Optimizing protein coordination to quantum dots with designer peptidyl linkers

Tetrameric Antibody Complexes and Affinity Tag Peptides for the Selective Immobilization and Imaging of Single Quantum Dots

Colloidal semiconductor quantum dots (QDs) are of widespread interest as fluorescent labels for bioanalysis and imaging applications. Single-particle measurements have proven to be a very powerful tool for better understanding the fundamental properties and behaviors of QDs and their bioconjugates; however, a recurring challenge is the immobilization of QDs in a solution-like environment that minimizes interactions with a bulk surface. Immobilization strategies for QD-peptide conjugates are particularly underdeveloped within this context. Here, we present a novel strategy for the selective immobilization of single QD-peptide conjugates using a combination of tetrameric antibody complexes (TACs) and affinity tag peptides. A glass substrate is modified with an adsorbed layer of concanavalin A (ConA) that binds a subsequent layer of dextran that minimizes nonspecific binding. A TAC with anti-dextran and anti-affinity tag antibodies binds to the dextran-coated glass surface and to the affinity tag sequence of QD-peptide conjugates. The result is spontaneous and sequence-selective immobilization of single QDs without any chemical activation or cross-linking. Controlled immobilization of multiple colors of QDs is possible using multiple affinity tag sequences. Experiments confirmed that this approach positions the QD away from the bulk surface. The method supports real-time imaging of binding and dissociation, measurements of Förster resonance energy transfer (FRET), tracking of dye photobleaching, and detection of proteolytic activity. We anticipate that this immobilization strategy will be useful for studies of QD-associated photophysics, biomolecular interactions and processes, and digital assays.

A Nanobody‐on‐Quantum Dot Displacement Assay for Rapid and Sensitive Quantification of the Epidermal Growth Factor Receptor (EGFR)

Biosensing approaches that combine small, engineered antibodies (nanobodies) with nanoparticles are often complicated. Here, we show that nanobodies with different C‐terminal tags can be efficiently attached to a range of the most widely used biocompatible semiconductor quantum dots (QDs). Direct implementation into simplified assay formats was demonstrated by designing a rapid and wash‐free mix‐and‐measure immunoassay for the epidermal growth factor receptor (EGFR). Terbium complex (Tb)‐labeled hexahistidine‐tagged nanobodies were specifically displaced from QD surfaces via EGFR‐nanobody binding, leading to an EGFR concentration‐dependent decrease of the Tb‐to‐QD Förster resonance energy transfer (FRET) signal. The detection limit of 80±20 pM (16±4 ng mL⁻¹) was 3‐fold lower than the clinical cut‐off concentration for soluble EGFR and up to 10‐fold lower compared to conventional sandwich FRET assays that required a pair of different nanobodies.

Preparation and Characterization of Quantum Dot-Peptide Conjugates Based on Polyhistidine Tags

Quantum dots (QDs) offer bright and robust photoluminescence among several other advantages in comparison to fluorescent dyes. In order to leverage the advantageous properties of QDs for applications in bioanalysis and imaging, simple and reliable methods for bioconjugation are required. One such method for conjugating peptides to QDs is the use of polyhistidine tags, which spontaneously bind to the surface of QDs. We describe protocols for assembling polyhistidine-tagged peptides to QDs and for characterizing the resultant QD-peptide conjugates. The latter include both electrophoretic and FRET-based protocols for confirming successful peptide assembly, estimating the maximum peptide loading capacity, and measuring the assembly kinetics. Sensors for protease activity and intracellular delivery are briefly noted as prospective applications of QD-peptide conjugates.

The symmetric designer protein Pizza as a scaffold for metal coordination

Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.

Phase Transfer and DNA Functionalization of Quantum Dots Using an Easy-to-Prepare, Low-Cost Zwitterionic Polymer

Small, stable, and bright quantum dots (QDs) are of interest in many biosensing and biomedical imaging applications, but current methodologies for obtaining these characteristics can be highly specialized or expensive. We describe a straightforward, low-cost protocol for functionalizing poly(isobutylene-alt-maleic anhydride) (PIMA) with moieties that anchor to the QD surface (histamine), impart hydrophilicity [(2-aminoethyl)trimethylammonium chloride (Me₃N⁺-NH₂)], and provide a platform for biofunctionalization via click chemistry (dibenzocyclooctyne (DBCO)). Guidelines to successfully use this polymer for QD ligand exchange are presented, and an example of biofunctionalization with DNA is shown. Stable QD-DNA conjugates are obtained with high yield and without requiring additional purification steps.

