High-affinity labeling and tracking of individual histidine-tagged proteins in live cells using Ni2+ tris-nitrilotriacetic acid quantum dot conjugates

Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane

Receptor for advanced glycation endproducts (RAGE) and toll-like receptor 4 (TLR4) are pattern-recognition receptors that bind to molecular patterns associated with pathogens, stress, and cellular damage. Diffusion plays an important role in receptor functionality in the cell membrane. However, there has been no prior investigation of the reciprocal effect of RAGE and TLR4 diffusion properties in the presence and absence of each receptor. This study reports how RAGE and TLR4 affect the mobility of each other in the human embryonic kidney (HEK) 293 cell membrane. Diffusion properties were measured using single-particle tracking (SPT) with quantum dots (QDs) that are selectively attached to RAGE or TLR4. The Brownian diffusion coefficients of RAGE and TLR4 are affected by the presence of the other receptor, leading to similar diffusion coefficients when both receptors coexist in the cell. When TLR4 is present, the average Brownian diffusion coefficient of RAGE increases by 40%, while the presence of RAGE decreases the average Brownian diffusion coefficient of TLR4 by 32%. Diffusion in confined membrane domains is not altered by the presence of the other receptor. The mobility of the cell membrane lipid remains constant whether one or both receptors are present. Overall, this work shows that the presence of each receptor can affect a subset of diffusion properties of the other receptor without affecting the mobility of the membrane.

The Utility of Fluorescence Recovery after Photobleaching (FRAP) to Study the Plasma Membrane

The plasma membrane of mammalian cells is involved in a wide variety of cellular processes, including, but not limited to, endocytosis and exocytosis, adhesion and migration, and signaling. The regulation of these processes requires the plasma membrane to be highly organized and dynamic. Much of the plasma membrane organization exists at temporal and spatial scales that cannot be directly observed with fluorescence microscopy. Therefore, approaches that report on the membrane's physical parameters must often be utilized to infer membrane organization. As discussed here, diffusion measurements are one such approach that has allowed researchers to understand the subresolution organization of the plasma membrane. Fluorescence recovery after photobleaching (or FRAP) is the most widely accessible method for measuring diffusion in a living cell and has proven to be a powerful tool in cell biology research. Here, we discuss the theoretical underpinnings that allow diffusion measurements to be used in elucidating the organization of the plasma membrane. We also discuss the basic FRAP methodology and the mathematical approaches for deriving quantitative measurements from FRAP recovery curves. FRAP is one of many methods used to measure diffusion in live cell membranes; thus, we compare FRAP with two other popular methods: fluorescence correlation microscopy and single-particle tracking. Lastly, we discuss various plasma membrane organization models developed and tested using diffusion measurements.

Molecular and cellular factors determining the functional pleiotropy of cytokines

Cytokines are soluble factors vital for mammalian physiology. Cytokines elicit highly pleiotropic activities, characterized by their ability to induce a wide spectrum of functional responses in a diverse range of cell subsets, which makes their study very challenging. Cytokines activate signalling via receptor dimerization/oligomerization, triggering activation of the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling pathway. Given the strong crosstalk and shared usage of key components of cytokine signalling pathways, a long-standing question in the field pertains to how functional diversity is achieved by cytokines. Here, we discuss how biophysical - for example, ligand-receptor binding affinity and topology - and cellular - for example, receptor, JAK and STAT protein levels, endosomal compartment - parameters contribute to the modulation and diversification of cytokine responses. We review how these parameters ultimately converge into a common mechanism to fine-tune cytokine signalling that involves the control of the number of Tyr residues phosphorylated in the receptor intracellular domain upon cytokine stimulation. This results in different kinetics of STAT activation, and induction of specific gene expression programs, ensuring the generation of functional diversity by cytokines using a limited set of signalling intermediaries. We describe how these first principles of cytokine signalling have been exploited using protein engineering to design cytokine variants with more specific and less toxic responses for immunotherapy.

