Robust and specific ratiometric biosensing using a copper-free clicked quantum dot-DNA aptamer sensor

In vitro study of a new theranostic smart niosomal nanostructure for direct delivery of docetaxel via anti-PSMA aptamer

In this study, a novel quantum dot (QD)-labeled specific anti-prostate-specific membrane antigen (PSMA) aptamer sequence was conjugated to a pH-responsive niosomal particle platform for delivery of docetaxel (DTX) components. The target cells were overexpressed PSMA. This strategy can minimize the systemic toxicity prevalent in DTX. Synthesis of pH-responsive niosomes was achieved by using thin-film hydration. The conjugation of the aptamer A10 to the niosomal particle was done via a disulfide bond. Furthermore, CdSe/ZnS QDs were fabricated using a hot-injection process, then were functionalized with mercapto propanoic acid (MPA) ligands and attached to the 3' terminal of aptamer via an Amide bind. Moreover, several characterization analyses including dynamic light scattering (DLS), zeta potential, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM), and transmission electron microscope (TEM) were performed. Additionally, 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) and apoptosis assays, as well as fluorescence microscopy, were used to assess the performance of the fabricated system. The data revealed a homogenous round-shaped population of niosomes with an average size of 200 nm and a negative surface charge was synthesized successfully. The FTIR and XRD evaluations confirmed the fabrication of both QDs and niosomes and the bioconjugation processes. The drug release happened in a controlled manner with a pH-sensitivity feature. The cellular uptake of aptamer-conjugated particles enhanced and consequently caused more cytotoxicity of prostate cancer cells with overexpression of PSMA. Furthermore, the QDs provided an ability to trace the treatment and its uptake via the targeted tissue. Overall, this study contributed to the development of a low-risk, highly specific platform for the delivery of both therapeutics and imaging agents.

Polyvalent Glycomimetic-Gold Nanoparticles Revealing Critical Roles of Glycan Display on Multivalent Lectin-Glycan Interaction Biophysics and Antiviral Properties

Multivalent lectin-glycan interactions (MLGIs) are widespread and vital for biology, making them attractive therapeutic targets. Unfortunately, the structural and biophysical mechanisms of several key MLGIs remain poorly understood, limiting our ability to design spatially matched glycoconjugates as potential therapeutics against specific MLGIs. We have recently demonstrated that natural oligomannose-coated nanoparticles are powerful probes for MLGIs. They can provide not only quantitative affinity and binding thermodynamic data but also key structural information (e.g, binding site orientation and mode) useful for designing glycoconjugate therapeutics against specific MLGIs. Despite success, how designing parameters (e.g., glycan type, density, and scaffold size) control their MLGI biophysical and antiviral properties remains to be elucidated. A synthetic pseudodimannose (psDiMan) ligand has been shown to selectively bind to a dendritic cell surface tetrameric lectin, DC-SIGN, over some other multimeric lectins sharing monovalent mannose specificity but having distinct cellular functions. Herein, we display psDiMan polyvalently onto gold nanoparticles (GNPs) of varying sizes (e.g., ∼5 and ∼13 nm, denoted as G5- and G13 psDiMan hereafter) to probe how the scaffold size and glycan display control their MLGI properties with DC-SIGN and the closely related lectin DC-SIGNR. We show that G5/13 psDiMan binds strongly to DC-SIGN, with sub-nM K ds, with affinity being enhanced with increasing scaffold size, whereas they show apparently no or only weak binding to DC-SIGNR. Interestingly, there is a minimal, GNP-size-dependent, glycan density threshold for forming strong binding with DC-SIGN. By combining temperature-dependent affinity and Van't Hoff analyses, we have developed a new GNP fluorescence quenching assay for MLGI thermodynamics, revealing that DC-SIGN-Gx-psDiMan binding is enthalpy-driven, with a standard binding ΔH 0 of ∼ -95 kJ mol-1, which is ∼4-fold that of the monovalent binding and is comparable to that measured by isothermal titration calorimetry. We further reveal that the enhanced DC-SIGN affinity with Gx-psDiMan with increasing GNP scaffold size is due to reduced binding entropy penalty and not due to enhanced favorable binding enthalpy. We further show that DC-SIGN binds tetravalently to a single Gx-psDiMan, irrespective of the GNP size, whereas DC-SIGNR binding is dependent on GNP size, with no apparent binding with G5, and weak cross-linking with G13. Finally, we show that Gx-psDiMans potently inhibit DC-SIGN-dependent augmentation of cellular entry of Ebola pseudoviruses with sub-nM EC50 values, whereas they exhibit no significant (for G5) or weak (for G13) inhibition against DC-SIGNR-augmented viral entry, consistent to their MLGI properties with DC-SIGNR in solution. These results have established Gx-psDiMan as a versatile new tool for probing MLGI affinity, selectivity, and thermodynamics, as well as GNP-glycan antiviral properties.

