Search

DNA nanotechnology has proven to be a powerful strategy for the bottom-up preparation of colloidal nanoparticle (NP) superstructures, enabling the coordination of multiple NPs with orientation and separation approaching nanometer precision. To do this, NPs are often conjugated with chemically modified, single-stranded (ss) DNA that can recognize complementary ssDNA on the DNA nanostructure. The limitation is that many NPs cannot be easily conjugated with ssDNA, and other conjugation strategies are expensive, inefficient, or reduce the specificity and/or precision with which NPs can be placed. As an alternative, the conjugation of nanoparticle-binding peptides and peptide nucleic acids (PNA) can produce peptide-PNA with distinct NP-binding and DNA-binding domains. Here, we demonstrate a simple application of this method to conjugate semiconductor quantum dots (QDs) directly to DNA nanostructures by means of a peptide-PNA with a six-histidine peptide motif that binds to the QD surface. With this method, we achieved greater than 90% capture efficiency for multiple QDs on a single DNA nanostructure while preserving both site specificity and precise spatial control of QD placement. Additionally, we investigated the effects of peptide-PNA charge on the efficacy of QD immobilization in suboptimal conditions. The results validate peptide-PNA as a viable alternative to ssDNA conjugation of NPs and warrant studies of other NP-binding peptides for peptide-PNA conjugation.

Synthetic DNA templated nanostructures offer an excellent platform for the precise spatial and orientational positioning of organic and inorganic nanomaterials. Previous reports have shown its applicability in the organization of plasmonic nanoparticles in a number of geometries for the purpose of realizing tunable nanoscale optical devices. However, translation of nanoparticle-DNA constructs to application requires additional efforts to increase scalability, reproducibility, and formation yields. Understanding all these factors is, in turn, predicated on in-depth analysis of each structure and comparing how formation changes with complexity. Towards the latter goal, we assemble seven unique plasmonic nanostructure symmetries of increasing complexity based on assembly of gold nanorods and nanoparticles on two different DNA origami templates, a DNA triangle and rhombus, and characterize them using gel electrophoresis, atomic force- and transmission electron microscopy, as well as optical spectroscopy. In particular, we focus on how much control can be elicited over yield, reproducibility, shape, size, inter-particle angles, gaps, and plasmon shifts as compared to expectations from computer simulations as structural complexity increases. We discuss how these results can contribute to establishing process principles for creating DNA templated plasmonic nanostructures.

Colloidal semiconductor quantum dots (QDs), metal nanoparticles, and cellulose paper are materials with numerous applications in bioanalysis and beyond. The functional properties of QDs and metal NPs are substantially different than those of cellulose, such that their integration with cellulose paper is potentially enabling for many applications. Here, we characterize and evaluate multiple chemistries that modify cellulose paper substrates for the affinity-based immobilization of QDs, gold nanoparticles (Au NPs), and platinum nanoparticles (Pt NPs). These chemistries include grafting of cellulose fibers with imidazole and dithiol groups, as well as the aminosilanization of cellulose fibers (both with and without subsequent grafting with dithiol groups). Cellulose modifications and nanoparticle immobilization are characterized by multiple techniques, including, but not limited to, X-ray photoelectron spectroscopy, scanning electron microscopy, and optical imaging, extinction, and fluorescence measurements. We demonstrate the on-paper immobilization of color-tuned mixtures of QDs, on-paper patterning of QDs by microcontact printing, and post-immobilization enhancement of energy transfer and model assays of protease activity. The robustness of QD photoluminescence is also evaluated between immobilization chemistries. Paper-immobilized Au NPs and Pt NPs are evaluated as potential substrates for SERS and as supported catalysts for a model decolorization reaction. Our cumulative results indicate that there may not be a one-size-fits-all immobilization chemistry. Instead, the immobilization chemistry should be tailored and optimized for the downstream application.

DNA-directed assembly of gold nanoparticles into precise two- and three-dimensional patterns has enabled bold advances in probing their optical properties such as the local enhancement in their surface plasmon resonance. DNA nanostructures synthesized using the principles of DNA origami have been programmed to contain unique capture sites for positioning metal nanoparticles in diverse geometries for applications in biosensing, therapy, and miniature electronics. However, to enable scalability beyond simple 2-3 nanoparticle architectures, it is important to understand the requirement for orthogonal capture sequences for attaching more than a single gold nanoparticle on a DNA nanostructure. In this work, we sought to assemble an angular gold nanorod-nanosphere-nanorod pattern on a DNA origami triangle with multiple capture sites utilizing a common capture sequence. Results indicate that gold nanospheres preferentially bound to all the capture sites on the DNA origami triangle and prevented attachment of gold nanorods. This suggests that requirement for orthogonal capture sites is correlated with the physical properties of the individual nanoparticle such as shape and size.