Magnetically purification/immobilization of poly histidine-tagged proteins by PEGylated magnetic graphene oxide nanocomposites

Carbon-based nanomaterials have many applications in biomedicine due to their unique mechanical, chemical, and biological properties. Among them, graphene has received special attention due to its very high specific surface area, high flexibility, and chemical stability. In this study, graphene oxide was first functionalized with amine groups (GO-NH₂) and then Fe₃O₄ nanoparticles were deposited on it using the hydrothermal method. In addition, polyethylene glycol (PEG) was attached to the magnetic graphene nanoparticles to increase their stability and solubility. Finally, PEGylated magnetic graphene nanocomposites were functionalized with nickel-nitrilotriacetic acid (NTA-Ni⁺²) to bind to the poly-histidine tag in recombinant proteins. The resulting nanocomposites (MG-PEG-NTA-Ni⁺²) were then used for magnetic immobilization and purification of recombinant β-NGF as a protein with his-tag sequence. Binding and purification were confirmed by FTIR and SDS-PAGE techniques, respectively. Importantly, differentiation of the PC12 cell line into neurons demonstrated that the purified β-NGF was fully functional. Our results suggest that MG-PEG-NTA-Ni⁺² nanocomposites may be a suitable alternative to commercial resins for rapid and specific protein immobilization and purification.

Semiconductor quantum dots in photoelectrochemical sensors from fabrication to biosensing applications

Semiconductor quantum dots (QDs) are a promising class of nanomaterials for developing new photoelectrodes and photoelectrochemistry systems for energy storage, transfer, and biosensing applications. These materials have unique electronic and photophysical properties and can be used as optical nanoprobes in displays, biosensors, imaging, optoelectronics, energy storage and energy harvesting. Researchers have recently been exploring the use of QDs in photoelectrochemical (PEC) sensors, which involve exciting a QD-interfaced photoactive material with a flashlight source and generating a photoelectrical current as an output signal. The simple surface properties of QDs also make them suitable for addressing issues related to sensitivity, miniaturization, and cost-effectiveness. This technology has the potential to replace current laboratory practices and equipment, such as spectrophotometers, used for testing sample absorption and emission. Semiconductor QD-based PEC sensors offer simple, fast, and easily miniaturized sensors for analyzing a variety of analytes. This review summarizes the various strategies for interfacing QD nanoarchitectures for PEC sensing, as well as their signal amplification. PEC sensing devices, particularly those used for the detection of disease biomarkers, biomolecules (glucose, dopamine), drugs, and various pathogens, have the potential to revolutionize the biomedical field. This review discusses the advantages of semiconductor QD-based PEC biosensors and their fabrication methods, with a focus on disease diagnostics and the detection of various biomolecules. Finally, the review provides prospects and considerations for QD-based photoelectrochemical sensor systems in terms of their sensitivity, speed, and portability for biomedical applications.

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.

Hybrid gold nanoparticle-quantum dot self-assembled nanostructures driven by complementary artificial proteins

Hybrid nanostructures are constructed by the direct coupling of fluorescent quantum dots and plasmonic gold nanoparticles. Self-assembly is directed by the strong affinity between two artificial α-repeat proteins that are introduced in the capping layers of the nanoparticles at a controlled surface density. The proteins have been engineered to exhibit a high mutual affinity, corresponding to a dissociation constant in the nanomolar range, towards the protein-functionalized quantum dots and gold nanoparticles. Protein-mediated self-assembly is evidenced by surface plasmon resonance and gel electrophoresis. The size and the structure of colloidal superstructures of complementary nanoparticles are analyzed by transmission electron microscopy and small angle X-ray scattering. The size of the superstructures is determined by the number of proteins per nanoparticle. The well-defined geometry of the rigid protein complex sets a highly uniform interparticle distance of 8 nm that affects the emission properties of the quantum dots in the hybrid ensembles. Our results open the route to the design of hybrid emitter-plasmon colloidal assemblies with controlled near-field coupling and better optical response.