Probing scaffold size effects on multivalent lectin-glycan binding affinity, thermodynamics and antiviral properties using polyvalent glycan-gold nanoparticles

Multivalent lectin-glycan interactions (MLGIs) are pivotal for viral infections and immune regulation. Their structural and biophysical data are thus highly valuable, not only for understanding their basic mechanisms but also for designing potent glycoconjugate therapeutics against target MLGIs. However, such information for some important MGLIs remains poorly understood, greatly limiting research progress. We have recently developed densely glycosylated nanoparticles, e.g., ∼4 nm quantum dots (QDs) or ∼5 nm gold nanoparticles (GNPs), as mechanistic probes for MLGIs. Using two important model lectin viral receptors, DC-SIGN and DC-SIGNR, we have shown that these probes can not only offer sensitive fluorescence assays for quantifying MLGI affinities, but also reveal key structural information (e.g., binding site orientation and binding mode) useful for MLGI targeting. However, the small sizes of the previous scaffolds may not be optimal for maximising MLGI affinity and targeting specificity. Herein, using α-manno-α-1,2-biose (DiMan) functionalised GNP (GNP-DiMan) probes, we have systematically studied how GNP scaffold size (e.g., 5, 13, and 27 nm) and glycan density (e.g., 100, 75, 50 and 25%) determine their MLGI affinities, thermodynamics, and antiviral properties. We have developed a new GNP fluorescence quenching assay format to minimise the possible interference of GNP's strong inner filter effect in MLGI affinity quantification, revealing that increasing the GNP size is highly beneficial for enhancing MLGI affinity. We have further determined the MLGI thermodynamics by combining temperature-dependent affinity and Van't Hoff analyses, revealing that GNP-DiMan-DC-SIGN/R binding is enthalpy driven with favourable binding Gibbs free energy changes (ΔG°) being enhanced with increasing GNP size. Finally, we show that increasing the GNP size significantly enhances their antiviral potency. Notably, the DiMan coated 27 nm GNP potently and robustly blocks both DC-SIGN and DC-SIGNR mediated pseudo-Ebola virus cellular entry with an EC50 of ∼23 and ∼49 pM, respectively, making it the most potent glycoconjugate inhibitor against DC-SIGN/R-mediated Ebola cellular infections. Our results have established GNP-glycans as a new tool for quantifying MLGI biophysical parameters and revealed that increasing the GNP scaffold size significantly enhances their MLGI affinities and antiviral potencies.

Micellular fluorescence resonance energy transfer based fluorescent ratiometric response to hydrocarbon analytes

Fluorescence resonance energy transfer (FRET) has been utilised to develop numerous selective and sensitive fluorescent ratiometric sensors. Typically, FRET-based fluorescent ratiometric sensors rely on chemical interactions between the sensor and analyte to illicit a response, thus unreactive hydrocarbons are a neglected analyte and a source for new sensors. By containing an unbound donor-acceptor system within micelles, energy transfer is enabled by spatial confinement. This offers the potential of a ratiometric response as a hydrocarbon analyte is added. Introducing a hydrocarbon analyte to this system causes micelles to swell, increasing the donor-acceptor distance and thus reducing the amount of observed energy transfer. We present InP/ZnS quantum dot donors interacting with a Nile Red acceptor, confined by cetyltrimethylammonium bromide (CTAB)-based micelles. We alleviated spatial confinement of the pair within micelles using common laboratory solvents to represent hydrocarbons, (toluene, hexane and octadecene). We constructed calibration curves for each solvent and found effective sensing ranges of 0.009-0.21, 0.008-0.27 and 0.003-0.06 M for toluene, hexane and octadecene, respectively. This study contributes towards the development of new hydrocarbon sensors utilising this new mechanism.

