at 20 °C for 1 hour with gentle shaking. After 1 hour, 2 mL of APTMS and 2 mL of TMPS are added and mixed, and the solution is incubated at 20 °C for 4 hours with gentle shaking. These spacer-coated AuNR@Ag particles are then centrifuged and resuspended in 1 mM CTAC to stop the spacer coating reaction. As another example, to coat AuNR@Ag particles corresponding to the spectrum shown in Figure 3, we follow the exact procedure described above and use AuNR@Ag with a major LSPR peak at approximately 510 nm and an absorbance of 45-50 nm. The use of a silane-based spacer layer is attractive because its thickness can be easily controlled by simply adjusting the stoichiometry of the reactants.

[0033] The spacer-coated AuNR@Ag nanostructures can be directly conjugated to at least one fluorescent agent, as shown in the second step of Figures 9 and 10. In various examples, the at least one fluorescent agent may comprise at least about 5, at least about 10, at least about 20, at least about 50, at least about 100, at least about 200, at least about 300, at least about 400, or at least about 500 fluorescent agents. The use of TMPS and APTMS as spacer growth layers exposes primary amine groups to the solvent, which are easily functionalized with amine-reactive fluorescent dyes, such as those containing N-hydroxysuccinimide (NHS) esters, isothiocyanates, tetrafluorophenyl (TFP) esters, or pentafluorophenyl (PFP). For the synthesis of plasmonic fluorophores, a single type of fluorescent dye and an appropriate plasmonic nanostructure core are generally selected so that the excitation maximum of the fluorescent dye is within about 50 nm of the significant LSPR peak of the plasmonic nanostructure. As an example, to label 1 mL of spacer-coated AuNR@Ag nanostructures corresponding to the spectrum in Figure 6 dissolved in 1 mM CTAC containing 0.5x phosphate-buffered saline at an absorbance of 20, 4 microliters of NHS-sulfo-cyanine 7.5 dissolved in dimethylformamide (DMF) at a concentration of 5 mg / mL is added and incubated at room temperature for 12 hours. As another example, to label 1 mL of spacer-coated AuNR@Ag nanostructures corresponding to the spectrum in Figure 3 dissolved in 1 mM CTAC containing 0.5x phosphate-buffered saline at an absorbance of 20, 2 microliters of the dye NHS-MB543 dissolved in dimethylformamide (DMF) at a concentration of 5 mg / mL is added and incubated at room temperature for 12 hours. Optimal labeling conditions can be found empirically for each dye / nanostructure combination, but should be chosen so that fluorescence per particle as a function of dye concentration is maximized.

[0034] By incorporating multiple different types of dye molecules into plasmonic fluorophores, spectrally unique plasmonic fluorophores with large Stokes shifts can be produced. As shown in Figure 7, by incorporating dye molecules capable of participating in Förster resonance energy transfer (FRET) into plasmonic fluorophores, it is possible to create plasmonic fluorophores with large Stokes shifts. Specifically, fluorescent dyes / drugs that form FRET pairs, FRET triplets, FRET quadruplets, or even FRET quintets can be incorporated. In a preferred embodiment, a suitable nanostructure core has high molar absorbance near the excitation maximum of the first donor dye molecule in the FRET chain (i.e., the dye molecule with the lowest excitation wavelength) and near the light source used for excitation, and therefore has a localized resonant plasmonic mode.

[0035] In one embodiment, a fluorescent nanocomposite structure may include a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, at least one fluorescent agent having a first maximum excitation wavelength (λEX1) and a first maximum emission wavelength (λEM1), and at least one fluorescent agent having a second maximum excitation wavelength (λEX2) and a second maximum emission wavelength (λEM2). The fluorescent nanocomposite structure can be excited with light at λEX1 and emit light at λEM2, such that the emission intensity of λEM2 is greater than the emission intensity of λEM1. Thus, the at least one fluorescent agent having λEX1 is a FRET donor for the at least one fluorescent agent having λEX2, which functions as a FRET acceptor. In some examples, the difference between at least one λLSPR and λEX1 is less than 100 nm, less than 75 nm, less than 50 nm, less than 25 nm, or less than 15 nm.

[0036] In some embodiments, the fluorescent nanocomposite can further contain a FRET triple, quadruple, or quintuple. For example, in the case of a FRET triple, the fluorescent nanocomposite can further include at least one fluorescent agent having a third maximum excitation wavelength (λEX3) and a third maximum emission wavelength (λEM3). The fluorescent nanocomposite structure can be excited with light at λEX1 and emit light at λEM3, such that the emission intensity of λEM3 is greater than the emission intensity of λEM1 or λEM2.