Current challenges in photodynamic therapy (PDT) include both the targeted delivery of the photosensitizer (PS) to the desired cellular location and the maintenance of PS efficacy. Zinc phthalocyanine (ZnPc), a macrocyclic porphyrin and a potent PS for PDT, undergoes photoexcitation to generate reactive singlet oxygen that kills cells efficiently, particularly when delivered to the plasma membrane. Like other commonly employed PS, ZnPc is highly hydrophobic and prone to self-aggregation in aqueous biological media. Further, it lacks innate subcellular targeting specificity. Cumulatively, these attributes pose significant challenges for delivery via traditional systemic drug delivery modalities. Here, we report the development and characterization of a liquid crystal nanoparticle (LCNP)-based formulation for the encapsulation and targeted tethering of ZnPc to the plasma membrane bilayer. ZnPc was coloaded with the organic fluorophore, perylene (PY), in the hydrophobic polymeric matrix of the LCNP core. PY facilitated the fluorescence-based tracking of the LCNP carrier while also serving as a Förster resonance energy transfer (FRET) donor to the ZnPc acceptor. This configuration availed efficient singlet oxygen generation via enhanced excitation of ZnPc from multiple surrounding PY energy donors. When excited in a FRET configuration, cuvette-based assays revealed that singlet oxygen generation from the ZnPc was ∼1.8-fold greater and kinetically 12 times faster compared to when the ZnPc was excited directly. The specific tethering of the LCNPs to the plasma membrane of HEK 293 T/17 and HeLa cells was achieved by surface functionalization of the NPs with PEGylated cholesterol. In HeLa cells, LCNPs coloaded with PY and ZnPc, when photoexcited in a FRET configuration, mediated 70% greater cell killing compared to LCNPs containing ZnPc alone (direct excitation of ZnPc). This was attributed to a significant increase of the oxidative stress in the cells during the PDT. Overall, this work details the ability of the LCNP platform to facilitate (1) the specific tethering of the PY-ZnPc FRET pair to the plasma membrane and (2) the FRET-mediated, augmented singlet oxygen generation for enhanced PDT relative to the direct excitation of ZnPc alone.

Combining biomolecules such as enzymes with nanoparticles has much to offer for creating next generation synergistically functional bionanomaterials. However, almost nothing is known about how these two disparate components interact at this critical biomolecular-materials interface to give rise to improved activity and emergent properties. Here we examine how the nanoparticle surface can influence and increase localized enzyme activity using a designer experimental system consisting of trypsin proteolysis acting on peptide-substrates displayed around semiconductor quantum dots (QDs). To minimize the complexity of analyzing this system, only the chemical nature of the QD surface functionalizing ligands were modified. This was accomplished by synthesizing a series of QD ligands that were either positively or negatively charged, zwitterionic, neutral, and with differing lengths. The QDs were then assembled with different ratios of dye-labeled peptide substrates and exposed to trypsin giving rise to progress curves that were monitored by Förster resonance energy transfer (FRET). The resulting trypsin activity profiles were analyzed in the context of detailed molecular dynamics simulations of key interactions occurring at this interface. Overall, we find that a combination of factors can give rise to a localized activity that was 35-fold higher than comparable freely diffusing enzyme-substrate interactions. Contributing factors include the peptide substrate being prominently displayed extending from the QD surface and not sterically hindered by the longer surface ligands in conjunction with the presence of electrostatic and other productive attractive forces between the enzyme and the QD surface. An intimate understanding of such critical interactions at this interface can produce a set of guidelines that will allow the rational design of next generation high-activity bionanocomposites and theranostics.

Ultrasmall noble metal and especially gold nanoclusters (AuNCs, ≤2 nm diameter in size) display a range of unique quantum confined and photophysical properties which are far different from their larger-sized nanoparticle counterparts or that of the bulk parent material. Amongst these properties, the photoluminescence of gold AuNCs has stimulated much interest for biological applications due to a combination of their small size, high photostability and range of emissions depending on size and surface stabilizing ligands, including near-IR emission. The dearth of robust Förster resonance energy transfer (FRET) donors and acceptors available to populate the latter spectral range is also driving strong interest in applying AuNCs for similar utility and especially for biosensing. However, the exact mechanism of how AuNCs engage in this type of energy transfer (ET) is still not defined and accumulating evidence indicates that it is not by a classical Förster process although, interestingly, many of the same characteristics and photophysical requirements seem to be present and even many-times required. Here, we summarize the state of the art in AuNC ET studies with a special emphasis on relevance to biological utility ranging from diagnostics to distance measurements along with describing the different ET mechanisms that have been ascribed with their use. Due to its corresponding importance in this discussion, we provide a brief overview of how these materials are synthesized, the current understanding of how their photoluminescence originates, and some related information on silver nanocluster (AgNC) ET along with related processes such as chemically-induced ET. A perspective and outlook on how this area will develop in the future is also provided.

Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.