Glycan-Gold Nanoparticles as Multifunctional Probes for Multivalent Lectin-Carbohydrate Binding: Implications for Blocking Virus Infection and Nanoparticle Assembly

Multivalent lectin-glycan interactions are widespread in biology and are often exploited by pathogens to bind and infect host cells. Glycoconjugates can block such interactions and thereby prevent infection. The inhibition potency strongly depends on matching the spatial arrangement between the multivalent binding partners. However, the structural details of some key lectins remain unknown and different lectins may exhibit overlapping glycan specificity. This makes it difficult to design a glycoconjugate that can potently and specifically target a particular multimeric lectin for therapeutic interventions, especially under the challenging in vivo conditions. Conventional techniques such as surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) can provide quantitative binding thermodynamics and kinetics. However, they cannot reveal key structural information, e.g., lectin's binding site orientation, binding mode, and interbinding site spacing, which are critical to design specific multivalent inhibitors. Herein we report that gold nanoparticles (GNPs) displaying a dense layer of simple glycans are powerful mechanistic probes for multivalent lectin-glycan interactions. They can not only quantify the GNP-glycan-lectin binding affinities via a new fluorescence quenching method, but also reveal drastically different affinity enhancing mechanisms between two closely related tetrameric lectins, DC-SIGN (simultaneous binding to one GNP) and DC-SIGNR (intercross-linking with multiple GNPs), via a combined hydrodynamic size and electron microscopy analysis. Moreover, a new term, potential of assembly formation (PAF), has been proposed to successfully predict the assembly outcomes based on the binding mode between GNP-glycans and lectins. Finally, the GNP-glycans can potently and completely inhibit DC-SIGN-mediated augmentation of Ebola virus glycoprotein-driven cell entry (with IC₅₀ values down to 95 pM), but only partially block DC-SIGNR-mediated virus infection. Our results suggest that the ability of a glycoconjugate to simultaneously block all binding sites of a target lectin is key to robust inhibition of viral infection.

Highly sensitive detection of carcinoembryonic antigen using copper-free click chemistry on the surface of azide cofunctionalized graphene oxide

In this study, we reported a highly sensitive method for detecting carcinoembryonic antigen (CEA) based on an azide cofunctionalized graphene oxide (GO-N₃) and carbon dot (CDs) biosensor system. Carbon dots-labeled DNA (CDs-DNA) combined with GO-N₃ using copper-free click chemistry (CFCC), which quenched the fluorescence of the CDs via fluorescence resonance energy transfer (FRET). Upon the addition of CEA, fluorescence was recovered due to the combination of CEA and aptamer. Under optimal conditions, the relative fluorescence intensity was linear with CEA concentration in the range of 0.01-1 ng/mL (R² = 0.9788), and the limit of detection (LOD) was 7.32 pg/mL (S/N = 3). This biosensor had a high sensitivity and good selectivity for CEA detection in serum samples, indicating that the novel sensor platform holds a great potential for CEA and other biomarkers in practical applications.

Photon induced quantum yield regeneration of cap-exchanged CdSe/CdS quantum rods for ratiometric biosensing and cellular imaging

Full water-dispersion of commercial hydrophobic CdSe/CdS core/shell quantum rods (QRs) was achieved by cap-exchange using a dihydrolipoic acid zwitterion ligand at a low ligand:QR molar ratio (LQMR) of 1000. However, this process almost completely quenched the QR fluorescence, greatly limiting its potential in downstream fluorescence based applications. Fortunately, we found that the QR fluorescence could be recovered by exposure to near ultra-violet to blue light radiation (e.g. 300-450 nm). These "reborn" QRs were found to be compact, bright, and stable, and were resistant to non-specific adsorption, which make them powerful fluorescent probes in broad biomedical applications. We demonstrated their potential in two model applications: first, the QRs were conjugated with His₈-tagged small antibody mimetic proteins (also known as Affimers) for the sensitive detection of target proteins via a Förster resonance energy transfer (FRET) readout strategy and second, the QR surface was functionalized with biotins for targeted imaging of cancer cells.