Picomolar Biosensing and Conformational Analysis Using Artificial Bidomain Proteins and Terbium-to-Quantum Dot Förster Resonance Energy Transfer

Although antibodies remain a primary recognition element in all forms of biosensing, functional limitations arising from their size, stability, and structure have motivated the development and production of many different artificial scaffold proteins for biological recognition. However, implementing such artificial binders into functional high-performance biosensors remains a challenging task. Here, we present the design and application of Förster resonance energy transfer (FRET) nanoprobes comprising small artificial proteins (αRep bidomains) labeled with a Tb complex (Tb) donor on the C-terminus and a semiconductor quantum dot (QD) acceptor on the N-terminus. Specific binding of one or two protein targets to the αReps induced a conformational change that could be detected by time-resolved Tb-to-QD FRET. These single-probe FRET switches were used in a separation-free solution-phase assay to quantify different protein targets at sub-nanomolar concentrations and to measure the conformational changes with sub-nanometer resolution. Probing ligand-receptor binding under physiological conditions at very low concentrations in solution is a special feature of FRET that can be efficiently combined with other structural characterization methods to develop, understand, and optimize artificial biosensors. Our results suggest that the αRep FRET nanoprobes have a strong potential for their application in advanced diagnostics and intracellular live-cell imaging of ligand-receptor interactions.

Quantum Dot Lipase Biosensor Utilizing a Custom-Synthesized Peptidyl-Ester Substrate

Lipases are an important class of lipid hydrolyzing enzymes that play significant roles in many aspects of cell biology and digestion; they also have large roles in commercial food and biofuel preparation and are being targeted for pharmaceutical development. Given these, and many other biotechnological roles, sensitive and specific biosensors capable of monitoring lipase activity in a quantitative manner are critical. Here, we describe a Förster resonance energy transfer (FRET)-based biosensor that originates from a custom-synthesized ester substrate displaying a peptide at one end and a dye acceptor at the other. These substrates were ratiometrically self-assembled to luminescent semiconductor quantum dot (QD) donors by metal affinity coordination using the appended peptide's terminal hexahistidine motif to give rise to the full biosensing construct. This resulted in a high rate of FRET between the QD donor and the proximal substrate's dye acceptor. The lipase hydrolyzed the intervening target ester bond in the peptide substrate which, in turn, displaced the dye acceptor containing component and altered the rate of FRET in a concentration-dependent manner. Specifics of the substrate's stepwise synthesis are described along with the sensors assembly, characterization, and application in a quantitative proof-of-concept demonstration assay that is based on an integrated Michaelis-Menten kinetic approach. The utility of this unique nanoparticle-based architecture within a sensor configuration is then discussed.

Quantum Dots and Gold Nanoparticles as Scaffolds for Enzymatic Enhancement: Recent Advances and the Influence of Nanoparticle Size

Nanoparticle scaffolds can impart multiple benefits onto immobilized enzymes including enhanced stability, activity, and recoverability. The magnitude of these benefits is modulated by features inherent to the scaffold–enzyme conjugate, amongst which the size of the nanoscaffold itself can be critically important. In this review, we highlight the benefits of enzyme immobilization on nanoparticles and the factors affecting these benefits using quantum dots and gold nanoparticles as representative materials due to their maturity. We then review recent literature on the use of these scaffolds for enzyme immobilization and as a means to dissect the underlying mechanisms. Detailed analysis of the literature suggests that there is a “sweet-spot” for scaffold size and the ratio of immobilized enzyme to scaffold, with smaller scaffolds and lower enzyme:scaffold ratios generally providing higher enzymatic activities. We anticipate that ongoing studies of enzyme immobilization onto nanoscale scaffolds will continue to sharpen our understanding of what gives rise to beneficial characteristics and allow for the next important step, namely, that of translation to large-scale processes that exploit these properties.

Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Förster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Quantum Dot-Based FRET Immunoassay for HER2 Using Ultrasmall Affinity Proteins

Engineered scaffold affinity proteins are used in many biological applications with the aim of replacing natural antibodies. Although their very small sizes are beneficial for multivalent nanoparticle conjugation and efficient Förster resonance energy transfer (FRET), the application of engineered affinity proteins in such nanobiosensing formats has been largely neglected. Here, it is shown that very small (≈6.5 kDa) histidine-tagged albumin-binding domain-derived affinity proteins (ADAPTs) can efficiently self-assemble to zwitterionic ligand-coated quantum dots (QDs). These ADAPT-QD conjugates are significantly smaller than QD-conjugates based on IgG, Fab', or single-domain antibodies. Immediate applicability by the quantification of the human epidermal growth factor receptor 2 (HER2) in serum-containing samples using time-gated Tb-to-QD FRET detection on the clinical benchtop immunoassay analyzer KRYPTOR is demonstrated here. Limits of detection down to 40 × 10^-12 m (≈8 ng mL^-1 ) are in a relevant clinical concentration range and outperform previously tested assays with antibodies, antibody fragments, and nanobodies.

Pursuing the Promise of Enzymatic Enhancement with Nanoparticle Assemblies

The growing emphasis on green chemistry, renewable resources, synthetic biology, regio-/stereospecific chemical transformations, and nanotechnology for providing new biological products and therapeutics is reinvigorating research into enzymatic catalysis. Although the promise is profound, many complex issues remain to be addressed before this effort will have a significant impact. Prime among these is to combat the degradation of enzymes frequently seen in ex vivo formats following immobilization to stabilize the enzymes for long-term application and to find ways of enhancing their activity. One promising avenue for progress on these issues is via nanoparticle (NP) display, which has been found in a number of cases to enhance enzyme activity while also improving long-term stability. In this feature article, we discuss the phenomenon of enhanced enzymatic activity at NP interfaces with an emphasis on our own work in this area. Important factors such as NP surface chemistry, bioconjugation approaches, and assay formats are first discussed because they can critically affect the observed enhancement. Examples are given of improved performance for enzymes such as phosphotriesterase, alkaline phosphatase, trypsin, horseradish peroxidase, and β-galactosidase and in configurations with either the enzyme or the substrate attached to the NP. The putative mechanisms that give rise to the performance boost are discussed along with how detailed kinetic modeling can contribute to their understanding. Given the importance of biosensing, we also highlight how this configuration is already making a significant contribution to NP-based enzymatic sensors. Finally, a perspective is provided on how this field may develop and how NP-based enzymatic enhancement can be extended to coupled systems and multienzyme cascades.

Impact of Anti-Biofouling Surface Coatings on the Properties of Nanomaterials and Their Biomedical Applications

Understanding and subsequently controlling non-specific interactions between engineered nanomaterials and biological environment have become increasingly important for further developing and advancing nanotechnology for biomedical applications. Such non-specific interactions, also known as the biofouling effect, mainly associate with the adsorption of biomolecules (such as proteins, DNAs, RNAs, and peptides) onto the surface of nanomaterials and the adhesion or uptake of nanomaterials by various cells. By altering the surface properties of nanomaterials the biofouling effect can lead to in situ changes of physicochemical properties, pharmacokinetics, functions, and toxicity of nanomaterials. This review provides discussions on the current understanding of the biofouling effect, the factors that affect the non-specific interactions associated with biofouling, and the impact of the biofouling effect on the performances and functions of nanomaterials. An overview of the development and applications of various anti-biofouling coating materials to preserve and improve the properties and functions of engineered nanomaterials for intended biomedical applications is also provided.

Kinetic enhancement in high-activity enzyme complexes attached to nanoparticles

Accumulating studies by many groups have found consistent enhancement in a wide variety of enzyme activities when they are displayed around nanoparticles. However, the underlying mechanism(s) that give rise to this phenomenon are still largely unknown. Herein, we develop a detailed reaction scheme that considers many of the various possible interactions between a substrate and a given enzyme-nanoparticle bioconjugate. The properties and some functional predictions that emanate from the reaction scheme were then tested using a model system where the homotetrameric beta-galactosidase enzyme complex was assembled with luminescent semiconductor nanocrystalline quantum dots displayed around its periphery. This type of assembly occurs as the ∼465 kDa enzyme complex is significantly larger than the 4.2 nm diameter green emitting quantum dots utilized. This unique architecture, in conjunction with the fact that this enzyme functions at or near the diffusion limit, provided a unique opportunity to selectively probe certain aspects of enzyme enhancement when attached to a nanoparticle with minimal potential perturbations to the native enzyme structure. Experimental assays were conducted where both free enzymes and quantum dot-decorated enzymes were compared directly in side-by-side samples and included formats where the kinetic processes were challenged with increasing viscosity and competitive inhibitors. The results strongly suggest that it is possible for there to be significant enhancements in an enzyme's catalytic rate or k_cat after attachment to a nanoparticle even when it is apparently diffusion limited without requiring any gross changes to the enzyme's structure. A discussion of how this reaction scheme and model can be applied to other systems is provided.