Multivalent Chelators for In Vivo Protein Labeling

With the advent of single-molecule methods, chemoselective and site-specific labeling of proteins evolved to become a central aspect in chemical biology as well as cell biology. Protein labeling demands high specificity, rapid as well as efficient conjugation, while maintaining low concentration and biocompatibility under physiological conditions. Generic methods that do not interfere with the function, dynamics, subcellular localization of proteins, and crosstalk with other factors are crucial to probe and image proteins in vitro and in living cells. Alternatives to enzyme-based tags or autofluorescent proteins are short peptide-based recognition tags. These tags provide high specificity, enhanced binding rates, bioorthogonality, and versatility. Here, we report on recent applications of multivalent chelator heads, recognizing oligohistidine-tagged proteins. The striking features of this system has facilitated the analysis of protein complexes by single-molecule approaches.

The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells

Small chemical/biological interaction pairs are at the forefront in tracing protein function and interaction at high signal-to-background ratios in cellular pathways. However, the optimal design of scaffold, linker, and chelator head still deserve systematic investigation to achieve the highest affinity and kinetic stability for in vitro and especially cellular applications. We report on a library of N-nitrilotriacetic acid (NTA)-based multivalent chelator heads (MCHs) built on linear, cyclic, and dendritic scaffolds and compare these with regard to their binding affinity and stability for the labeling of cellular His-tagged proteins. Furthermore, we describe a new approach for tracing cellular target proteins at picomolar probe concentrations in cells. Finally, we outline fundamental differences between the MCH scaffolds and define a cyclic trisNTA chelator that displays the highest affinity and kinetic stability of all reported reversible, low-molecular-weight interaction pairs.

A Fluorescent Chemosensor for Zn2+ Based on a C3-Symmetrical and Pre-Organized 2,2′,2″-Nitrilotribenzoic Acid Material

A C3-symmetrical 4,4″,4⁗-nitrilotris(2′-methyl-[1,1′-biphenyl]-3-carboxylic acid) (4) derived from nitrilotriacetic acid (NTA) was found to selectively bind Zinc(ii) ions both in DMSO or MeOH. A synergistic effect of the anionic counter ion SO42− on the sensing behaviour of 4 to metal ions was clearly observed in DMSO. Interestingly, 4 showed a rapid hypochromatic shift in emission ascribed to the deprotonation and the concomitant formation of a 4–metal complex upon the addition of Zn2+ ions, instead of the bathochromic shift and emission enhancement attributed to the SO42−-involved hydrogen-bonding interaction for Ni2+, Li+, Mg2+, and Na+ ions at ratios below 1:1 in DMSO. The observed sensing process of sulfate salts associated with the SO42−-involved hydrogen-bonding interaction, deprotonation, and the concomitant complexation can also be clearly monitored by titration methods utilising UV-vis, fluorescence, and NMR spectroscopy in solution. In comparison with 4, compound 1 showed an obvious difference in the binding interaction with zinc sulfate in MeOH, probably owing to the decreased acidity. Anion-induced hydrogen-bonding interactions and deprotonation of the COOH protons in the excited state also endowed 4 versatile spectroscopic properties. The addition of F− and SO42− anions resulted in a remarkable enhancement probably related with a rigidifying effect. 2,2′,2″-Nitrilotribenzoic acid can be utilised as a potential scaffold to build a series of conjugated fluorescent sensors by its chelation effect owing to the rigid cavity pre-organised by the triphenylamine moiety and the carboxylic groups and the conjugation extension in the 4,4′,4″ positions.

Fluorescent probes for nanoscopy: four categories and multiple possibilities

Nanoscopy enables breaking down the light diffraction limit and reveals the nanostructures of objects being studied using light. In 2014, three scientists pioneered the development of nanoscopy and won the Nobel Prize in Chemistry. This recognized the achievement of the past twenty years in the field of nanoscopy. However, fluorescent probes used in the field of nanoscopy are still numbered. Here, we review the currently available four categories of probes and existing methods to improve the performance of probes.

His-tag based in situ labelling of progeny viruses for real-time single virus tracking in living cells

Tracking virus infection events in live cells is useful for understanding the mechanism of virus infection, and fluorescent labelling is a critical step. Herein a noninvasive strategy for labelling viruses with His-tags was developed by in situ modifying the cell surface proteins with polypeptides containing His-tags during progeny virus assembly. The His-tagged viruses were further conjugated with Ni²⁺-nitrilotriacetate complex modified quantum dots, and retained their infectivity for real-time single virus tracking in living cells.

HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors

The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Measurement of phosphorylation of p42/44 mitogen-activated protein kinase and of cell growth demonstrated that the HaloTag fusion proteins were biologically active. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins.

Quantum dots: bright and versatile in vitro and in vivo fluorescence imaging biosensors

Colourful cells and tissues: semiconductor quantum dots and their versatile applications in multiplexed bioimaging research.

Aptamer-mediated indirect quantum dot labeling and fluorescent imaging of target proteins in living cells

Protein labeling for dynamic living cell imaging plays a significant role in basic biological research, as well as in clinical diagnostics and therapeutics. We have developed a novel strategy in which the dynamic visualization of proteins within living cells is achieved by using aptamers as mediators for indirect protein labeling of quantum dots (QDs). With this strategy, the target protein angiogenin was successfully labeled with fluorescent QDs in a minor intactness model, which was mediated by the aptamer AL6-B. Subsequent living cell imaging analyses indicated that the QDs nanoprobes were selectively bound to human umbilical vein endothelial cells, gradually internalized into the cytoplasm, and mostly localized in the lysosome organelle, indicating that the labeled protein retained high activity. Compared with traditional direct protein labeling methods, the proposed aptamer-mediated strategy is simple, inexpensive, and provides a highly selective, stable, and intact labeling platform that has shown great promise for future biomedical labeling and intracellular protein dynamic analyses.

Multiplexed modular genetic targeting of quantum dots

While DNA-directed nanotechnology is now a well-established platform for bioinspired nanoscale assembly in vitro, the direct targeting of various nanomaterials in living biological systems remains a significant challenge. Hybrid biological systems with integrated and targeted nanomaterials may have interesting and exploitable properties, so methods for targeting various nanomaterials to precise biological locations are required. Fluorescence imaging has benefited from the use of nanoparticles with superior optical properties compared to fluorescent organic dyes or fluorescent proteins. While single-particle tracking (SPT) in living cells with genetically encoded proteins is limited to very short trajectories, the high photon output of genetically targeted and multiplexed quantum dots (QDs) would enable long-trajectory analysis of multiple proteins. However, challenges with genetic targeting of QDs limit their application in these experiments. In this report, we establish a modular method for targeting QD nanoparticles selectively to multiple genetically encoded tags by precomplexing QD-streptavidin conjugates with cognate biotinylated hapten molecules. This approach enables labeling and SPT of multiple genetically encoded proteins on living cells at high speed and can label expressed proteins in the cytosol upon microinjection into living cells. While we demonstrate labeling with three distinct QD conjugates, the approach can be extended to other specific hapten-affinity molecule interactions and alternative nanoparticles, enabling precise directed targeting of nanoparticles in living biological systems.

Revisiting 30 years of biofunctionalization and surface chemistry of inorganic nanoparticles for nanomedicine

In the last 30 years we have assisted to a massive advance of nanomaterials in material science. Nanomaterials and structures, in addition to their small size, have properties that differ from those of larger bulk materials, making them ideal for a host of novel applications. The spread of nanotechnology in the last years has been due to the improvement of synthesis and characterization methods on the nanoscale, a field rich in new physical phenomena and synthetic opportunities. In fact, the development of functional nanoparticles has progressed exponentially over the past two decades. This work aims to extensively review 30 years of different strategies of surface modification and functionalization of noble metal (gold) nanoparticles, magnetic nanocrystals and semiconductor nanoparticles, such as quantum dots. The aim of this review is not only to provide in-depth insights into the different biofunctionalization and characterization methods, but also to give an overview of possibilities and limitations of the available nanoparticles.