The design of nanoparticles is critical for their efficient use in many applications ranging from biomedicine to sensing and energy. While shape and size are responsible for the properties of the inorganic nanoparticle core, the choice of ligands is of utmost importance for the colloidal stability and function of the nanoparticles. Moreover, the selection of ligands employed in nanoparticle synthesis can determine their final size and shape. Ligands added after nanoparticle synthesis infer both new properties as well as provide enhanced colloidal stability. In this article, we provide a comprehensive review on the role of the ligands with respect to the nanoparticle morphology, stability, and function. We analyze the interaction of nanoparticle surface and ligands with different chemical groups, the types of bonding, the final dispersibility of ligand-coated nanoparticles in complex media, their reactivity, and their performance in biomedicine, photodetectors, photovoltaic devices, light-emitting devices, sensors, memory devices, thermoelectric applications, and catalysis.

Luminescent semiconductor quantum dots (QDs) are one of the more popular nanomaterials currently utilized within biological applications. However, what is not widely appreciated is their growing role as versatile energy transfer (ET) donors and acceptors within a similar biological context. The progress made on integrating QDs and ET in biological configurations and applications is reviewed in detail here. The goal is to provide the reader with (1) an appreciation for what QDs are capable of in this context, (2) how this field has grown over a relatively short time span, and, in particular, (3) how QDs are steadily revolutionizing the development of new biosensors along with a myriad of other photonically active nanomaterial-based bioconjugates. An initial discussion of QD materials along with key concepts surrounding their preparation and bioconjugation is provided given the defining role these aspects play in the QDs ability to succeed in subsequent ET applications. The discussion is then divided around the specific roles that QDs provide as either Förster resonance energy transfer (FRET) or charge/electron transfer donor and/or acceptor. For each QD-ET mechanism, a working explanation of the appropriate background theory and formalism is articulated before examining their biosensing and related ET utility. Other configurations such as incorporation of QDs into multistep ET processes or use of initial chemical and bioluminescent excitation are treated similarly. ET processes that are still not fully understood such as QD interactions with gold and other metal nanoparticles along with carbon allotropes are also covered. Given their maturity, some specific applications ranging from in vitro sensing assays to cellular imaging are separated and discussed in more detail. Finally a perspective on how this field will continue to evolve is provided.

Graphical abstract, Highlights • Single domain antibody—rhizavidin fusion bioconjugated biotin coated quantum dots. • Provided facile and effective method to orient antibodies on QD surface. • Accomplished improved production of His-tagged rhizavidin (RZh) in E. coli. • 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.

Bio-inspired, hybrid architectures employing quantum dots (QDs) appended with functionally active biomolecules such as enzymes have the potential to be utilized in numerous applications. Some examples include nanosensors for medical diagnostics, chemical/biological threat detection, as well as “bio-factories” in complex industrial synthetic processes. The main advantage in creating these nanofactories is increased rates in catalysis and efficiency when enzymes are associated with nanoscaffolds, as shown in numerous studies. However, the mechanism for this enhancement remains elusive. Gaining a fundamental, mechanistic understanding of enzyme-QD nanostructures is important in the development of numerous device applications. In this work, we review an array of enzymes attached to QDs and generate a hypothesis in regards to the unique architecture of the enzyme-nanoparticle (NP) construct that leads to increases in catalysis. We highlight work with phosphotiresterase (PTE) attached to two distinctly sized QDs in neutralizing a simulant nerve agent, as well as in other enzyme systems.

Strong, flexible, and transparent materials have garnered tremendous interest in recent years as materials and electronics manufacturers pursue devices that are bright, flexible, durable, tailorable, and lightweight. Depending on the starting components, polymers fabricated using thiol–yne chemistry have been shown to be exceptionally strong and/or flexible, while also being amenable to modification by the incorporation of nanoparticles. In the present work, novel ligands were synthesized and used to functionalize quantum dots (QDs) of various diameters. The functionalized QDs were then incorporated into thiol–yne prepolymer matrices. These matrices were subsequently polymerized to form QD thiol–yne nanocomposite polymers. To demonstrate the versatility of the fabrication process, the prepolymers were either thermally cured or photopolymerized. The resulting transparent nanocomposites expressed the size-specific color of the QDs within them when exposed to ultraviolet irradiation, demonstrating that QDs can be incorporated into thiol–yne polymers without significantly altering QD expression. With the inclusion of QDs, thiol–yne nanocomposite polymers are promising candidates for use in numerous applications including as device display materials, optical lens materials, and/or sensor materials.

All bacteria shed outer membrane vesicles (OMVs) loaded with a diverse array of small molecules, proteins, and genetic cargo. In this study we sought to hijack the bacterial cell export pathway to simultaneously produce, package, and release an active enzyme, phosphotriesterase (PTE). To accomplish this goal the SpyCatcher/SpyTag (SC/ST) bioconjugation system was utilized to produce a PTE-SpyCatcher (PTE-SC) fusion protein and a SpyTagged transmembrane porin protein (OmpA-ST), known to be abundant in OMVs. Under a range of physiological conditions the SpyTag and SpyCatcher domains interact with one another and form a covalent isopeptide bond driving packaging of PTE into forming OMVs. The PTE-SC loaded OMVs are characterized for size distribution, number of vesicles produced, cell viability, packaged PTE enzyme kinetics, OMV loading efficiency, and enzyme stability following iterative cycles of freezing and thawing. The PTE-loaded OMVs exhibit native-like enzyme kinetics when assayed with paraoxon as a substrate. PTE is often toxic to expression cultures and has a tendency to lose activity with improper handling. The coexpression of OmpA-ST with PTE-SC, however, greatly improved the overall PTE production levels by mitigating toxicity through exporting of the PTE-SC and greatly enhanced packaged enzyme stability against iterative cycles of freezing and thawing.