Nanoparticle cellular uptake by dendritic wedge peptides: achieving single peptide facilitated delivery

Significant efforts are being undertaken to optimize the cargo carrying capacity and especially the cellular delivery efficiency of functionalized nanoparticles for applications in biological research and pharmacological delivery. One approach to increasing nanoparticle surface cargo display capacity is to decrease the number of moieties required for mediating cellular delivery by improving their efficiency. We describe a series of multivalent cell penetrating peptide (CPP) dendrimers that facilitate rapid cellular delivery of prototypical nanoparticle-semiconductor quantum dots (QDs). The modular CPP dendrimers were assembled through an innovative convergent oxime ligation strategy between (Arg₉)_n motifs and a dendritic QD-coordination scaffold. Dendrimeric peptides sequentially incorporate a terminal (His)₆ motif for metal-affinity QD coordination, a Pro₉ spacer, a branching poly-lysine scaffold, and wedged display of (Arg₉)_n binding motifs with n = 1×, 2×, 4×, 8×, 16× multivalency. QD dendrimer display capacity was estimated using structural simulations and QD-(Arg₉)_1-16 conjugates characterized by dynamic light scattering along with surface plasmon resonance-based binding assays to heparan sulfate proteoglycan surfaces. Cellular uptake via endocytosis was confirmed and peptide delivery kinetics investigated as a function of QD-(Arg₉)_1-16 conjugate exposure time and QD assembly ratio where cellular viability assays reflected no overt cytotoxicity. The ability of single dendrimer conjugates to facilitate cellular uptake was confirmed for QD-(Arg₉)_2-16 repeats along with the ability to deliver >850 kDa of protein cargo per QD. Minimizing the number of CPPs required for cellular uptake is critical for expanding nanoparticle cargo carrying capacity and can allow for inclusion of additional sensors, therapeutics and contrast agents on their surface.

Nanomaterial-based sensors for the detection of biological threat agents

The danger posed by biological threat agents and the limitations of modern detection methods to rapidly identify them underpins the need for continued development of novel sensors. The application of nanomaterials to this problem in recent years has proven especially advantageous. By capitalizing on large surface/volume ratios, dispersability, beneficial physical and chemical properties, and unique nanoscale interactions, nanomaterial-based biosensors are being developed with sensitivity and accuracy that are starting to surpass traditional biothreat detection methods, yet do so with reduced sample volume, preparation time, and assay cost. In this review, we start with an overview of bioagents and then highlight the breadth of nanoscale sensors that have recently emerged for their detection.

Conjugation of biotin-coated luminescent quantum dots with single domain antibody-rhizavidin fusions

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Single domain antibody—rhizavidin fusion bioconjugated biotin coated quantum dots.

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Provided facile and effective method to orient antibodies on QD surface.

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Accomplished improved production of His-tagged rhizavidin (RZh) in E. coli.

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Demonstrated utility of RZh as a replacement for tetrameric biotin binders.

Straightforward and effective methods are required for the bioconjugation of proteins to surfaces and particles. Previously we demonstrated that the fusion of a single domain antibody with the biotin binding molecule rhizavidin provided a facile method to coat biotin-modified surfaces with a highly active and oriented antibody. Here, we constructed similar single domain antibody—rhizavidin fusions as well as unfused rhizavidin with a His-tag. The unfused rhizavidin produced efficiently and its utility for assay development was demonstrated in surface plasmon resonance experiments. The single domain antibody-rhizavidin fusions were utilized to coat quantum dots that had been prepared with surface biotins. Preparation of antibody coated quantum dots by this means was found to be both easy and effective. The prepared single domain antibody-quantum dot reagent was characterized by surface plasmon resonance and applied to toxin detection in a fluoroimmunoassay sensing format.

Improving detection sensitivity by oriented bioconjugation of antibodies to quantum dots with a flexible spacer arm for immunoassay

The impacts of conjugation method and spacer arm for antibody covalent coupling with quantum dots on their biodetection performance are experimentally disclosed.