High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies

There is significant demand for experimental approaches to aid protein localization in electron microscopy micrographs and ultimately in three-dimensional reconstructions of macromolecular assemblies. We report preparation and use of a reagent consisting of tris-nitrilotriacetic acid (tris-NTA) conjugated with a monofunctional gold nanoparticle ((AuNP)tris-NTA) for site-specific, non-covalent labeling of protein termini fused to a histidine-tag (His-tag). Multivalent binding of tris-NTA to a His-tag via complexed Ni(II) ions results in subnanomolar affinity and a defined 1:1 stoichiometry. Precise localization of (AuNP)tris-NTA labeled proteins by electron microscopy is further ensured by the reagent's short conformationally restricted linker. We used (AuNP)tris-NTA to localize His-tagged proteins in an oligomeric ATPase and in the bacterial 50S ribosomal subunit. (AuNP)tris-NTA can specifically bind to the target proteins in these assemblies and is clearly discernible. Our labeling reagent should find broad application in noncovalent, site-specific labeling of protein termini to pinpoint their location in macromolecular assemblies.

Photoligation combined with zwitterion-modified lipoic acid ligands provides compact and biocompatible quantum dots

We describe the design and synthesis of a series of compact ligands made of lipoic acid (LA)-based coordinating anchors and hydrophilic zwitterion groups. This ligand design is combined with a novel photoligation strategy to promote the transfer of QDs to polar and buffer media. This approach has provided hydrophilic QDs that exhibit great colloidal stability over a broad range of pHs and in the presence of cell culture media. Our photoligation strategy drastically improves previous phase transfer methods by eliminating the need for chemical reduction of the dithiolane ring using NaBH4 prior to the cap exchange, and it is adapted to several LA-based ligands. We also found that QDs stabilized with these compact zwitterionic ligands are fully compatible with metal-histidine-driven self-assembly where the protein activity is maintained after forming conjugation with the QDs.

Multifarious determinants of cytokine receptor signaling specificity

Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.

Multidentate zwitterionic ligands provide compact and highly biocompatible quantum dots

Hydrophilic functional semiconductor nanocrystals that are also compact provide greatly promising platforms for use in bioinspired applications and are thus highly needed. To address this, we designed a set of metal coordinating ligands where we combined two lipoic acid groups, bis(LA)-ZW, (as a multicoordinating anchor) with a zwitterion group for water compatibility. We further combined this ligand design with a new photoligation strategy, which relies on optical means instead of chemical reduction of the lipoic acid, to promote the transfer of CdSe-ZnS QDs to buffer media. In particular, we found that the QDs photoligated with this zwitterion-terminated bis(lipoic) acid exhibit great colloidal stability over a wide range of pHs, to an excess of electrolytes, and in the presence of growth media and reducing agents, in addition to preserving their optical and spectroscopic properties. These QDs are also stable at nanomolar concentrations and under ambient conditions (room temperature and white light exposure), a very promising property for fluorescent labeling in biology. In addition, the compact ligands permitted metal-histidine self-assembly between QDs photoligated with bis(LA)-ZW and two different His-tagged proteins, maltose binding protein and fluorescent mCherry protein. The remarkable stability of QDs capped with these multicoordinating and compact ligands over a broad range of conditions and at very small concentrations, combined with the compatibility with metal-histidine conjugation, could be very useful for a variety of applications, ranging from protein tracking and ligand-receptor binding to intracellular sensing using energy transfer interactions.

Combining ligand design with photoligation to provide compact, colloidally stable, and easy to conjugate quantum dots

We describe the design and synthesis of two compact multicoordinating (lipoic acid-appended) zwitterion ligands for the capping of luminescent quantum dots, QDs. This design is combined with a novel and easy to implement photoligation strategy to promote the in situ ligand exchange and transfer of the QDs to buffer media. This method involves the irradiation of the native hydrophobic nanocrystals in the presence of the ligands, which promotes in situ cap exchange and phase transfer of the QDs, eliminating the need for a chemical reduction of the dithiolane groups. Applied to the present LA-zwitterion ligands, this route has provided QDs with high photoluminescence yields and excellent colloidal stability over a broad range of conditions, including acidic and basic pH, in the presence of growth media and excess salt conditions. The small lateral extension of the capping layer allowed easy conjugation of the QDs to globular proteins expressing a terminal polyhistidine tag, where binding is promoted by metal-affinity interactions between the accessible Zn-rich surface and imidazoles in the terminal tag of the proteins. The ability to carry out conjugation in acidic as well as basic conditions opens up the possibility to use such self-assembled QD-protein conjugates in various biological applications.