A simple magnetic nanoparticle-poly-enzyme nanobead sandwich assay for direct, ultrasensitive DNA detection

A simple magnetic nanoparticle (MNP)-poly-enzyme nanobead sandwich assay for direct detection of ultralow levels of unlabeled target-DNA is developed. This approach uses a capture-DNA covalently linked to a dense PEGylated polymer encapsulated MNP and a biotinylated signal-DNA to sandwich the target-DNA. A DNA ligation is then followed to offer high discrimination between the perfect-match and single-base mismatch target-DNAs. Only the presence of a perfect-match target can covalently link the biotinylated signal-DNA onto the MNP surface for subsequent binding to a polymer nanobead tagged with thousands of copies of high-activity neutravidin-horseradish peroxidase (NAV-HRP) for great enzymatic signal amplification. Combining the advantages of the dense MNP surface PEGylation to reduce non-specific adsorption (assay background) and the powerful signal amplification of poly-enzyme nanobead, this assay can directly quantify the target-DNA down to single digit attomolar with a large linear dynamic range of 5 orders of magnitude (from 10^-18 to 10^-13M).

A versatile and accessible polymer coating for functionalizable zwitterionic quantum dots with high DNA grafting efficiency

Efficient and versatile functionalization of poly(anhydride maleic-alt-isobutylene) (PIMA), with economical commercial reagents, results in the one-step/one-day production of a copper-free click chemistry-ready carboxybetaine-like coating for quantum dots (QDs). The QDs are bright and stable in aqueous media and easily grafted with DNA with >95% efficiency.

Quantum dots in biomedical applications

Semiconducting nanoparticles, more commonly known as quantum dots, possess unique size and shape dependent optoelectronic properties. In recent years, these unique properties have attracted much attention in the biomedical field to enable real-time tissue imaging (bioimaging), diagnostics, single molecule probes, and drug delivery, among many other areas. The optical properties of quantum dots can be tuned by size and composition, and their high brightness, resistance to photobleaching, multiplexing capacity, and high surface-to-volume ratio make them excellent candidates for intracellular tracking, diagnostics, in vivo imaging, and therapeutic delivery. We discuss recent advances and challenges in the molecular design of quantum dots are discussed, along with applications of quantum dots as drug delivery vehicles, theranostic agents, single molecule probes, and real-time in vivo deep tissue imaging agents. We present a detailed discussion of the biodistribution and toxicity of quantum dots, and highlight recent advances to improve long-term stability in biological buffers, increase quantum yield following bioconjugation, and improve clearance from the body. Last, we present an outlook on future challenges and strategies to further advance translation to clinical application. STATEMENT OF SIGNIFICANCE: Semiconducting nanoparticles, commonly known as quantum dots, possess unique size and shape dependent electrical and optical properties. In recent years, they have attracted much attention in biomedical imaging to enable diagnostics, single molecule probes, and real-time imaging of tumors. This review discusses recent advances and challenges in the design of quantum dots, and highlights how these strategies can further advance translation to clinical applications.

Sensing with photoluminescent semiconductor quantum dots

Fluorescent sensors benefit from high signal-to-noise and multiple measurement modalities, enabling a multitude of applications and flexibility of design. Semiconductor nanocrystal quantum dots (QDs) are excellent fluorophores for sensors because of their extraordinary optical properties. They have high thermal and photochemical stability compared to organic dyes or fluorescent proteins and are extremely bright due to their large molar cross-sections. In contrast to organic dyes, QD emission profiles are symmetric, with relatively narrow bandwidths. In addition, the size tunability of their emission color, which is a result of quantum confinement, make QDs exceptional emitters with high color purity from the ultra-violet to near infrared wavelength range. The role of QDs in sensors ranges from simple fluorescent tags, as used in immunoassays, to intrinsic sensors that utilize the inherent photophysical response of QDs to fluctuations in temperature, electric field, or ion concentration. In more complex configurations, QDs and biomolecular recognition moieties like antibodies are combined with a third component to modulate the optical signal via energy transfer. QDs can act as donors, acceptors, or both in energy transfer-based sensors using Förster resonance energy transfer (FRET), nanometal surface energy transfer (NSET), or charge or electron transfer. The changes in both spectral response and photoluminescent lifetimes have been successfully harnessed to produce sensitive sensors and multiplexed devices. While technical challenges related to biofunctionalization and the high cost of laboratory-grade fluorimeters have thus far prevented broad implementation of QD-based sensing in clinical or commercial settings, improvements in bioconjugation methods and detection schemes, including using simple consumer devices like cell phone cameras, are lowering the barrier to broad use of more sensitive QD-based devices.