[0037] As shown in Figure 7, FRET dyes can be conjugated to the same spacer layer, with a thickness of 1 nm to 10 nm, preferably 2 to 5 nm. Alternatively, as shown in Figure 7, FRET dyes can be conjugated to different spacer layers, where the shortest wavelength donor dye is conjugated to the first spacer layer and the acceptor dye is conjugated to a second spacer layer covering the first spacer layer and having a thickness of 1 nm to 3 nm. This layer-by-layer scheme can be expanded to accommodate FRET triple, quadruple, and quintuple dyes. Furthermore, a mixed scheme can be combined with the layer-by-layer scheme. For example, the first layer can be coated with only the donor dye, and the second layer can be coated with a mixture of another dye pair that functions as a FRET acceptor for the donor dye and a donor for the longer wavelength acceptor dye.

[0038] As an example, spacer-coated AuNR@Ag nanostructures corresponding to the spectrum shown in Figure 3 are coated with the FRET pair FITC and Cy3 in a 1:1 stoichiometry. Figure 8 shows the resulting emission spectrum of this plasmonic fluorophore when excited at 470 nm. When excited at 470 nm, this plasmonic fluorophore exhibits suppressed emission at the FITC emission maximum near 520 nm and strong emission near the Cy3 emission maximum near 570 nm, both indicative of efficient FRET. In the absence of FITC, which serves as the donor molecule, the same plasmonic fluorophore containing only Cy3 is minimally excited by 470 nm light. As a further example, spacer-coated AuNR@Ag nanostructures corresponding to the spectrum shown in Figure 3 are coated with the FRET triplet FITC, Cy3, and Cy5 in a 1:1:1 stoichiometry. Figure 8 also shows the resulting emission spectrum of this plasmonic fluorophore when excited at 470 nm. In this embodiment, both FITC and Cy3 fluorescence are suppressed, and Cy5 fluorescence is enhanced.In the absence of FITC, the fluorescence of Cy3-Cy5 particles is minimized when excited at 470 nm.In the absence of Cy3, FITC fluorescence is minimally suppressed, and Cy5 fluorescence can be minimized due to the low FRET efficiency of FITC as a donor.The optimal labeling stoichiometry is selected to maximize the fluorescence of the final acceptor (i.e., the dye with the longest emission wavelength) while minimizing donor dye fluorescence. By matching appropriate nanostructures (i.e., those with a significant LSPR mode near the excitation maximum (λ) of the shortest wavelength donor and in the vicinity of the excitation source), selecting appropriate FRET dye chains to facilitate resonance energy transfer, and optimizing the labeling stoichiometry to maximize the fluorescence of the plasmonic fluorophore at the emission maximum (λ) of the longest wavelength acceptor dye in the FRET dye chain while suppressing the fluorescence of the donor dye, multiple spectrally unique long Stokes shift plasmonic fluorophores can be created.Table 1 below provides examples of dye chain combinations that can be used to create unique plasmonic fluorophores with the excitation and emission wavelengths given in column 1. These are non-limiting examples, and those skilled in the art will recognize that spectrally similar dyes (i.e., having excitation and emission maxima within 15 nm of the dyes listed below) can be substituted to achieve the same effect. For example, Alexa488 can be substituted with FITC or Cy2 without significant difference if the labeling stoichiometry is optimized. As another example, Alexa546 can be substituted with MB543, tetramethylrhodamine, or Cy3. As another example, Alexa633 can be substituted with Cy5 or IRDye 650.

[0039] [Table 1-1]

[0040] [Table 1-2]