The intrinsic properties of quantum dots (QDs) and the growing ability to interface them controllably with living cells has far-reaching potential applications in probing cellular processes such as membrane action potential. We demonstrate that an electric field typical of those found in neuronal membranes results in suppression of the QD photoluminescence (PL) and, for the first time, that QD PL is able to track the action potential profile of a firing neuron with millisecond time resolution. This effect is shown to be connected with electric-field-driven QD ionization and consequent QD PL quenching, in contradiction with conventional wisdom that suppression of the QD PL is attributable to the quantum confined Stark effect.

Enzymes provide the critical means by which to catalyze almost all biological reactions in a controlled manner. Methods to harness and exploit their properties are of strong current interest to the growing field of biotechnology. In contrast to depending upon recombinant genetic approaches, a growing body of evidence suggests that apparent enzymatic activity can be enhanced when located at a nanoparticle interface. We use semiconductor quantum dots (QDs) as a well-defined and easily bioconjugated nanoparticle along with Escherichia coli-derived alkaline phosphatase (AP) as a prototypical enzyme to seek evidence for this process in a de novo model system. We began by first assessing whether the relatively large dimeric AP protein (∼100 kDa) can be assembled onto two differentially sized green and red CdSe/ZnS core/shell QDs in a ratiometric and structurally controlled manner; such assembly is necessary to minimize heterogeneity within the bioconjugate and provide intimate control over the experimental form...

Forster resonance energy transfer (FRET)-based assemblies currently comprise a significant portion of intracellularly based sensors. Although extremely useful, the fluorescent protein pairs typically utilized in such sensors are still plagued by many photophysical issues including significant direct acceptor excitation, small changes in FRET efficiency, and limited photostability. Luminescent semiconductor nanocrystals or quantum dots (QDs) are characterized by many unique optical properties including size-tunable photoluminescence, broad excitation profiles coupled to narrow emission profiles, and resistance to photobleaching, which can cumulatively overcome many of the issues associated with use of fluorescent protein FRET donors. Utilizing QDs for intracellular FRET-based sensing still requires significant development in many areas including materials optimization, bioconjugation, cellular delivery and assay design and implementation. We are currently developing several QD-based FRET sensors for various intracellular applications. These include sensors targeting intracellular proteolytic activity along with those based on theranostic nanodevices for monitoring drug release. The protease sensor is based on a unique design where an intracellularly expressed fluorescent acceptor protein substrate assembles onto a QD donor following microinjection, forming an active complex that can be monitored in live cells over time. In the theranostic configuration, the QD is conjugated to a carrier protein-drug analogue complex to visualize real-time intracellular release of the drug from its carrier in response to an external stimulus. The focus of this talk will be on the design, properties, photophysical characterization and cellular application of these sensor constructs.

Luminescent semiconductor quantum dots (QDs) play an important role in optical biosensing and, in particular, in FRET (Forster resonance energy transfer)-based luminescent probes. The QD materials that form the basis for these probes are in actuality quite heterogeneous and consist of different types of QDs with variations in material compositions, surface coatings, and available biofunctionalization strategies. To optimize their role in active sensors that rely on FRET, extensive physicochemical characterization is required. A technique that can provide precise information about size, shape, and bioconjugation properties of different QD-biomolecule conjugates from a single sample and measurement under actual experimental biosensing conditions would therefore be highly important for advancing QDs to a next generation nanobiosensing tool. Here, we present a detailed FRET study on a large set of QD-biomolecule conjugates, which allows for a homogeneous solution-phase size, shape, and bioconjugation analysis of peptide and protein self-assembled QDs at subnanomolar concentrations and with subnanometer resolution. Direct incorporation of luminescent Tb-complexes (Tb) in the peptides or proteins leads to Tb-to-QD FRET upon assembly to the different QD surfaces. Luminescence decay times and time-gated intensities, which precisely decode the FRET interactions, provide a wealth of useful information on the underlying composite structure and even biochemical functionality. In contrast to other high-resolution techniques, which require rather sophisticated instrumentation, well-defined experimental conditions, and low sample throughput, our technique uses a commercial time-resolved fluorescence plate reader for very fast and simple data acquisition of many aqueous samples in a standard microtiter plate.

DNA can process information through sequence-based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two-component sensor incorporating a chimeric peptide-DNA substrate is evaluated here as a protease-to-DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye-labeled peptide-DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross-talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.