Functionalized quantum dots for biosensing and bioimaging and concerns on toxicity

Considerable efforts have been devoted to the development of novel functionalized nanomaterials for bio-oriented applications. With unique optical properties and molar scale production, colloidal photoluminescent quantum dots (QDs) have been properly functionalized with controlled interfaces as new class of optical probes with extensive use in biomedical research. In this review, we present a brief summary on the current research interests of using fine engineered QDs as a nanoplatform for biomedical sensing and imaging applications. In addition, recent concerns on the potential toxic effects of QDs are described as a general guidance for the development on QD formulations in future studies.

Electrostatically controlled quantum dot monofunctionalization for interrogating the dynamics of protein complexes in living cells

Quantum dots (QD) are powerful labels for probing diffusion and interaction dynamics of proteins on the single molecule level in living cells. Protein cross-linking due to multifunctional QD strongly affects these properties. This becomes particularly critical when labeling interaction partners with QDs for interrogating the dynamics of complexes. We have here implemented a generic method for QD monofunctionalization based on electrostatic repulsion of a highly negatively charged peptide carrier. On the basis of this method, monobiotinylated QDs were prepared with high yield as confirmed by single molecule assays. These QDs were successfully employed for probing the assembly and diffusion dynamics of binary and ternary cytokine-receptor complexes on the surface of living cells by dual color single QD tracking. Thus, sequential and dynamic recruitment of the type I interferon receptor subunits by the ligand could be observed.

Quantum dot targeting with lipoic acid ligase and HaloTag for single-molecule imaging on living cells

We present a methodology for targeting quantum dots to specific proteins on living cells in two steps. In the first step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches 10-bromodecanoic acid onto a 13 amino acid recognition sequence that is genetically fused to a protein of interest. In the second step, quantum dots derivatized with HaloTag, a modified haloalkane dehalogenase, react with the ligated bromodecanoic acid to form a covalent adduct. We found this targeting method to be specific, fast, and fully orthogonal to a previously reported and analogous quantum dot targeting method using E. coli biotin ligase and streptavidin. We used these two methods in combination for two-color quantum dot visualization of different proteins expressed on the same cell or on neighboring cells. Both methods were also used to track single molecules of neurexin, a synaptic adhesion protein, to measure its lateral diffusion in the presence of neuroligin, its trans-synaptic adhesion partner.

Quantum dots: synthesis, bioapplications, and toxicity

This review introduces quantum dots (QDs) and explores their properties, synthesis, applications, delivery systems in biology, and their toxicity. QDs are one of the first nanotechnologies to be integrated with the biological sciences and are widely anticipated to eventually find application in a number of commercial consumer and clinical products. They exhibit unique luminescence characteristics and electronic properties such as wide and continuous absorption spectra, narrow emission spectra, and high light stability. The application of QDs, as a new technology for biosystems, has been typically studied on mammalian cells. Due to the small structures of QDs, some physical properties such as optical and electron transport characteristics are quite different from those of the bulk materials.

Comprehensive analysis of the effects of CdSe quantum dot size, surface charge, and functionalization on primary human lung cells

The growing potential of quantum dots (QDs) in applications as diverse as biomedicine and energy has provoked much dialogue about their conceivable impact on human health and the environment at large. Consequently, there has been an urgent need to understand their interaction with biological systems. Parameters such as size, composition, surface charge, and functionalization can be modified in ways to either enhance biocompatibility or reduce their deleterious effects. In the current study, we simultaneously compared the impact of size, charge, and functionalization alone or in combination on biological responses using primary normal human bronchial epithelial cells. Using a suite of cellular end points and gene expression analysis, we determined the biological impact of each of these properties. Our results suggest that positively charged QDs are significantly more cytotoxic compared to negative QDs. Furthermore, while QDs functionalized with long ligands were found to be more cytotoxic than those functionalized with short ligands, negative QDs functionalized with long ligands also demonstrated size-dependent cytotoxicity. We conclude that QD-elicited cytotoxicity is not a function of a single property but a combination of factors. The mechanism of toxicity was found to be independent of reactive oxygen species formation, as cellular viability could not be rescued in the presence of the antioxidant n-acetyl cysteine. Further exploring these responses at the molecular level, we found that the relatively benign negative QDs increased gene expression of proinflammatory cytokines and those associated with DNA damage, while the highly toxic positive QDs induced changes in genes associated with mitochondrial function. In an attempt to tentatively "rank" the contribution of each property in the observed QD-induced responses, we concluded that QD charge and ligand length, and to a lesser extent, size, are key factors that should be considered when engineering nanomaterials with minimal bioimpact (charge > functionalization > size).

