Stable small quantum dots for synaptic receptor tracking on live neurons

Enzyme-Responsive Modular Peptides Enhance Tumor Penetration of Quantum Dots via Charge Reversal Strategy

Quantum dots (QDs) are colloidal semiconductor nanoparticles acting as fluorescent probes for detection, disease diagnosis, and photothermal and photodynamic therapy. However, their performance in cancer treatment is limited by inadequate tumor accumulation and penetration due to the larger size of nanoparticles compared to small molecules. To address this challenge, charge reversal nanoparticles offer an effective strategy to prolong blood circulation time and achieve enhanced endocytosis and tumor penetration. In this study, we leveraged the overexpressed γ-glutamyl transpeptidase (GGT) in many human tumors and developed a library of modular peptides to serve as water-soluble surface ligands of QDs. We successfully transferred the QDs from the organic phase to the aqueous phase within 5 min. And through systematic tuning of the peptide sequence, we optimized the fluorescent stability of QDs and their charge reversal behavior in response to GGT. The resulting optimal peptide stabilized QDs in aqueous solution with a high fluorescent retention rate of 93% after three months and realized the surface charge reversal of QDs triggered by GGT in vitro. The binding between the peptide and QD surface was investigated by using saturation transfer differential nuclear magnetic resonance (STD NMR). Thanks to its charge reversal ability, the GGT-responsive QDs exhibited enhanced cellular uptake in GGT-expressing cancer cells and deeper penetration in the 3D multicellular spheroids. This enzyme-responsive modular peptide can lead to specific tumor targeting and deeper tumor penetration, holding great promise to enhance the treatment efficacy of QD-based theranostics.

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments

Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.

Compact, Fast Blinking Cd-Free Quantum Dots for Super-Resolution Fluorescence Imaging

Quantum dots (QDs) can be used as fluorescent probes in single molecule localization microscopy to achieve subdiffraction limit resolution (super-resolution fluorescence imaging). However, the toxicity of Cd in the prototypical CdSe-based QDs can limit their use in biological applications. Furthermore, commercial CdSe QDs are usually modified with relatively thick shells of both inorganic and organic materials to render them in the 10-20 nm size range, which is relatively large for biological labels. In this report, we present compact (4-6 nm) CuInS2/ZnS (CIS/ZnS) and compare them to commercially sourced CdSe/ZnS QDs for their blinking behavior, localization precision and super-resolution imaging. Although commercial CdSe/ZnS QDs are brighter than the more compact Cd-free CIS/ZnS QD, both give comparable results of 4.5-5.0-fold improvement in imaging resolution over conventional TIRF imaging of actin filaments. This likely results from the fact that CIS/ZnS QDs show very short on-times and long off times which leads to less overlap in the point spread functions of emitting CIS/ZnS QD labels on the actin filaments at the same labeling density. These results demonstrate that CIS/ZnS QDs are an excellent candidate to complement and perhaps even replace the larger and more toxic CdSe-based QDs for robust single- molecule super-resolution imaging.

Significance of Capping Agents of Colloidal Nanoparticles from the Perspective of Drug and Gene Delivery, Bioimaging, and Biosensing: An Insight

The over-growth and coagulation of nanoparticles is prevented using capping agents by the production of stearic effect that plays a pivotal role in stabilizing the interface. This strategy of coating the nanoparticles’ surface with capping agents is an emerging trend in assembling multipurpose nanoparticles that is beneficial for improving their physicochemical and biological behavior. The enhancement of reactivity and negligible toxicity is the outcome. In this review article, an attempt has been made to introduce the significance of different capping agents in the preparation of nanoparticles. Most importantly, we have highlighted the recent progress, existing roadblocks, and upcoming opportunities of using surface modified nanoparticles in nanomedicine from the drug and gene delivery, bioimaging, and biosensing perspectives.