The Current Status and Future Outlook of Quantum Dot-Based Biosensors for Plant Virus Detection

Enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR), widely used for the detection of plant viruses, are not easily performed, resulting in a demand for an innovative and more efficient diagnostic method. This paper summarizes the characteristics and research trends of biosensors focusing on the physicochemical properties of both interface elements and bioconjugates. In particular, the topological and photophysical properties of quantum dots (QDs) are discussed, along with QD-based biosensors and their practical applications. The QD-based Fluorescence Resonance Energy Transfer (FRET) genosensor, most widely used in the biomolecule detection fields, and QD-based nanosensor for Rev-RRE interaction assay are presented as examples. In recent years, QD-based biosensors have emerged as a new class of sensor and are expected to open opportunities in plant virus detection, but as yet there have been very few practical applications (Table 3). In this article, the details of those cases and their significance for the future of plant virus detection will be discussed.

Inorganic Nanoparticles as Donors in Resonance Energy Transfer for Solid-Phase Bioassays and Biosensors

Bioassays for the rapid detection and quantification of specific nucleic acids, proteins, and peptides are fundamental tools in many clinical settings. Traditional optical emission methods have focused on the use of molecular dyes as labels to track selective binding interactions and as probes that are sensitive to environmental changes. Such dyes can offer good detection limits based on brightness but typically have broad emission bands and suffer from time-dependent photobleaching. Inorganic nanoparticles such as quantum dots and upconversion nanoparticles are photostable over prolonged exposure to excitation radiation and tend to offer narrow emission bands, providing a greater opportunity for multiwavelength multiplexing. Importantly, in contrast to molecular dyes, nanoparticles offer substantial surface area and can serve as platforms to carry a large number of conjugated molecules. The surface chemistry of inorganic nanoparticles offers both challenges and opportunities for the control of solubility and functionality for selective molecular interactions by the assembly of coatings through coordination chemistry. This report reviews advances in the compositional design and methods of conjugation of inorganic quantum dots and upconversion nanoparticles and the assembly of combinations of nanoparticles to achieve energy exchange. Our interest is the exploration of configurations where the modified nanoparticles can be immobilized to solid substrates for the development of bioassays and biosensors that operate by resonance energy transfer (RET).

Dissecting Multivalent Lectin-Carbohydrate Recognition Using Polyvalent Multifunctional Glycan-Quantum Dots

Multivalent protein-carbohydrate interactions initiate the first contacts between virus/bacteria and target cells, which ultimately lead to infection. Understanding the structures and binding modes involved is vital to the design of specific, potent multivalent inhibitors. However, the lack of structural information on such flexible, complex, and multimeric cell surface membrane proteins has often hampered such endeavors. Herein, we report that quantum dots (QDs) displayed with a dense array of mono-/disaccharides are powerful probes for multivalent protein-glycan interactions. Using a pair of closely related tetrameric lectins, DC-SIGN and DC-SIGNR, which bind to the HIV and Ebola virus glycoproteins (EBOV-GP) to augment viral entry and infect target cells, we show that such QDs efficiently dissect the different DC-SIGN/R-glycan binding modes (tetra-/di-/monovalent) through a combination of multimodal readouts: Förster resonance energy transfer (FRET), hydrodynamic size measurement, and transmission electron microscopy imaging. We also report a new QD-FRET method for quantifying QD-DC-SIGN/R binding affinity, revealing that DC-SIGN binds to the QD >100-fold tighter than does DC-SIGNR. This result is consistent with DC-SIGN's higher trans-infection efficiency of some HIV strains over DC-SIGNR. Finally, we show that the QDs potently inhibit DC-SIGN-mediated enhancement of EBOV-GP-driven transduction of target cells with IC50 values down to 0.7 nM, matching well to their DC-SIGN binding constant (apparent Kd = 0.6 nM) measured by FRET. These results suggest that the glycan-QDs are powerful multifunctional probes for dissecting multivalent protein-ligand recognition and predicting glyconanoparticle inhibition of virus infection at the cellular level.