Luminescent nanoparticles and their use for in vitro and in vivo diagnostics

Fluorescence spectroscopy has been shown to be a useful tool for a broad variety of biological and medical applications. Many of the analytical methods, as used for tumor marker and gene mutation detection, recognition of pathogens or monitoring of cell-related processes, are based on the labeling of the investigating object with luminescent nanoparticles. Owing to their size, which is comparable to that of biomolecules, and to their extraordinary optical properties, luminescent nanoparticles could well improve the sensitivity and flexibility of current detection techniques. This article provides a general overview of the synthesis, properties and application of luminescent semiconductor, metal and inorganic nanoparticles for in vitro and in vivo diagnostics, also reflecting the aspect of biocompatibility.

Luminescent quantum dots as platforms for probing in vitro and in vivo biological processes

In this report we review some of the recent progress made for enhancing the biocompatibility of luminescent quantum dots (QDs) and for developing targeted bio-inspired applications centered on live cell imaging and sensing. We start with a detailed analysis of the surface functionalization strategies developed thus far, and discuss their effectiveness for providing long term stability of the quantum dots in biological media, to changes in pH and to added electrolytes. We then discuss the available conjugation techniques to couple QDs to a variety of biological receptors and compare their effectiveness. In particular, we highlight the implementation of new strategies such as the use of copper-free cyclo-addition reaction (CLICK) chemistry and chemo-selective ligation. We then discuss the advances made for intracellular delivery where ideas such as receptor-driven endocytosis and uptake promoted by cell penetrating peptides are used. We then describe a few representative examples where QDs have been used to investigate specific cell biology processes. Such processes include binding of QDs conjugated to the nerve growth factor to membrane specific receptors and intracellular uptake, tracking of membrane protein at the single molecule level, and recognition of ligand bound QDs by T cell receptors. We conclude by discussing issues of toxicity associated with the use of QDs in biology.

Quantum dots to tail single bio-molecules inside living cells

In the last two decades, the single particle and single molecule approach became more and more popular to investigate the activity and the mechano-chemical properties of biological molecules. The inherent limit of these assays was that the molecules of interest were observed in vitro, out of their natural environment, the cell. Several recent works have shown the possibility to overcome this limit, to extend this approach to living cells and to observe the details of many cellular processes at the molecular level. In this review we discuss the use of semiconductor quantum dots to perform single particle and single molecule tracking in the cell. We refer to other articles for the technical aspects of this method. Here, after an introduction on the advantages provided by these nanoparticles, we restrict ourselves to some examples, mainly related to intracellular transport and molecular motor activity. These will illustrate the important role played by semiconductor quantum dots as fluorescent nano-reporters in in cell single molecule approach in modern biology and biophysics.

Enabling biomedical research with designer quantum dots

Quantum Dots (QDs) are a new class of semiconductor nanoparticulate luminophores, which are actively researched for novel applications in biology and nanomedicine. In this review, the recent progress in the design and applications of QD labels for in vitro and in vivo imaging of cells is presented. Surface chemical engineering of hydrophobic QDs is required to render them water soluble and biocompatible. Further surface modification and attachment of bioactive molecules to the surface of QDs, such as peptides, aptamers, or antibodies are intensively explored for targeted imaging of living cells, and disease states in animals. Specially designed surface coatings can drastically decrease nonspecific interactions between QDs and cells, minimize degradation of QDs under in vivo physiological conditions, reduce the cytotoxicity of QDs, and prolong circulation lifetimes in animals. New generations of QD probes are also promising for imaging cellular processes at the single-molecule level. Ultimately, QDs as components of complex therapeutic nanosystems are poised to contribute significantly to the field of personalized medicine.