In clinical diagnostics, homogeneous time-resolved (TR) FRET immunoassays are used for fast and highly sensitive detection of biomarkers in serum samples. The most common immunoassay format is based on europium chelate or cryptate donors and allophycocyanin acceptors. Replacing europium donors with terbium complexes and the acceptors with QDs offers large photophysical advantages for multiplexed diagnostics, because the Tb-complex can be used as FRET donor for QD acceptors of different colors. Water-soluble and biocompatible QDs are commercially available or can be synthesized in the laboratory using many available recipes from the literature. Apart from the semiconductor material composition, an important aspect of choosing the right QD for TR-FRET assays is the thickness of the QD coating, which will influence the photophysical properties and long-term stability as well as the donor-acceptor distance and FRET efficiency. Here we present a detailed time-resolved spectroscopic study of three different QDs with an emission maximum around 605 nm for their application as FRET acceptors (using a common Tb donor) in TR-bioassays: (i) Invitrogen/Life Technologies Qdot605, (ii) eBioscience eFluorNC605 and iii) ter-polymer stabilized CdSe/CdS/ZnS QDs synthesized in our laboratories. All FRET systems are very stable and possess large Förster distances (7.4-9.1 nm), high FRET efficiencies (0.63-0.80) and low detection limits (0.06-2.0 pM) within the FRET-bioassays. Shapes, sizes and the biotin/QD ratio of the biocompatible QDs could be determined directly in the solution phase bioassays at subnanomolar concentrations. Both commercial amphiphilic polymer/lipid encapsulated QDs and self-made ligand-exchanged QDs provide extremely low detection limits for highly sensitive TR-FRET bioassays.

Understanding the relationships between the physicochemical properties of engineered nanomaterials and their toxicity is critical for environmental and health risk analysis. However, this task is confounded by material diversity, heterogeneity of published data and limited sampling within individual studies. Here, we present an approach for analysing and extracting pertinent knowledge from published studies focusing on the cellular toxicity of cadmium-containing semiconductor quantum dots. From 307 publications, we obtain 1,741 cell viability-related data samples, each with 24 qualitative and quantitative attributes describing the material properties and experimental conditions. Using random forest regression models to analyse the data, we show that toxicity is closely correlated with quantum dot surface properties (including shell, ligand and surface modifications), diameter, assay type and exposure time. Our approach of integrating quantitative and categorical data provides a roadmap for interrogating the wide-ranging toxicity data in the literature and suggests that meta-analysis can help develop methods for predicting the toxicity of engineered nanomaterials. Literature data mining and knowledge extraction (known as meta-analysis) can be used to derive the relationships between toxicological outcome and the physicochemical properties of cadmium-containing quantum dots.

We characterize energy transfer between luminescent 1.5 nm diameter gold nanocrystal (AuNC) acceptors and three structurally/functionally-distinct classes of emissive donors including organic dyes, metal chelates and semiconductor quantum dots (QDs). Energy transfer efficiencies within the donor-AuNC assemblies were evaluated with steady-state and time-resolved measurements. Donor quenching was observed for every donor-acceptor pair although AuNC sensitization was only observed from metal-chelates and QDs. Results were analyzed with Forster’s dipole-dipole coupling model (FRET) and dipole-metal damping models including nanosurface energy transfer (NSET) and nanovolume energy transfer (NVET). FRET dramatically underestimated energy transfer efficiencies while the damping models provided qualitatively better fits to the data although neither fully reproduces the experimental data. Analysis suggests that organic dye donor quenching without corresponding AuNC sensitization results from enhanced intersystem crossing between dye singlet and triplet states driven by AuNC magnetic dipoles. We further consider factors that account for the unique electronic properties of the ultra-small luminescent AuNCs including the high excited state densities, rapid dephasing time and strong electron confinement as well as paramagnetic properties. Overall, the results provide insight into requirements necessary for realizing applications based on AuNC acceptor sensitization.

Nanosensors employing quantum dots (QDs) and enzyme substrates with fluorescent moieties offer tremendous promise for disease surveillance/diagnostics and as high-throughput co-factor assays. Advantages of QDs over other nanoscaffolds include their small size and inherent photochemical properties such as size tunable fluorescence, ease in attaching functional moieties, and resistance to photobleaching. These properties make QDs excellent Forster Resonance Energy Transfer (FRET) donors; well-suited for rapid, optical measurement applications. We report enzyme sensors designed with a single FRET donor, the QD donor acting as a scaffold to multiple substrates or acceptors. The QD-sensor follows the concrete activity of the enzyme, as compared to the most common methodologies that quantify the enzyme amount or its mRNA precursor. As the sensor reports on the enzyme activity in real-time we can actively follow the kinetics of the enzyme. Though classic Michaelis-Menten (MM) parameters can be obtained to describe the activity. In the course of these experiments deviations, both decreasing and increasing the kinetics, from the common MM model were observed upon close examinations. From these observations additional experiments were undertaken to understand the varying mechanisms. Different enzymes can present different deviations depending on the chosen target, e.g. trypsin appears to present a positive hopping mechanism while collagenase demonstrates a QD caused reversible inhibition.