Quantum Dots with a Compact Amphiphilic Zwitterionic Coating

Generally speaking, it is difficult to keep nanomaterials encapsulated in amphiphilic polymers like octylamine-grafted poly(acrylic acid) (OPA) compact in coating-layer, with a small hydrodynamic size. Here, we prepared stable hydrophilic quantum dots (QDs) via encapsulation in ∼3 nm-long amphiphilic and zwitterionic (AZ) molecules. After encapsulation with AZ molecules, the coated QDs are only 2.1 nm thicker in coating, instead of 5.4 nm with OPA. Meanwhile, the hydrodynamic sizes of CdSe/CdS, ZnCdSeS, ZnCdSe/ZnS, and CdSe/ZnS QDs encapsulated in AZ molecules (AZ-QDs) are less than 15 nm, and 6-7 nm smaller than those of QDs in OPA (OPA-QDs). Notably, both extracellular and intracellular nonspecific binding of AZ-QDs is approximately 100-folds lower than that of OPA-QDs.

Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging

Quantum dots (QDs) are a class of semiconductor nanocrystal used broadly as fluorescent emitters for analytical studies in the life sciences. These nanomaterials are particularly valuable for single-particle imaging and tracking applications in cells and tissues. An ongoing technological goal is to reduce the hydrodynamic size of QDs to enhance access to sterically hindered biological targets. Multidentate polymer coatings are a focus of these efforts and have resulted in compact and stable QDs with hydrodynamic diameters near 10 nm. New developments are needed to reach smaller sizes to further enhance transport through pores in cells and tissues. Here, we describe how structural characteristics of linear multidentate copolymers determine hydrodynamic size, colloidal stability, and biomolecular interactions of coated QDs. We tune copolymer composition, degree of polymerization, and hydrophilic group length, and coat polymers on CdSe and (core)shell (HgCdSe)CdZnS QDs. We find that a broad range of polymer structures and compositions yield stable colloidal dispersions; however, hydrodynamic size minimization and nonspecific binding resistance can only be simultaneously achieved within a narrow range of properties, requiring short polymers, balanced compositions, and small nanocrystals. In quantitative single-molecule imaging assays in synapses of live neurons, size reduction progressively increases labeling specificity of neurotransmitter receptors. Our findings provide a design roadmap to next-generation QDs with sizes approaching fluorescent protein labels that are the standard of many live-cell biomolecular studies.

Antibody Self-Assembly Maximizes Cytoplasmic Immunostaining Accuracy of Compact Quantum Dots

Antibody conjugates of quantum dots (QDs) are expected to transform immunofluorescence staining by expanding multiplexed analysis and improving target quantification. Recently, a new generation of small QDs coated with multidentate polymers has improved QD labeling density in diverse biospecimens, but new challenges prevent their routine use. In particular, these QDs exhibit nonspecific binding to fixed cell nuclei and their antibody conjugates have random attachment orientations. This report describes four high-efficiency chemical approaches to conjugate antibodies to compact QDs. Methods include click chemistry and self-assembly through polyhistidine coordination, both with and without adaptor proteins that directionally orient antibodies. Specific and nonspecific labeling are independently analyzed after application of diverse blocking agent classes, and a new assay is developed to quantitatively measure intracellular labeling density based on microtubule stain connectivity. Results show that protein conjugation to the QD surface is required to simultaneously eliminate nonspecific binding and maintain antigen specificity. Of the four conjugation schemes, polyhistidine-based coordination of adaptor proteins with antibody self-assembly yields the highest intracellular staining density and the simplest conjugation procedure. Therefore, antibody and adaptor protein orientation, in addition to blocking optimization, are important determinants of labeling outcomes, insights that can inform translational development of these more compact nanomaterials.

Quantum Dots for Improved Single-Molecule Localization Microscopy

Colloidal semiconductor quantum dots (QDs) have long established their versatility and utility for the visualization of biological interactions. On the single-particle level, QDs have demonstrated superior photophysical properties compared to organic dye molecules or fluorescent proteins, but it remains an open question as to which of these fundamental characteristics are most significant with respect to the performance of QDs for imaging beyond the diffraction limit. Here, we demonstrate significant enhancement in achievable localization precision in QD-labeled neurons compared to neurons labeled with an organic fluorophore. Additionally, we identify key photophysical parameters of QDs responsible for this enhancement and compare these parameters to reported values for commonly used fluorophores for super-resolution imaging.