Ratiometric fluorescent pH nanoprobes based on in situ assembling of fluorescence resonance energy transfer between fluorescent proteins

pH-dependent protein adsorption on mesoporous silica nanoparticle (MSN) was examined as a unique means for pH monitoring. Assuming that the degree of protein adsorption determines the distance separating protein molecules, we examined the feasibility of nanoscale pH probes based on fluorescence resonance energy transfer (FRET) between two fluorescent proteins (mTurquoise2 and mNeonGreen, as donor and acceptor, respectively). Since protein adsorption on MSN is pH-sensitive, both fluorescent proteins were modified to make their isoelectric points (pIs) identical, thus achieving comparable adsorption between the proteins and enhancing FRET signals. The adsorption behaviors of such modified fluorescent proteins were examined along with ratiometric FRET signal generation. Results demonstrated that the pH probes could be manipulated to show feasible sensitivity and selectivity for pH changes in hosting solutions, with a good linearity observed in the pH range of 5.5-8.0. In a demonstration test, the pH probes were successfully applied to monitor progress of enzymatic reactions. Such an "in situ-assembling" pH sensor demonstrates a promising strategy in developing nanoscale fluorescent protein probes. Graphical abstract Working principle of the developed pH sensor TNS; and FRET Ratio (I₅₂₈/I₄₆₀) as a function of pH under different protein feed ratios (mNeonGreen to mTurquoise2).

Ultraefficient Cap-Exchange Protocol To Compact Biofunctional Quantum Dots for Sensitive Ratiometric Biosensing and Cell Imaging

An ultraefficient cap-exchange protocol (UCEP) that can convert hydrophobic quantum dots (QDs) into stable, biocompatible, and aggregation-free water-dispersed ones at a ligand:QD molar ratio (LQMR) as low as 500, some 20-200-fold less than most literature methods, has been developed. The UCEP works conveniently with air-stable lipoic acid (LA)-based ligands by exploiting tris(2-carboxylethyl phosphine)-based rapid in situ reduction. The resulting QDs are compact (hydrodynamic radius, R_h, < 4.5 nm) and bright (retaining > 90% of original fluorescence), resist nonspecific adsorption of proteins, and display good stability in biological buffers even with high salt content (e.g., 2 M NaCl). These advantageous properties make them well suited for cellular imaging and ratiometric biosensing applications. The QDs prepared by UCEP using dihydrolipoic acid (DHLA)-zwitterion ligand can be readily conjugated with octa-histidine (His₈)-tagged antibody mimetic proteins (known as Affimers). These QDs allow rapid, ratiometric detection of the Affimer target protein down to 10 pM via a QD-sensitized Förster resonance energy transfer (FRET) readout signal. Moreover, compact biotinylated QDs can be readily prepared by UCEP in a facile, one-step process. The resulting QDs have been further employed for ratiometric detection of protein, exemplified by neutravidin, down to 5 pM, as well as for fluorescence imaging of target cancer cells.

Förster resonance energy transfer and excited state life time reduction of rhodamine 6G with NiO nanorods in PVP films

In the present study, we report the preparation of NiO nanorods (NNR) and its Förster resonant energy transfer (FRET) behaviour with rhodamine 6G (R6G) in a Polyvinyl pyrrolidone (PVP) polymer matrix. The prepared nanocomposite polymer (NCP) films contain PVP and R6G whose concentrations are kept constant and different concentrations of NNR. Spectral overlap between the absorption and fluorescence spectrum of R6G and NNR shows the possibility of FRET phenomena to be occurring in the prepared NCP films. Steady state and time resolved fluorescence measurements are carried out at two excitation wavelengths (330 and 510nm) to study the energy transfer process between R6G and NNR in the PVP host. The obtained results show that the energy transfer is from R6G (serves as a donor) to NNR (functions as an acceptor). Calculated radiative efficiencies, donor-acceptor distances and average lifetime also confirm the energy transfer from R6G to NNR.