[0041] In some embodiments, the plasmonic fluorophore may further comprise a scaffold layer. In one example, after coating with a fluorescent dye, the next step in preparing the plasmonic fluorophore may be adding a scaffold layer. The scaffold layer serves several purposes, including preventing nonspecific adsorption in immunoassays (when an appropriate blocking reagent is used), stabilizing the fluorescent dye-labeled plasmonic fluorophore, and serving as a base onto which targeting elements used in biorecognition, such as biotin, streptavidin, nucleic acids, or antibodies, can be easily conjugated. While the scaffold layer is not absolutely essential, as these targeting elements can be attached directly to the spacer layer, the scaffold layer provides additional labeling versatility and improves plasmonic fluorophore stabilization. Figure 9 shows an example of a process for creating an antibody-coated plasmonic fluorophore using bovine serum albumin (BSA) as a scaffold layer. In this process, the fluorescent dye-labeled plasmonic fluorophore is incubated with a mixture of biotinylated and native BSA in solution for approximately 30 minutes with sonication. The labeling density can be easily adjusted by changing the ratio of biotinylated BSA to native BSA from 100% to 1%. Furthermore, the degree of biotinylated BSA labeling can be varied from 1 to 10 biotins using an amine-reactive biotinylation reagent such as NHS-PEG4-biotin. By adjusting the ratio of biotinylated BSA to native BSA, combined with the degree of biotinylation, the density and distribution of biotin on the surface of the plasmonic fluorophore can be freely controlled. The BSA scaffold layer can be further crosslinked using glutaraldehyde or another suitable crosslinking agent to increase stability.

[0042] In one embodiment, the plasmonic fluorophore may further comprise at least one biotin-binding molecule on the spacer coating and / or scaffold layer. For example, the at least one biotin-binding molecule may comprise at least about 2, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 biotin-binding molecules. Non-limiting examples of biotin-binding molecules include streptavidin, neutravidin, and avidin. For example, after coating with a BSA / biotinylated BSA scaffold layer, the plasmonic fluorophore may be functionally reactive with streptavidin and used to specifically detect streptavidin in biological assays. It may also be coated with streptavidin to produce a streptavidin-functionalized plasmonic fluorophore, which can be used to specifically detect biotinylated reagents in biological assays. These streptavidin-coated plasmonic fluorophores can be further modified with another biotinylation reagent, such as an antibody, as shown in Figure 9. As another example, biotinylated BSA can be replaced with BSA functionalized with a "click" chemical reactive moiety, such as trans-cyclooctene (TCO) conjugated to BSA via an NHS-TCO reagent or tetrazine (Tz) conjugated to BSA via an NHS-tetrazine reagent, and a scaffold layer can be formed using a mixture of BSA:BSA-TCO or BSA-Tz, as shown in Figure 10. Those skilled in the art will recognize that any click reaction pair, including but not limited to an azide-alkyne pair in a copper-catalyzed click reaction, can be used in place of TCO / TZ. Furthermore, as shown in Figure 10, it is possible to conjugate a targeting element (e.g., streptavidin, antibody, nucleic acid, etc.) to a click-functionalized plasmonic fluorophore by incubating the click-functionalized plasmonic fluorophore with the targeting element labeled with a complementary click moiety.

[0043] In one embodiment, the plasmonic fluorophore may further comprise at least one peptide-loaded MHC (pMHC) molecule on its outer surface. In various examples, the pMHC molecule may be biotinylated, and the biotinylated pMHC may be attached to a biotin-binding molecule on the spacer coating and / or scaffold layer. The at least one biotinylated pMHC molecule may comprise at least about 2, at least about 4, at least about 8, at least about 12, at least about 16, at least about 20, at least about 24, at least about 28, at least about 32, at least about 36, at least about 40, or at least about 48 pMHC molecules. Plasmonic fluorophores conjugated with pMHC represent a highly attractive platform for MHC tetramer assays or tetramer staining, which are used to identify antigen-specific T cells containing T cell receptors (TCRs) that specifically recognize the peptide loaded on the pMHC. The standard reagent used to identify antigen-specific T cells in so-called MHC-tetramer assays (also known as tetramer staining) is fluorescently labeled streptavidin bound to four biotinylated pMHC molecules. Because single pMHC-receptor complexes have relatively weak affinity, combining four pMHC molecules into a single complex via streptavidin increases avidity, and therefore apparent affinity. This concept has been further expanded by linking multiple MHC tetramer molecules together, for example, to create pMHC dodecamers. Another alternative is to attach pMHC to fluorescently labeled dextran to create so-called dextramers. Disclosed herein are methods and compositions for creating plasmonic fluorophores decorated with many, preferably 8-40 or more, MHC molecules.