Optimizing Quantum Dot Probe Size for Single-Receptor Imaging

Quantum dots (QDs) are nanocrystals with bright fluorescence and long-term photostability, attributes particularly beneficial for single-molecule imaging and molecular counting in the life sciences. The size of a QD nanocrystal determines its physicochemical and photophysical properties, both of which dictate the success of imaging applications. Larger nanocrystals typically have better optical properties, with higher brightness, red-shifted emission, reduced blinking, and greater stability. However, larger nanocrystals introduce molecular-labeling biases due to steric hindrance and nonspecific binding. Here, we systematically analyze the impact of nanocrystal size on receptor labeling in live and fixed cells. We designed three (core)shell QDs with red emission (600-700 nm) and crystalline sizes of 3.2, 5.5, and 8.3 nm. After coating with the same multidentate polymer, hydrodynamic sizes were 9.2 nm (QD9.2), 13.3 nm (QD13.3), and 17.4 nm (QD17.4), respectively. The QDs were conjugated to streptavidin and applied as probes for biotinylated neurotransmitter receptors. QD9.2 exhibited the highest labeling specificity for receptors in the narrow synaptic cleft (∼20-30 nm) in living neurons. However, for dense receptor labeling for molecular counting in live and fixed HeLa cells, QD13.3 yielded the highest counts. Nonspecific binding rose sharply for hydrodynamic sizes larger than 13.3 nm, with QD17.4 exhibiting particularly diminished specificity. Our comparisons further highlight needs to continue engineering the smallest QDs to increase single-molecule intensity, suppress blinking frequency, and inhibit nonspecific labeling in fixed and permeabilized cells. These results lay a foundation for designing QD probes with further reduced sizes to achieve unbiased labeling for quantitative and single-molecule imaging.

Engineering the Bio-Nano Interface Using a Multifunctional Coordinating Polymer Coating

In the past three decades, interest in using nanoparticles as diagnostic tools to interrogate various biosystems has witnessed remarkable growth. For instance, it has been shown that nanoparticle probes enable the study of cellular processes at the single molecule level. These advances provide new opportunities for understanding fundamental problems in biology, innovation in medicine, and the treatment of diseases. A multitude of nanoparticles have been designed to facilitate in vitro or in vivo sensing, imaging, and diagnostics. Some of those nanoparticle platforms are currently in clinical trials or have been approved by the U.S. Food and Drug Administration. Nonetheless, using nanoparticles in biology is still facing several obstacles, such as poor colloidal stability under physiological conditions, nonspecific interactions with serum proteins, and low targeting efficiency in biological fluids, in addition to issues of uncontrolled biodistribution and cytotoxicity. All these problems are primarily controlled by the surface stabilizing coating used.In this Account, we summarize recent progress made in our laboratory focused on the development of multifunctional polymers as coordinating ligands, to tailor the surface properties of nanoparticles and facilitate their application in biology. We first detail the advantageous features of the coating strategy, followed by a discussion of the key parameters in the ligand design. We then describe the synthesis and use of a series of multicoordinating polymers as ligands optimized for coating quantum dots (QDs), gold nanoparticles (AuNPs), and magnetic nanoparticles (MNPs), with a focus on (i) how to improve the colloidal stability and antifouling performance of materials in biological conditions; (ii) how to design highly compact coating, without compromising colloidal stability; and (iii) how to tailor the surface functionalities to achieve conjugation to target biomolecules. We also highlight the ability of a phase transfer strategy, mediated by UV irradiation, to promote rapid ligand exchange while preserving the integrity of key functional groups. We then summarize the bioconjugation approaches applied to polymer-coated nanoparticles, with emphasis on the ability of metal-histidine self-assembly and click chemistry, to control the final nanoparticle bioconjugates. Finally, we demonstrate the use of polymer-coated nanoparticles for sensor design based on redox-active interactions and peptide-mediated intracellular delivery. We anticipate that the coating design presented in this Account would advance the integration of nanoparticles into biology and medicine.