Dynamics of lesion processing by bacterial nucleotide excision repair proteins

Single-molecule approaches permit an unrivalled view of how complex systems operate and have recently been used to understand DNA-protein interactions. These tools have enabled advances in a particularly challenging problem, the search for damaged sites on DNA. DNA repair proteins are present at the level of just a few hundred copies in bacterial cells to just a few thousand in human cells, and they scan the entire genome in search of their specific substrates. How do these proteins achieve this herculean task when their targets may differ from undamaged DNA by only a single hydrogen bond? Here we examine, using single-molecule approaches, how the prokaryotic nucleotide excision repair system balances the necessity for speed against specificity. We discuss issues at a theoretical, biological, and technical level and finally pose questions for future research.

Aqueous phase transfer of InP/ZnS nanocrystals conserving fluorescence and high colloidal stability

Small thiol-containing amino acids such as cysteine are appealing surface ligands for transferring semiconductor quantum dots (QDs) from organic solvents to the aqueous phase. They provide a compact hydrodynamic diameter and low nonspecific binding in biological environment. However, cysteine-capped QDs generally exhibit modest colloidal stability in water and their fluorescence quantum yield (QY) is significantly reduced as compared to organics. We demonstrate that during phase transfer the deprotonation of the thiol group by carefully adjusting the pH is of crucial importance for increasing the binding strength of cysteine to the QD surface. As a result, the colloidal stability of cysteine-capped InP/ZnS core/shell QDs is extended from less than one day to several months. The developed method is of very general character and can be used also with other hydrophilic thiols and various other types of QDs, e.g., CdSe/CdS/ZnS and CuInS(2)/ZnS QDs as well as CdSe and CdSe/CdS nanorods. We show that the observed decrease of QY upon phase transfer with cysteine is related to the generation of cysteine dimer, cystine. This side-reaction implies the formation of disulfide bonds, which efficiently trap photogenerated holes and inhibit radiative recombination. On the other hand, this process is not irreversible. By addition of an appropriate reducing agent, tris(2-carboxyethyl)phosphine hydrochloride (TCEP), the QY can be partially recovered. When TCEP is already added during the phase transfer, the QY of cysteine-capped InP/ZnS QDs can be maintained almost quantitatively. Finally, we show that penicillamine is a promising alternative to cysteine for the phase transfer of QDs, as it is much less prone to disulfide formation.

Quantum dots find their stride in single molecule tracking

Thirteen years after the demonstration of quantum dots as biological imaging agents, and nine years after the initial commercial introduction of bioconjugated quantum dots, the brightness and photostability of the quantum dots has enabled a range of investigations using single molecule tracking. These materials are being routinely utilized by a number of groups to track the dynamics of single molecules in reconstituted biophysical systems and on living cells, and are especially powerful for investigations of single molecules over long timescales with short exposure times and high pointing accuracy. New approaches are emerging where the quantum dots are used as 'hard-sphere' probes for intracellular compartments. Innovations in quantum dot surface modification are poised to substantially expand the utility of these materials.

ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding

The extent to which ligand occupancy and dimerization contribute to erbB1 signaling is controversial. To examine this, we utilized two-color Quantum Dot tracking for visualization of erbB1 homodimerization and quantification of the dimer off rate (k_off) on living cells. Kinetic parameters were extracted using a 3-state Hidden Markov Model to identify transition rates between free, co-confined, and dimerized states. We report that dimers composed of 2 ligand-bound receptors are long-lived and their k_off is independent of kinase activity. By comparison, unliganded dimers have >4-fold faster k_off. Transient co-confinement of receptors promotes repeated encounters and enhances dimer formation. Mobility decreases >6-fold when ligand-bound receptors dimerize. Blockade of erbB1 kinase activity or disruption of actin networks results in faster diffusion of receptor dimers. These results implicate both signal propagation and the cortical cytoskeleton in reduced mobility of signaling-competent erbB1 dimers.