[0044] The resulting composition has several advantages over existing materials: 1) the plasmonic fluorophore itself is at least 50 times brighter than conventional fluorophores, including PE, resulting in a higher signal; 2) the presence of multiple pMHC molecules (at least 12) provides the pMHC-modified plasmonic fluorophore with very high avidity / apparent affinity; and 3) the physical size of the pMHC-modified plasmonic fluorophore (longest dimension >50 nm) allows binding of cell surface receptors over a larger area, meaning that T cells with lower receptor densities can be detected. In some embodiments, the plasmonic fluorophore has a fluorescence intensity at least 50 times greater, at least 100 times greater, at least 200 times greater, at least 300 times greater, at least 400 times greater, or at least 500 times greater than the fluorescence intensity of the fluorophore alone.

[0045] In an exemplary embodiment, pMHC-modified plasmonic fluorophores can be assembled by combining streptavidin-conjugated plasmonic fluorophores with biotinylated pMHC molecules by adding streptavidin-coated plasmonic fluorophores to a solution containing a molar excess of biotinylated pMHC molecules. Here, the molar excess is determined relative to the molar concentration of streptavidin in the solution containing the streptavidin-conjugated plasmonic fluorophores, as shown in Figure 11. The pMHC-decorated plasmonic fluorophores can be separated from free pMHC by centrifugation. After the reaction, an excess of free biotin can be added before centrifugation to ensure all biotin-binding sites are occupied, thereby minimizing potential cross-linking and aggregation. The density of pMHC on the surface of the plasmonic fluorophores in this design can be easily altered by simply changing the ratio of biotinylated BSA to BSA used in the preparation of the plasmonic fluorophores, by changing the degree of biotinylation of the BSA, or both. This ultimately has the effect of altering the number of streptavidin molecules present on the surface of the plasmonic fluorophore. It should be noted that the BSA coating in this context functions as a scaffold and can be substituted for many different proteins and other polymers that can perform similar functions. Furthermore, biotin can be directly incorporated into the silane spacer layer (e.g., using biotin-PEG-silane), or biotin-PEG-NHS ester can be attached via exposed amines, similar to how fluorescent dyes are conjugated. In this scenario, streptavidin can be directly conjugated via these biotin molecules, eliminating the need for a scaffold.

[0046] In another embodiment, a pMHC-modified plasmonic fluorophore can be assembled by combining a plasmonic fluorophore containing a reactive click chemistry moiety with pMHC labeled with a complementary click moiety (e.g., a plasmonic fluorophore labeled with TCO-PEG-NHS ester and a pMHC labeled with tetrazine-PEG-NHS ester). In this scenario, PEG acts as a spacer to improve conjugation efficiency but may be omitted. PEG can be 2 to 24 monomer units long). In this "clicked" pMHC embodiment, the plasmonic fluorophore is first coated with a mixture of TCO-labeled BSA and free BSA, where the TCO-BSA ratio can range from 100% to approximately 5%, ideally 80% to approximately 10%. This TCO-plasmonic fluorophore can then be incubated with a molar excess of tetrazine-labeled pMHC molecules. The density of pMHC on the surface of the plasmonic fluorophore can be altered simply by changing the ratio of TCO-BSA to BSA. In another embodiment, an MHC molecule is engineered to have an unpaired cysteine ​​at the C-terminus or in a solvent-exposed loop, and a reactive click moiety is added to the MHC molecule via a sulfhydryl-reactive reagent (e.g., maleimide-PEG-Tz or maleimide-PEG-TCO), which can then be conjugated to a complementary functionalized plasmonic fluorophore.

[0047] Typically, MHC molecules are expressed in bacterial cultures and contain a biotinylation tag, such as BSP or AviTag. After purification and refolding of the MHC molecule, this tag is modified with a biotin ligase, such as BirA, which site-specifically adds a biotin molecule. Click versions of plasmonic fluorophores can be used to directly link appropriately modified MHC molecules. Genetic code expansion techniques can be used to site-specifically introduce non-standard amino acids into proteins. Using this strategy, at least one natural amino acid in an MHC molecule, for example in the C-terminal region, can be replaced with a non-standard amino acid containing a click-reactive moiety. An exemplary amino acid that can react with a Tz-functionalized plasmonic fluorophore is TCO. * -L-lysine (TCO * The click-functionalized nonstandard amino acid is simply added to the growth medium, thereby incorporating it into the MHC protein at the specific site. The click-functionalized nonstandard amino acid is then added to the growth medium, thereby incorporating it into the MHC protein at the specific site. The click-functionalized nonstandard amino acid is then added to the growth medium, thereby incorporating it into the MHC protein at the specific site. The advantage of this approach is the elimination of the addition of a biotin ligase recognition sequence to the MHC and the elimination of a ligation reaction using biotin ligase. This same approach can be applied to click-functionalized antibodies and other biologically expressed molecules, which can then be conjugated to complementary click-functionalized plasmonic fluorophores.