Zwitterion and Oligo(ethylene glycol) Synergy Minimizes Nonspecific Binding of Compact Quantum Dots

Quantum dots (QDs) are a class of fluorescent nanocrystals in development as labels for molecular imaging in cells and tissues. Recently, coatings for quantum dots based on multidentate polymers have improved labeling performance in a range of bioanalytical applications, primarily due to reduced probe hydrodynamic size. Now, an ongoing challenge is to eliminate nonspecific binding between these small probes and cellular components that mask specifically labeled molecules. Here, we describe insights into controlling and minimizing intermolecular interactions governing nonspecific binding using multidentate polymers with tunable hydrophilic functional groups that are cationic, anionic, zwitterionic (ZW), or nonionic (oligoethylene glycol; OEG). By fixing surface-binding groups and polymer length, coated colloids have similar sizes but diverse physicochemical properties. We measure binding to globular proteins, fixed cells, and living cells and observe a substantial improvement in nonspecific binding resistance when surfaces are functionalized with a combination of ZW and OEG. The independent underlying effects of counterion adsorption and flexibility appear to synergistically resist adsorption when combined, particularly for fixed cells enriched in both charged and hydrophobic moieties. We further show that ZW-OEG QDs are stable under diverse conditions and can be self-assembled with antibodies to specifically label surface antigens on living cells and cytoplasmic proteins in fixed cells. This surface engineering strategy can be adopted across the diverse range of colloidal materials currently in use and in development for biomedical applications to optimize their molecular labeling specificity.

Pin1 Binding to Phosphorylated PSD-95 Regulates the Number of Functional Excitatory Synapses

The post-synaptic density protein 95 (PSD-95) plays a central role in excitatory synapse development and synaptic plasticity. Phosphorylation of the N-terminus of PSD-95 at threonine 19 (T19) and serine 25 (S25) decreases PSD-95 stability at synapses; however, a molecular mechanism linking PSD-95 phosphorylation to altered synaptic stability is lacking. Here, we show that phosphorylation of T19/S25 recruits the phosphorylation-dependent peptidyl-prolyl cis-trans isomerase (Pin1) and reduces the palmitoylation of Cysteine 3 and Cysteine 5 in PSD-95. This reduction in PSD-95 palmitoylation accounts for the observed loss in the number of dendritic PSD-95 clusters, the increased AMPAR mobility, and the decreased number of functional excitatory synapses. We find the effects of Pin1 overexpression were all rescued by manipulations aimed at increasing the levels of PSD-95 palmitoylation. Therefore, Pin1 is a key signaling molecule that regulates the stability of excitatory synapses and may participate in the destabilization of PSD-95 following the induction of synaptic plasticity.

Short-Wave Infrared Quantum Dots with Compact Sizes as Molecular Probes for Fluorescence Microscopy

Materials with short-wave infrared (SWIR) emission are promising contrast agents for in vivo animal imaging, providing high-contrast and high-resolution images of blood vessels in deep tissues. However, SWIR emitters have not been developed as molecular labels for microscopy applications in the life sciences, which require optimized probes that are bright, stable, and small. Here, we design and synthesize semiconductor quantum dots (QDs) with SWIR emission based on HgxCd1-xSe alloy cores red shifted to the SWIR by epitaxial deposition of thin HgxCd1-xS shells with a small band gap. By tuning alloy composition alone, the emission can be shifted across the visible-to-SWIR (VIR) spectra while maintaining a small and equal size, allowing direct comparisons of molecular labeling performance across a broad range of wavelength. After coating with click-functional multidentate polymers, the VIR-QD spectral series has high quantum yield in the SWIR (14-33%), compact size (13 nm hydrodynamic diameter), and long-term stability in aqueous media during continuous excitation. We show that these properties enable diverse applications of SWIR molecular probes for fluorescence microscopy using conjugates of antibodies, growth factors, and nucleic acids. A broadly useful outcome is a 10-55-fold enhancement of the signal-to-background ratio at both the single-molecule level and the ensemble level in the SWIR relative to visible wavelengths, primarily due to drastically reduced autofluorescence. We anticipate that VIR-QDs with SWIR emission will enable ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluorescence.

Ligand-conjugated quantum dots for fast sub-diffraction protein tracking in acute brain slices

Semiconductor quantum dots (QDs) have demonstrated utility in long-term single particle tracking of membrane proteins in live cells in culture. To extend the superior optical properties of QDs to more physiologically relevant cell platforms, such as acute brain slices, we examine the photophysics of compact ligand-conjugated CdSe/CdS QDs using both ensemble and single particle analysis in brain tissue media. We find that symmetric core passivation is critical for both photostability in oxygenated media and for prolonged single particle imaging in brain slices. We then demonstrate the utility of these QDs by imaging single dopamine transporters in acute brain slices, achieving 20 nm localization precision at 10 Hz frame rates. These findings detail design requirements needed for new QD probes in complex living environments, and open the door to physiologically relevant studies that capture the utility of QD probes in acute brain slices.