Combining semiconductor quantum dots and bioscaffolds into nanoscale energy transfer devices

Significant advances have been made in the development of nanoscale devices capable of exciton transport via Förster resonance energy transfer. Several requirements must be met for effective operation, including a reliable energy-harvesting source along with highly organized, precisely placed energy relay elements. For the latter, biological scaffolds such as DNA provide a customizable, symmetric, and stable structure that can be site-specifically modified with organic fluorophores. Here, advancements in nanoscale energy transfer devices incorporating semiconductor nanocrystals and bioscaffolds are reviewed with discussion of biofunctionalization, linker chemistries, design considerations, and concluding with applications in light harvesting, multiplexed biosensing, and optical logic.

Advances in nanoparticle imaging technology for vascular pathologies

Nanoparticle imaging agents for vascular pathologies are in development, and some agents are already in clinical trials. Untargeted agents, with long circulation, are excellent blood-pool agents, but molecularly targeted agents have significant advantages due to the signal enhancement possible with nanoparticle presentation of the contrast agent molecules. Molecular targets that are accessible directly from the vasculature are optimal for such agents. Targets that are removed from the vasculature, such as those on tumor cell surfaces, have limited accessibility owing to the enhanced permeation and retention effect. Yet, efforts at molecular targeting have tested small molecules, peptides, antibodies, and most recently aptamers as possible targeting ligands. The future is bright for nanoparticle-based imaging of vascular pathologies.

Understanding How Nanoparticle Attachment Enhances Phosphotriesterase Kinetic Efficiency

As a specific example of the enhancement of enzymatic activity that can be induced by nanoparticles, we investigate the hydrolysis of the organophosphate paraoxon by phosphotriesterase (PTE) when the latter is displayed on semiconductor quantum dots (QDs). PTE conjugation to QDs underwent extensive characterization including structural simulations, electrophoretic mobility shift assays, and dynamic light scattering to confirm orientational and ratiometric control over enzyme display which appears to be necessary for enhancement. PTE hydrolytic activity was then examined when attached to ca. 4 and 9 nm diameter QDs in comparison to controls of freely diffusing enzyme alone. The results confirm that the activity of the QD conjugates significantly exceeded that of freely diffusing PTE in both initial rate (∼4-fold) and enzymatic efficiency (∼2-fold). To probe kinetic acceleration, various modified assays including those with increased temperature, presence of a competitive inhibitor, and increased viscosity were undertaken to measure the activation energy and dissociation rates. Cumulatively, the data indicate that the higher activity is due to an acceleration in enzyme-product dissociation that is presumably driven by the markedly different microenvironment of the PTE-QD bioconjugate's hydration layer. This report highlights how a specific change in an enzymatic mechanism can be both identified and directly linked to its enhanced activity when displayed on a nanoparticle. Moreover, the generality of the mechanism suggests that it could well be responsible for other examples of nanoparticle-enhanced catalysis.

An enzymatically-sensitized sequential and concentric energy transfer relay self-assembled around semiconductor quantum dots

The ability to control light energy within de novo nanoscale structures and devices will greatly benefit their continuing development and ultimate application. Ideally, this control should extend from generating the light itself to its spatial propagation within the device along with providing defined emission wavelength(s), all in a stand-alone modality. Here we design and characterize macromolecular nanoassemblies consisting of semiconductor quantum dots (QDs), several differentially dye-labeled peptides and the enzyme luciferase which cumulatively demonstrate many of these capabilities by engaging in multiple-sequential energy transfer steps. To create these structures, recombinantly-expressed luciferase and the dye-labeled peptides were appended with a terminal polyhistidine sequence allowing for controlled ratiometric self-assembly around the QDs via metal-affinity coordination. The QDs serve to provide multiple roles in these structures including as central assembly platforms or nanoscaffolds along with acting as a potent energy harvesting and transfer relay. The devices are activated by addition of coelenterazine H substrate which is oxidized by luciferase producing light energy which sensitizes the central 625 nm emitting QD acceptor by bioluminescence resonance energy transfer (BRET). The sensitized QD, in turn, acts as a relay and transfers the energy to a first peptide-labeled Alexa Fluor 647 acceptor dye displayed on its surface. This dye then transfers energy to a second red-shifted peptide-labeled dye acceptor on the QD surface through a second concentric Förster resonance energy transfer (FRET) process. Alexa Fluor 700 and Cy5.5 are both tested in the role of this terminal FRET acceptor. Photophysical analysis of spectral profiles from the resulting sequential BRET-FRET-FRET processes allow us to estimate the efficiency of each of the transfer steps. Importantly, the efficiency of each step within this energy transfer cascade can be controlled to some extent by the number of enzymes/peptides displayed on the QD. Further optimization of the energy transfer process(es) along with potential applications of such devices are finally discussed.