A main goal of bionanotechnology and nanoparticle (NP)-mediated drug delivery (NMDD) continues to be the development of novel biomaterials that can controllably modulate the activity of the NP-associated therapeutic cargo. One of the desired subcellular locations for targeted delivery in NMDD is the plasma membrane. However, the controlled delivery of hydrophobic cargos to the membrane bilayer poses significant challenges including cargo precipitation and lack of specificity. Here, we employ a liquid crystal NP (LCNP)-based delivery system for the controlled partitioning of a model dye cargo from within the NP core into the plasma membrane bilayer. During synthesis of the NPs, the water-insoluble model dye cargo, 3,3'-dioctadecyloxacarbocyanine perchlorate (DiO), was efficiently incorporated into the hydrophobic LCNP core as confirmed by multiple spectroscopic analyses. Conjugation of a PEGylated cholesterol derivative to the NP surface (DiO-LCNP-PEG-Chol) facilitated the localization of the dye-loaded NPs to lipid raft microdomains in the plasma membrane in HEK 293T/17 cell. Analysis of DiO cellular internalization kinetics revealed that when delivered as a LCNP-PEG-Chol NP, the half-life of DiO membrane residence time (30 min) was twice that of free DiO (DiO(free)) (15 min) delivered from bulk solution. Time-resolved laser scanning confocal microscopy was employed to visualize the passive efflux of DiO from the LCNP core and its insertion into the plasma membrane bilayer as confirmed by Förster resonance energy transfer (FRET) imaging. Finally, the delivery of DiO as a LCNP-PEG-Chol complex resulted in the attenuation of its cytotoxicity; the NP form of DiO exhibited ∼30-40% less toxicity compared to DiO(free). Our data demonstrate the utility of the LCNP platform as an efficient vehicle for the combined membrane-targeted delivery and physicochemical modulation of molecular cargos using lipid raft-mediated tethering.

Designer DNA structures have garnered much interest as a way of assembling novel nanoscale architectures with exquisite control over the positioning of discrete molecules or nanoparticles. Exploiting this potential for a variety of applications such as light-harvesting, molecular electronics, or biosensing is contingent on the degree to which various nanoarchitectures with desired molecular functionalizations can be realized, and this depends critically on characterization. Many techniques exist for analyzing DNA-organized nanostructures; however, these are almost never used in concert because of overlapping concerns about their differing character, measurement environments, and the disparity in DNA modification chemistries and probe structure or size. To assess these concerns and to see what might be gleaned from a multimodal characterization, we intensively study a single DNA nanostructure using a multiplicity of methods. Our test bed is a linear 100 base-pair double-stranded DNA that has been modified by a variety of chemical handles, dyes, semiconductor quantum dots, gold nanoparticles, and electroactive labels. To this we apply a combination of physical/optical characterization methods including electrophoresis, atomic force microscopy, transmission electron microscopy, dynamic light scattering, Förster resonance energy transfer, voltammetry, and structural modeling. In general, the results indicate that the differences among the techniques are not so large as to prevent their effective use in combination, that the data tend to be corroborative, and that differences observed among them can actually be quite informative.

Understanding how to controllably modulate the efficiency of energy transfer in Förster resonance energy transfer (FRET)-based assemblies is critical to their implementation as sensing modalities. This is particularly true for sensing assemblies that are to be used as the basis for real time intracellular sensing of intracellular processes and events. We use a quantum dot (QD) donor -mCherry acceptor platform that is engineered to self-assemble in situ wherein the protein acceptor is expressed via transient transfection and the QD donor is microinjected into the cell. QD-protein assembly is driven by metal-affinity interactions where a terminal polyhistidine tag on the protein binds to the QD surface. Using this system, we show the ability to modulate the efficiency of the donor–acceptor energy transfer process by controllably altering either the ligand coating on the QD surface or the precise location where the QD-protein assembly process occurs. Intracellularly, a short, zwitterionic ligand mediates more efficient FRET relative to longer ligand species that are based on the solubilizing polymer, poly(ethylene glycol). We further show that a greater FRET efficiency is achieved when the QD-protein assembly occurs free in the cytosol compared to when the mCherry acceptor is expressed tethered to the inner leaflet of the plasma membrane. In the latter case, the lower FRET efficiency is likely attributable to a lower expression level of the mCherry acceptor at the membrane combined with steric hindrance. Our work points to some of the design considerations that one must be mindful of when developing FRET-based sensing schemes for use in intracellular sensing.