[0048] Further provided herein is a method for identifying T cells having specific T cell receptors. In one embodiment, the method may include providing a sample containing T cells, contacting the sample containing T cells with a fluorescent nanocomposite structure, spatially separating the T cells, exciting the fluorescent nanocomposite structure with a wavelength of light that induces fluorescence emission, and detecting the T cells labeled with the fluorescent nanocomposite structure. In some examples, the T cells may be spatially separated using flow cytometry.

[0049] The fluorescent nanocomposite structure may contain at least one major histocompatibility complex (MHC) molecule loaded with a peptide (pMHC) capable of specifically binding to T cells containing a receptor specific for the peptide. In some embodiments, the fluorescent nanocomposite structure includes a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR), at least one spacer coating, and at least one fluorescent agent having a maximum excitation wavelength. The fluorescent nanocomposite structure has a fluorescence intensity at least 500 times greater than that of the at least one fluorescent agent alone. [Example]

[0050] Example 1: Preparation of streptavidin-functionalized plasmonic fluorophores One milliliter of plasmonic fluorophore labeled with a fluorescent agent with an absorbance of 20 at the LSPR wavelength was centrifuged to form a pellet. 990 μL of the supernatant was removed. In a separate microcentrifuge tube, 200 μL of biotinylated BSA solution (at least a 100-fold molar excess relative to the plasmonic fluorophore to be coated) was added to an appropriate buffer (e.g., 50 mM carbonate-bicarbonate buffer, pH 9). The entire plasmonic fluorophore pellet was transferred to the biotinylated BSA solution and sonicated in a water bath for 30 minutes. The solution was removed from the sonic water bath and incubated at 4°C for 15 hours. The biotinylated BSA-coated plasmonic fluorophore solution was centrifuged to form a pellet, and then all but 10 μL of the supernatant was removed. In a separate microcentrifuge tube, 200 μL of streptavidin solution (at least a 50-fold molar excess relative to the plasmonic fluorophore to be coated) was added to an appropriate buffer (e.g., 50 mM carbonate-bicarbonate buffer, pH 9). The entire pellet of biotinylated BSA-coated plasmonic fluorophores was transferred to a streptavidin solution and incubated for 2 hours. This solution was centrifuged to form a pellet, and the supernatant was removed. The pellet was then resuspended in an appropriate buffer (e.g., 50 mM carbonate-bicarbonate buffer, pH 9, containing 1% BSA). This process was repeated two more times to remove unbound streptavidin.

[0051] Example 2: Construction of pMHC-functionalized plasmonic fluorophores Streptavidin-functionalized plasmonic fluorophores (Strep-PF) similar to those described in Example 1 were adjusted to an absorbance of 20 at their LSPR wavelength, and 1 mL was removed and placed in a microcentrifuge tube. This solution was centrifuged to pellet the Strep-PF, and approximately 990 μL of supernatant was removed. In a separate microcentrifuge tube, 400 μL of an 8 μM (368 μg / mL peptide-MHC I complex or 232 μg / mL peptide-MHC II) solution was added to a compatible buffer, e.g., 1× phosphate-buffered saline (PBS) pH 7.4, on ice. The entire centrifuged Strep-PF pellet was transferred to the MHC-peptide complex solution, which was vortexed for 10 seconds and then incubated at 4°C for 2 hours. This reaction could be used directly or, optionally, blocked by adding a molar excess of biotin and then used.

[0052] Example 3: Plate-based assay confirming that plasmonic fluorophores are functionalized with pMHC A simple method to confirm that the plasmonic fluorophore was conjugated to pMHC was to perform an immunoassay against the MHC moiety. This was done by coating a microtiter plate with an antibody specific to the MHC moiety (either anti-β2-microglobulin or an anti-MHC class-specific antibody) at a concentration of 1 μg / mL in PBS. The plate was then blocked with an appropriate blocking agent (e.g., 1% BSA in 1X PBS) and washed with an appropriate detergent (e.g., 1X PBS containing 0.05% Tween 20). A specific amount of solution containing the plasmonic fluorophore conjugated to pMHC was then incubated in the plate for 10 minutes, removed, and the plate was washed with an appropriate detergent. Plasmonic fluorophore fluorescence on the plate surface was then detected using an appropriate reader and compared with that of a control well of a microtiter plate not coated with an antibody specific to the MHC moiety. Because the MHC complex rapidly dissociates in the absence of peptide binding, this procedure confirmed that the pMHC complex was functionally active.