Multifunctional Polymer Ligand Interface CdZnSeS/ZnS Quantum Dot/Cy3-Labeled Protein Pairs as Sensitive FRET Sensors

High-quality CdZnSeS/ZnS alloyed core/thick-shell quantum dots (QDs) as energy donors were first exploited in Förster resonance energy transfer (FRET) applications. A highly efficient ligand-exchange method was used to prepare low toxicity, high quantum yield, stabile, and biocompatible CdZnSeS/ZnS QDs densely capped with multifunctional polymer ligands containing dihydrolipoic acid (DHLA). The resulting QDs can be applied to construct QDs-based Förster resonance energy transfer (FRET) systems by their high affinity interaction with dye cyanine 3 (Cy3)-labeled human serum albumin (HSA). This QD-based FRET protein complex can serve as a sensitive sensor for probing the interaction of clofazimine with proteins using fluorescence spectroscopic techniques. The ability of FRET imaging both in vitro and in vivo not only reveals that the current FRET system can remain intact for 2 h but also confirms the potential of the FRET system to act as a nanocarrier for intracellular protein delivery or to serve as an imaging probe for cancer diagnosis.

Quantum dots-DNA bioconjugates: synthesis to applications

Semiconductor nanoparticles particularly quantum dots (QDs) are interesting alternatives to organic fluorophores for a range of applications such as biosensing, imaging and therapeutics. Addition of a programmable scaffold such as DNA to QDs further expands the scope and applicability of these hybrid nanomaterials in biology. In this review, the most important stages of preparation of QD-DNA conjugates for specific applications in biology are discussed. Special emphasis is laid on (i) the most successful strategies to disperse QDs in aqueous media, (ii) the range of different conjugation with detailed discussion about specific merits and demerits in each case, and (iii) typical applications of these conjugates in the context of biology.

Ratiometric fluorescence, electrochemiluminescence, and photoelectrochemical chemo/biosensing based on semiconductor quantum dots

Ratiometric fluorescent sensors, which can provide built-in self-calibration for correction of a variety of analyte-independent factors, have attracted particular attention for analytical sensing and optical imaging with the potential to provide a precise and quantitative analysis. A wide variety of ratiometric sensing probes using small fluorescent molecules have been developed. Compared with organic dyes, exploiting semiconductor quantum dots (QDs) in ratiometric fluorescence sensing is even more intriguing, owing to their unique optical and photophysical properties that offer significant advantages over organic dyes. In this review, the main photophysical mechanism for generating dual-emission from QDs for ratiometry is discussed and categorized in detail. Typically, dual-emission can be obtained either with energy transfer from QDs to dyes or with independent dual fluorophores of QDs and dye/QDs. The recent discovery of intrinsic dual-emission from Mn-doped QDs offers new opportunities for ratiometric sensing. Particularly, the signal transduction of QDs is not restricted to fluorescence, and electrochemiluminescence and photoelectrochemistry from QDs are also promising for sensing, which can be made ratiometric for correction of interferences typically encountered in electrochemistry. All these unique photophysical properties of QDs lead to a new avenue of ratiometry, and the recent progress in this area is addressed and summarized here. Several interesting applications of QD-based ratiometry are presented for the determination of metal ions, temperature, and biomolecules, with specific emphasis on the design principles and photophysical mechanisms of these probes.

Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein-Ligand Interactions

A highly efficient cap-exchange approach for preparing compact, dense polyvalent mannose-capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein-ligand interactions.

Compact, Polyvalent Mannose Quantum Dots as Sensitive, Ratiometric FRET Probes for Multivalent Protein-Ligand Interactions

A highly efficient cap-exchange approach for preparing compact, dense polyvalent mannose-capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC-SIGN and DC-SIGNR (collectively termed as DC-SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC-SIGN, but not its closely related receptor DC-SIGNR, which is further confirmed by its specific blocking of DC-SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC-SIGN binds more efficiently to densely packed mannosides. A FRET-based thermodynamic study reveals that the binding is enthalpy-driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein-ligand interactions.

Fast, Ratiometric FRET from Quantum Dot Conjugated Stabilized Single Chain Variable Fragments for Quantitative Botulinum Neurotoxin Sensing

Botulinum neurotoxin (BoNT) presents a significant hazard under numerous realistic scenarios. The standard detection scheme for this fast-acting toxin is a lab-based mouse lethality assay that is sensitive and specific, but slow (∼2 days) and requires expert administration. As such, numerous efforts have aimed to decrease analysis time and reduce complexity. Here, we describe a sensitive ratiometric fluorescence resonance energy transfer scheme that utilizes highly photostable semiconductor quantum dot (QD) energy donors and chromophore conjugation to compact, single chain variable antibody fragments (scFvs) to yield a fast, fieldable sensor for BoNT with a 20-40 pM detection limit, toxin quantification, adjustable dynamic range, sensitivity in the presence of interferents, and sensing times as fast as 5 min. Through a combination of mutations, we achieve stabilized scFv denaturation temperatures of more than 60 °C, which bolsters fieldability. We also describe adaptation of the assay into a microarray format that offers persistent monitoring, reuse, and multiplexing.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.