Effective biological application of nanocrystalline semiconductor quantum dots continues to be hampered by the lack of easily implemented and widely applicable labeling chemistries. Here, we introduce two new orthogonal nanocrystal bioconjugation chemistries that overcome many of the labeling issues associated with currently utilized approaches. These chemistries specifically target either (1) the ubiquitous amines found on proteins or (2) thiols present in either antibody hinge regions or recombinantly introduced into other proteins to facilitate site-specific labeling. The amine chemistry incorporates aniline-catalyzed hydrazone bond formation, while the sulfhydryl chemistry utilizes nanocrystals displaying surface activated maleimide groups. Both reactive chemistries are rapidly implemented, yielding purified nanocrystal-protein bioconjugates in as little as 3 h. Following initial characterization of the nanocrystal materials, the wide applicability and strong multiplexing potential of these chemistries are demonstrated in an array of applications including immunoassays, immunolabeling in both cellular and tissue samples, in vivo cellular uptake, and flow cytometry. Side-by-side comparison of the immunolabeled cells suggested a functional equivalence between results generated with the amine and thiol-labeled antibody-nanocrystal bioconjugates in that format. Three-color labeling was achieved in the cellular uptake format, with no significant toxicity observed while simultaneous five-color labeling of different epitopes was demonstrated for the immunolabeled tissue sample. Novel labeling applications are also facilitated by these chemistries, as highlighted by the ability to directly label cellular membranes in adherent cell cultures with the thiol-reactive chemistry.

Enzymes are important players in multiple applications, be it bioremediation, biosynthesis, or as reporters. The business of catalysis and inhibition of enzymes is a multibillion dollar industry and understanding the kinetics of commercial enzymes can have a large impact on how these systems are optimized. Recent advances in nanotechnology have opened up the field of nanoparticle (NP) and enzyme conjugates and two principal architectures for NP conjugate systems have been developed. In the first example the enzyme is bound to the NP in a persistent manner, here we find that key factors such as directed enzyme conjugation allow for enhanced kinetics. Through controlled comparative experiments we begin to tease out specific mechanisms that may account for the enhancement. The second system is based on dynamic interactions of the enzymes with the NP. The enzyme substrate is bound to the NP and the enzyme is free in solution. Here again we find that there are many variables , such as substrate positioning and NP selection, that modify the kinetics.

Nanosensors employing quantum dots (QDs) with appended biofunctional moieties offer tremendous promise for disease surveillance/diagnostics and chemical/biological threat activity. Their small size permits cell penetration and their inherent photochemical properties are well-suited for rapid, optical measurement. The effectiveness of enzymes immobilized on QDs, however, are not completely understood, hindering development of chemical/biological sensors and remediation materials. Here, we analyze enzyme effectiveness for the neutralization of a simulant nerve agent when attached to two distinctly-sized QDs. Two sizes of QDs, 525 or 625 nm, were appended with DHLA ligands to improve aqueous stability and prevent aggregation. Various molar ratios of de novo phosphotriesterase trimer (PTE3) were rapidly self-assembled via spontaneous metal coordination of the PTE oligohistidine tag onto the Zn2+-rich QD surface. PTE catalyzes the detoxification of organophosphate pesticides (e.g, paraoxon, an analog of sarin) to p-nitrophenol whose absorbance can be measured at 405 nm. The optimal ratio of PTE3 to 525 nm and 625 nm QD’s was determined to be 12 and 24, respectively. The enhanced enzyme performance in both cases is most likely due to increased enzyme-substrate interactions from improvements in enzyme orientation, enzyme density, and substrate diffusion on or near the QD. Development of these nansosensors as optical-based biosensors (e.g., within compact microfluidic devices) may greatly improve the sensitivity of conventional biological/chemical detection schemes.

Glycan moiety of glycoproteins plays an essential role in its biological activity in vivo, and the analysis of glycosylation is of great importance in the development of protein therapeutics. In this study, we report a rapid and simple detection of protein glycosylation based on the fluorescence resonance energy transfer (FRET) between concanavalin A-conjugated gold nanoparticles (ConA-AuNPs) and dextran-conjugated quantum dots (Dex-QDs). The increased photoluminescence (PL) signals of Dex-QDs due to the competitive inhibition of glycoproteins were well correlated with the glycosylation chain length of glucose oxidases as well as the mannosylation degree of bovine serum albumin (BSA). The parallel analysis of the diversely mannosylated BSAs using an image analyzer further demonstrated the potential of this new technique in high-throughput screening of glycoprotein and carbohydrate therapeutics.

Nanostructured magnetic materials (NMMs)[1] have attracted much attention recently because of their broad biotechnological applications including support matrices for enzyme immobilization,[2] immunoassays,[3] drug delivery,[4] and biosensors.[ 5] Specifically, the easy separation and controlled placement of NMMs by means of an external magnetic field enables their application in the development of immobilized enzyme processes[2] and the construction of magnetically controllable bio-electrocatalytic systems.[5, 6] Herein, we demonstrate the use of immobilized enzymes in NMMs for magnetically switchable bio-electrocatalysis.