[0053] Example 4: Identification of T cell populations capable of recognizing specific peptides Prepare cells of interest (e.g., CD8-positive T cells) at 2 x 10 6 Cells were added to a microcentrifuge tube in a well of a 96-well microtiter plate. The volume was adjusted to 200 μL with an appropriate cell staining buffer (e.g., 1X PBS containing 5% fetal bovine serum). 2 μL of pMHC-functionalized plasmonic fluorophore solution was added as in Example 2, where the pMHC contained the peptide of interest, and the mixture was incubated on ice in the dark for 30 minutes. The cells were washed twice with staining buffer and resuspended in 200 μL of staining buffer. The cells were analyzed using a flow cytometer with appropriate settings to detect the specific fluorescent signal of the plasmonic fluorophore used. Titration of the concentration of pMHC-functionalized plasmonic fluorophore may be necessary for optimal performance.

[0054] While several embodiments have been described, those skilled in the art will recognize that various modifications, alternative configurations, and equivalents may be used without departing from the spirit of the present invention. Moreover, certain well-known processes and elements have not been described to avoid unnecessarily obscuring the present invention. Accordingly, the above description should be interpreted as illustrative, and not as limiting the scope of the present invention. The following claims are intended to cover all general and specific features described herein, as well as all statements of scope of the methods and compositions of the present invention that may be said to lie therebetween as a matter of language. [1] A fluorescent nanocomposite structure comprising: a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR); at least one spacer coating; at least one fluorescent agent having an excitation wavelength maximum (λ); at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC); The fluorescent nanocomposite structure has a fluorescence intensity that is at least 500 times greater than the fluorescence intensity of the at least one fluorescent agent alone. [2] The fluorescent nanocomposite structure according to [1], wherein the difference between the at least one λLSPR and the λEX is less than 75 nm. [3] The fluorescent nanocomposite structure according to [1], wherein the plasmonic nanostructure is a silver-coated gold nanorod (AuNR@Ag). [4] The fluorescent nanocomposite structure according to [1], wherein the at least one fluorescent agent comprises at least about 5, at least about 10, at least about 20, at least about 50, at least about 100, at least about 200, at least about 300, at least about 400, or at least about 500 fluorescent agents. [5] The fluorescent nanocomposite structure according to [1] above, wherein the spacer coating has a thickness of about 1 nm to about 20 nm. [6] The fluorescent nanocomposite structure according to [1] above, further comprising a biotin-binding molecule. [7] The fluorescent nanocomposite structure according to [6], wherein the at least one biotin-binding molecule comprises at least about 2, at least about 5, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 biotin-binding molecules. [8] The fluorescent nanocomposite structure according to [6], wherein the biotin-binding molecule is streptavidin, neutravidin, or avidin. [9] The fluorescent nanocomposite structure according to [1], wherein the at least one pMHC molecule comprises at least about 2, at least about 4, at least about 8, at least about 12, at least about 16, at least about 20, at least about 24, at least about 28, at least about 32, at least about 36, at least about 40, or at least about 48 pMHC molecules.

[10] The fluorescent nanocomposite structure according to [6], wherein the at least one pMHC molecule is biotinylated.

[11] The fluorescent nanocomposite structure according to [1], further comprising a scaffold layer covering the spacer coating.

[12] A fluorescent nanocomposite structure comprising: a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR); at least one spacer coating; at least one fluorescent agent having a first maximum excitation wavelength (λEX1) and a first maximum emission wavelength (λEM1); at least one fluorescent agent having a second maximum excitation wavelength (λEX2) and a second maximum emission wavelength (λEM2); The fluorescent nanocomposite structure is excited by light of λEX1 and can emit light of λEM2; A fluorescent nanocomposite structure, wherein the intensity of the emission at λEM2 is greater than the intensity of the emission at λEM1.

[13] The fluorescent nanocomposite structure according to

[12] , wherein the difference between the at least one λLSPR and the λEX1 is less than 75 nm.

[14] The fluorescent nanocomposite structure according to

[12] , wherein the at least one fluorescent agent having λEX1 is a FRET donor for the at least one fluorescent agent having λEX2 which functions as a FRET acceptor.