Thioflavin T as an Efficient G-Quadruplex Inducer for the Highly Sensitive Detection of Thrombin Using a New Föster Resonance Energy Transfer System

We report a new Föster resonance energy transfer (FRET) system that uses a special dye, thioflavin T (ThT), as an energy acceptor and a water-soluble conjugated polymer (CP) with high fluorescence as an energy donor. A simple, label-free, and sensitive strategy for the detection of thrombin in buffer and in diluted serum was designed based on this new system using ThT as an efficient inducer of the G-quadruplex. The difference between the blank and the positive samples was amplified due to distinctive FRET signals because thrombin has little effect on the intercalation of ThT into the G-quadruplex. In the absence of the target, ThT induces the aptamer to form a G-quadruplex and intercalates into it with strong fluorescence. The electrostatic attractions between the negatively charged G-quadruplex and positively charged CP allow a short donor-acceptor distance, resulting in a high FRET signal. However, in the presence of the target, the aptamer forms a G-quadruplex-thrombin complex first, followed by the intercalation of ThT into the G-quadruplex. A long distance exists between the donor and acceptor due to the strong steric hindrance from the large-sized thrombin, which leads to a low FRET signal. Compared with previously reported strategies based on the FRET between the CP and dye, our strategy is label-free, and the sensitivity was improved by an order of magnitude. Our strategy also shows the advantages of being simple, rapid (about 50 min), sensitive, label-free, and low-cost in comparison to strategies based on the FRET between quantum dots and dyes.

DNA-regulated silver nanoclusters for label-free ratiometric fluorescence detection of DNA

Two kinds of DNA-regulated Ag nanoclusters were one-pot synthesized on an oligonucleotide, and delicately utilized in the design of a label-free ratiometric fluorescence strategy for DNA detection with simplicity and high sensitivity.

QD-Based FRET Probes at a Glance

The unique optoelectronic properties of quantum dots (QDs) give them significant advantages over traditional organic dyes, not only as fluorescent labels for bioimaging, but also as emissive sensing probes. QD sensors that function via manipulation of fluorescent resonance energy transfer (FRET) are of special interest due to the multiple response mechanisms that may be utilized, which in turn imparts enhanced flexibility in their design. They may also function as ratiometric, or "color-changing" probes. In this review, we describe the fundamentals of FRET and provide examples of QD-FRET sensors as grouped by their response mechanisms such as link cleavage and structural rearrangement. An overview of early works, recent advances, and various models of QD-FRET sensors for the measurement of pH and oxygen, as well as the presence of metal ions and proteins such as enzymes, are also provided.

Recent progress in quantum dot based sensors

Recent progress in quantum dot (QD) based chemo- and biosensors for various applications is summarized.

Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients

We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L(-1)). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.

Recent developments in antibody-based assays for the detection of bacterial toxins

Considering the urgent demand for rapid and accurate determination of bacterial toxins and the recent promising developments in nanotechnology and microfluidics, this review summarizes new achievements of the past five years. Firstly, bacterial toxins will be categorized according to their antibody binding properties into low and high molecular weight compounds. Secondly, the types of antibodies and new techniques for producing antibodies are discussed, including poly- and mono-clonal antibodies, single-chain variable fragments (scFv), as well as heavy-chain and recombinant antibodies. Thirdly, the use of different nanomaterials, such as gold nanoparticles (AuNPs), magnetic nanoparticles (MNPs), quantum dots (QDs) and carbon nanomaterials (graphene and carbon nanotube), for labeling antibodies and toxins or for readout techniques will be summarized. Fourthly, microscale analysis or minimized devices, for example microfluidics or lab-on-a-chip (LOC), which have attracted increasing attention in combination with immunoassays for the robust detection or point-of-care testing (POCT), will be reviewed. Finally, some new materials and analytical strategies, which might be promising for analyzing toxins in the near future, will be shortly introduced.