Detecting kallikrein proteolytic activity with peptide-quantum dot nanosensors

Contamination and adulterants in both naturally derived and synthetic drugs pose a serious threat to the worldwide medical community. Developing rapid and sensitive sensors/devices to detect these hazards is thus a continuing need. We describe a hydrophilic semiconductor quantum dot (QD)-peptide Förster resonance energy transfer (FRET) nanosensor for monitoring the activity of kallikrein, a key proteolytic enzyme functioning at the initiation of the blood clotting cascade. Kallikrein is also activated by the presence of an oversulfated contaminant recently found in preparations of the drug heparin. Quantitatively monitoring the activity of this enzyme within a nanosensor format has proven challenging because of inherent steric and kinetic considerations. Our sensor is designed around a central QD donor platform which displays controlled ratios of a modular peptidyl substrate. This peptide, in turn, sequentially expresses a terminal oligohistidine motif that mediates the rapid self-assembly of peptides to the QD surface, a linker-spacer sequence to extend the peptide away from the QD surface, a kallikrein recognized-cleavage site, and terminates in an acceptor dye-labeling site. Hydrophilic QDs prepared with compact, zwitterionic surface coatings were first evaluated for their ability to self-assemble the dye-labeled peptide substrates. An optimized two-step protocol was then utilized where high concentrations of peptide were initially digested with purified human kallikrein and samples collected at distinct time points were subsequently diluted into QD-containing solutions for assaying. This sensor provided a quantitative FRET-based readout for monitoring kallikrein activity and comparison to a calibration curve allowed estimation of the relevant Michaelis-Menten kinetic descriptors. The results further suggest that almost any protease should be amenable to a QD-based FRET assay format with appropriate design considerations.

Zwitterionic-coated "stealth" nanoparticles for biomedical applications: recent advances in countering biomolecular corona formation and uptake by the mononuclear phagocyte system

Nanoparticles represent highly promising platforms for the development of imaging and therapeutic agents, including those that can either be detected via more than one imaging technique (multi-modal imaging agents) or used for both diagnosis and therapy (theranostics). A major obstacle to their medical application and translation to the clinic, however, is the fact that many accumulate in the liver and spleen as a result of opsonization and scavenging by the mononuclear phagocyte system. This focused review summarizes recent efforts to develop zwitterionic-coatings to counter this issue and render nanoparticles more biocompatible. Such coatings have been found to greatly reduce the rate and/or extent of non-specific adsorption of proteins and lipids to the nanoparticle surface, thereby inhibiting production of the "biomolecular corona" that is proposed to be a universal feature of nanoparticles within a biological environment. Additionally, in vivo studies have demonstrated that larger-sized nanoparticles with a zwitterionic coating have extended circulatory lifetimes, while those with hydrodynamic diameters of ≤5 nm exhibit small-molecule-like pharmacokinetics, remaining sufficiently small to pass through the fenestrae and slit pores during glomerular filtration within the kidneys, and enabling efficient excretion via the urine. The larger particles represent ideal candidates for use as blood pool imaging agents, whilst the small ones provide a highly promising platform for the future development of theranostics with reduced side effect profiles and superior dose delivery and image contrast capabilities.

A sensitive quantum dots-based "OFF-ON" fluorescent sensor for ruthenium anticancer drugs and ctDNA