[15] The fluorescent nanocomposite structure according to

[12] , further comprising at least one fluorescent agent having a third maximum excitation wavelength (λEX3) and a third maximum emission wavelength (λEM3), wherein the fluorescent nanocomposite structure is excited with light of λEX1 and can emit light of λEM3, and the emission intensity of λEM3 is greater than the emission intensity of λEM1 or λEM2.

[16] 1. A method for identifying T cells having a specific T cell receptor, the method comprising: providing a sample containing T cells; contacting the sample containing T cells with a fluorescent nanocomposite structure comprising at least one major histocompatibility complex (MHC) molecule (pMHC) loaded with a peptide, wherein the pMHC is capable of specifically binding to T cells containing a receptor specific for the peptide; spatially separating the T cells; exciting the fluorescent nanocomposite structure with a wavelength of light that induces fluorescence emission; and detecting the T cells labeled with the fluorescent nanocomposite structure.

[17] The fluorescent nanocomposite structure comprises: a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR); at least one spacer coating; at least one fluorescent agent having an excitation wavelength maximum; The method according to

[16] , wherein the fluorescent nanocomposite structure has a fluorescence intensity that is at least 500 times greater than the fluorescence intensity of the at least one fluorescent agent alone.

[18] The method of

[16] above, wherein the T cells are spatially separated using flow cytometry.

Claims

1. A fluorescent nanocomposite structure comprising: a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR); at least one spacer coating; at least one fluorescent agent having a maximum excitation wavelength (λ) conjugated to a surface of said spacer coating; and at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC) conjugated to said spacer coating; the fluorescent nanocomposite structure has a fluorescence intensity that is at least 500 times greater than the fluorescence intensity of the at least one fluorescent agent alone; A fluorescent nanocomposite structure, wherein the plasmonic nanostructures are silver-coated gold nanorods (AuNR@Ag).

2. 10. The fluorescent nanocomposite structure of claim 1, wherein the difference between said at least one λLSPR and said λEX is less than 75 nm.

3. 10. The fluorescent nanocomposite structure of claim 1, wherein the at least one fluorescent agent comprises at least 5, at least 10, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400, or at least 500 fluorescent agent molecules.

4. 2. The fluorescent nanocomposite structure of claim 1, wherein the spacer coating has a thickness of 1 nm to 20 nm.

5. 10. The fluorescent nanocomposite structure of claim 1, further comprising a biotin-binding molecule.

6. 6. The fluorescent nanocomposite structure of claim 5, wherein the at least one biotin-binding molecule comprises at least 2, at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 biotin-binding molecules.

7. The fluorescent nanocomposite structure of claim 5 , wherein the biotin-binding molecule is streptavidin, neutravidin, or avidin.

8. 10. The fluorescent nanocomposite structure of claim 1, wherein the at least one pMHC molecule comprises at least 2, at least 4, at least 8, at least 12, at least 16, at least 20, at least 24, at least 28, at least 32, at least 36, at least 40, or at least 48 pMHC molecules.

9. The fluorescent nanocomposite structure of claim 5 , wherein the at least one pMHC molecule is biotinylated.

10. The fluorescent nanocomposite structure of claim 1 further comprising a scaffold layer overlying said spacer coating.

11. 1. A method for identifying T cells having a specific T cell receptor, the method comprising: providing a sample containing T cells; contacting the sample containing T cells with a fluorescent nanocomposite structure comprising at least one peptide-loaded major histocompatibility complex (MHC) molecule (pMHC) conjugated to a spacer coating, wherein the pMHC is capable of specifically binding to T cells containing a receptor specific for the peptide; spatially separating the T cells; exciting the fluorescent nanocomposite structure with a wavelength of light that induces fluorescence emission; detecting the T cells labeled with the fluorescent nanocomposite structure; The fluorescent nanocomposite structure comprises: a plasmonic nanostructure having at least one localized surface plasmon resonance wavelength (λLSPR); at least one of said spacer coatings; at least one fluorescent agent having a maximum excitation wavelength conjugated to a surface of said spacer coating; the fluorescent nanocomposite structure has a fluorescence intensity that is at least 500 times greater than the fluorescence intensity of the at least one fluorescent agent alone; The method, wherein the plasmonic nanostructures are silver-coated gold nanorods (AuNR@Ag).

12. 12. The method of claim 11, wherein the T cells are spatially separated using flow cytometry.

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