Nanoparticle (NP) display potentially offers a new way to both stabilize and, in many cases, enhance enzyme activity over that seen for native protein in solution. However, the large, globular and sometimes multimeric nature of many enzymes limits their ability to attach directly to the surface of NPs, especially when the latter are colloidally stabilized with bulky PEGylated ligands. Engineering extended protein linkers into the enzymes to achieve direct attachment through the PEG surface often detrimentally alters the enzymes catalytic ability. Here, we demonstrate an alternate, hybrid biomaterials-based approach to achieving directed enzyme assembly on PEGylated NPs. We self-assemble a unique architecture consisting of a central semiconductor quantum dot (QD) scaffold displaying controlled ratios of extended peptide-DNA linkers which penetrate through the PEG surface to directly couple enzymes to the QD surface. As a test case, we utilize phosphotriesterase (PTE), an enzyme of bio-defense interest due to its ability to hydrolyze organophosphate nerve agents. Moreover, this unique approach still allows PTE to maintain enhanced activity while also suggesting the ability of DNA to enhance enzyme activity in and of itself.

Treatments for autoimmunity - diseases where the immune system mistakenly attacks self-molecules - are not curative and leave patients immunocompromised. New studies aimed at more specific treatments reveal development of inflammation or tolerance is influenced by the form self-antigens are presented. Using a mouse model of multiple sclerosis (MS), we show for the first time that quantum dots (QDs) can be used to generate immunological tolerance by controlling the density of self-antigen on QDs. These assemblies display dense arrangements of myelin self-peptide associated with disease in MS, are uniform in size (

Photonic wires were constructed by sequentially arranging up to 7 fluorophores along a concatenated DNA scaffold. This yielded nanostructures displaying from one- to six-energy transfer steps where end-to-end efficiency reflected the multiple underlying photophysical processes and the ability of long-range interactions to compensate for localized non-ideal dye behaviour.

Biocompatible nanoparticles have recently attracted significant attention due to increasing interest in their use for biological sensing, cellular labeling and in vivo imaging. Semiconductor quantum dots (QDs) with good colloidal stability as well as small hydrodynamic sizes are particularly useful within these applications. We have developed a series of dihydrolipoic acid (DHLA) based surface ligands to enhance the colloidal stability and biocompatibility of water soluble QDs. Modification of DHLA with poly(ethylene glycol) derivatives provided the QDs with extended colloidal stability over a wide pH range and under high salt concentrations, which contrasts with the limited colloidal stability provided by DHLA alone. Functionalization of the PEG termini enabled one to have easy access to the QD surface and construct a variety of stable QD-biomolecules conjugates. A series of DHLA-based compact ligands with zwitterionic character has also been explored to develop compact sized QDs without sacrificing the colloidal stability. Despite their smaller sizes than the PEG analogs, the QDs coated with the zwitterionic ligands still have excellent colloidal stability and minimize nonspecific interactions in biological environments. Recent studies of thiol-based multidentate ligands and ligand exchange methods further improved the colloidal stability and fluorescence quantum yields.

We describe a new, single pot, aqueous phase method for synthesizing water soluble gold nanoparticles (AuNPs) over a size range of 15–130 nm. Poly(ethylene glycol)-appended thioctic acid ligands were used to control the growth rates and stabilize the AuNPs. Critical factors that enable the controlled growth of the AuNPs over this size range include the pH, the choice of reducing agent, the reaction temperature and the sequential addition of gold precursor and ligand with specific ligand-to-gold ratios. We describe the synthetic procedure in detail. Optical and structural characterization of the AuNPs was accomplished using UV–vis absorption spectroscopy, dynamic light scattering, and transmission and scanning electron microscopy.

Rapid and sensitive assay of proteases and their inhibition in a high-throughput manner is of great significance in the diagnostic and pharmaceutical fields. We developed a multiplexed assay system of proteases and their inhibition by measuring the energy transfer between quantum dots (QDs) and gold nanoparticles (AuNPs) on a glass slide. In this system, while the photoluminescence (PL) of donor QDs immobilized on a surface was quenched due to the presence of AuNPs (energy acceptor) in close proximity, the protease activity caused modulation in the efficiency of the energy transfer between the acceptor and donor, thus enabling the protease assay. In comparison to the QD-dye system, the conjugate of the QD-AuNP gave rise to higher energy transfer efficiency, resulting in quantitative assay of proteases with more sensitivity. When matrix metalloproteinase, caspase, and thrombin were tested, a multiplexed assay was successfully achieved since the AuNP could be used as a common energy acceptor in conjunction with QDs having different colors. Our system is anticipated to find applications in the diagnosis of protease-related diseases and screening of potential drugs with high sensitivity in a high-throughput way.

An inhibition assay method was developed based on the modulation in the FRET efficiency between quantum dots (QDs) and gold nanoparticles (AuNPs) in the presence of the molecules which inhibit the interactions between QD- and AuNP-conjugated biomolecules. For the functionalization, AuNPs were first stabilized by chemisorption of n-alkanethiols and then capped with the first generation polyamidoamine (G1 PAMAM) dendrimers. By employing a streptavidin−biotin couple as a model system, avidin was quantitatively analyzed as an inhibitor by sensing the change in photoluminescence (PL) quenching of SA−QDs by biotin−AuNPs. The detection limit for avidin was about 10 nM. It is anticipated that the PL quenching-based sensing system can be used for the quantitative analysis and high throughput screening of molecules which inhibit the specific biomolecular interactions.