In this contribution, a simple and sensitive fluorescent sensor for the determination of both the three ruthenium anticancer drugs (1 to 3) and calf thymus DNA (ctDNA) was established based on the CdTe quantum dots (QDs) fluorescence "OFF-ON" mode. Under the experimental conditions, the fluorescence of CdTe QDs can be effectively quenched by ruthenium anticancer drugs because of the surface binding of these drugs on CdTe QDs and the subsequent photoinduced electron transfer (PET) process from CdTe QDs to ruthenium anticancer drugs, which render the system into fluorescence "OFF" status. The system can then be "ON" after the addition of ctDNA which brought the restoration of CdTe QDs fluorescence intensity, since ruthenium anticancer drugs broke away from the surface of CdTe QDs and inserted into double helix structure of ctDNA. The fluorescence quenching effect of the CdTe QDs-ruthenium anticancer drugs systems was mainly concentration dependent, which could be used to detect three ruthenium anticancer drugs. The limits of detection were 5.5 × 10(-8) M for ruthenium anticancer drug 1, 7.0 × 10(-8) M for ruthenium anticancer drug 2, and 7.9× 10(-8) M for ruthenium anticancer drug 3, respectively. The relative restored fluorescence intensity was directly proportional to the concentration of ctDNA in the range of 1.0 × 10(-8) M ∼ 3.0 × 10(-7) M, with a correlation coefficient (R) of 0.9983 and a limit of detection of 1.1 × 10(-9) M. The relative standard deviation (RSD) for 1.5 × 10(-7) M ctDNA was 1.5% (n = 5). There was almost no interference to some common chemical compounds, nucleotides, amino acids, and proteins. The proposed method was applied to the determination of ctDNA in three synthetic samples with satisfactory results. The possible reaction mechanism of CdTe QDs fluorescence "OFF-ON" was further investigated. This simple and sensitive approach possessed some potential applications in the investigation of interaction between drug molecules and DNA.

Nanobodies and nanocrystals: highly sensitive quantum dot-based homogeneous FRET immunoassay for serum-based EGFR detection

Semiconductor quantum dot nanocrystals (QDs) for optical biosensing applications often contain thick polyethylene glycol (PEG)-based coatings in order to retain the advantageous QD properties in biological media such as blood, serum or plasma. On the other hand, the application of QDs in Förster resonance energy transfer (FRET) immunoassays, one of the most sensitive and most common fluorescence-based techniques for non-competitive homogeneous biomarker diagnostics, is limited by such thick coatings due to the increased donor-acceptor distance. In particular, the combination with large IgG antibodies usually leads to distances well beyond the common FRET range of approximately 1 to 10 nm. Herein, time-gated detection of Tb-to-QD FRET for background suppression and an increased FRET range is combined with single domain antibodies (or nanobodies) for a reduced distance in order to realize highly sensitive QD-based FRET immunoassays. The "(nano)(2) " immunoassay (combination of nanocrystals and nanobodies) is performed on a commercial clinical fluorescence plate reader and provides sub-nanomolar (few ng/mL) detection limits of soluble epidermal growth factor receptor (EGFR) in 50 μL buffer or serum samples. Apart from the first demonstration of using nanobodies for FRET-based immunoassays, the extremely low and clinically relevant detection limits of EGFR demonstrate the direct applicability of the (nano)(2-) assay to fast and sensitive biomarker detection in clinical diagnostics.

Evaluation of diverse peptidyl motifs for cellular delivery of semiconductor quantum dots

Cell-penetrating peptides (CPPs) have rapidly become a mainstay technology for facilitating the delivery of a wide variety of nanomaterials to cells and tissues. Currently, the library of CPPs to choose from is still limited, with the HIV TAT-derived motif still being the most used. Among the many materials routinely delivered by CPPs, nanoparticles are of particular interest for a plethora of labeling, imaging, sensing, diagnostic, and therapeutic applications. The development of nanoparticle-based technologies for many of these uses will require access to a much larger number of functional peptide motifs that can both facilitate cellular delivery of different types of nanoparticles to cells and be used interchangeably in the presence of other peptides and proteins on the same surface. Here, we evaluate the utility of four peptidyl motifs for their ability to facilitate delivery of luminescent semiconductor quantum dots (QDs) in a model cell culture system. We find that an LAH4 motif, derived from a membrane-inserting antimicrobial peptide, and a chimeric sequence that combines a sweet arrow peptide with a portion originating from the superoxide dismutase enzyme provide effective cellular delivery of QDs. Interestingly, a derivative of the latter sequence lacking just a methyl group was found to be quite inefficient, suggesting that even small changes can have significant functional outcomes. Delivery was effected using 1 h incubation with cells, and fluorescent counterstaining strongly suggests an endosomal uptake process that requires a critical minimum number or ratio of peptides to be displayed on the QD surface. Concomitant cytoviability testing showed that the QD-peptide conjugates are minimally cytotoxic in the model COS-1 cell line tested. Potential applications of these peptides in the context of cellular delivery of nanoparticles and a variety of other (bio)molecules are discussed.