Bright sub-20-nm cathodoluminescent nanoprobes for electron microscopy

Electron microscopy has been instrumental in our understanding of complex biological systems. Although electron microscopy reveals cellular morphology with nanoscale resolution, it does not provide information on the location of different types of proteins. An electron-microscopy-based bioimaging technology capable of localizing individual proteins and resolving protein-protein interactions with respect to cellular ultrastructure would provide important insights into the molecular biology of a cell. Here, we synthesize small lanthanide-doped nanoparticles and measure the absolute photon emission rate of individual nanoparticles resulting from a given electron excitation flux (cathodoluminescence). Our results suggest that the optimization of nanoparticle composition, synthesis protocols and electron imaging conditions can lead to sub-20-nm nanolabels that would enable high signal-to-noise localization of individual biomolecules within a cellular context. In ensemble measurements, these labels exhibit narrow spectra of nine distinct colours, so the imaging of biomolecules in a multicolour electron microscopy modality may be possible.

Advances in Nanomaterials for Brain Microscopy

Microscopic imaging of the brain continues to reveal details of its structure, connectivity, and function. To further improve our understanding of the emergent properties and functions of neural circuits, new methods are necessary to directly visualize the relationship between brain structure, neuron activity, and neurochemistry. Advances in engineering the chemical and optical properties of nanomaterials concurrent with developments in deep-tissue microscopy hold tremendous promise for overcoming the current challenges associated with in vivo brain imaging, particularly for imaging the brain through optically-dense brain tissue, skull, and scalp. To this end, developments in nanomaterials offer much promise toward implementing tunable chemical functionality for neurochemical targeting and sensing, and fluorescence stability for long-term imaging. In this review, we summarize current brain microscopy methods and describe the diverse classes of nanomaterials recently leveraged as contrast agents and functional probes for microscopic optical imaging of the brain.

A Revised View on the Role of Surface AMPAR Mobility in Tuning Synaptic Transmission: Limitations, Tools, and Alternative Views

Calcium dynamics in presynaptic terminals regulate the response dynamics of most central excitatory synapses. However, this dogma has been challenged by the hypothesis that mobility of the postsynaptic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype glutamate receptors (AMPAR) plays a role in tuning fast excitatory synaptic transmission. In this review, we reevaluate the factors regulating postsynaptic AMPAR mobility, reassess the modeling parameters, analyze the experimental tools, and end by providing alternative ideas stemming from recent results. In particular, newer methods of labeling AMPARs with small fluorophores in live neurons, combined with super-resolution microscopy and sub-second dynamics, lends support to the idea that AMPARs are primarily within the synapse, are greatly constrained, and have much slower mobility than previously thought. We discuss new experiments which may be necessary to readdress the role of postsynaptic AMPAR mobility in tuning fast excitatory synaptic transmission.

Minimizing ATP depletion by oxygen scavengers for single-molecule fluorescence imaging in live cells

The stability of organic dyes against photobleaching is critical in single-molecule tracking and localization microscopy. Since oxygen accelerates photobleaching of most organic dyes, glucose oxidase is commonly used to slow dye photobleaching by depleting oxygen. As demonstrated here, pyranose-2-oxidase slows bleaching of Alexa647 dye by ∼20-fold. However, oxygen deprivation may pose severe problems for live cells by reducing mitochondrial oxidative phosphorylation and ATP production. We formulate a method to sustain intracellular ATP levels in the presence of oxygen scavengers. Supplementation with metabolic intermediates including glyceraldehyde, glutamine, and α-ketoisocaproate maintained the intracellular ATP level for at least 10 min by balancing between FADH₂ and NADH despite reduced oxygen levels. Furthermore, those metabolites supported ATP-dependent synthesis of phosphatidylinositol 4,5-bisphosphate and internalization of PAR2 receptors. Our method is potentially relevant to other circumstances that involve acute drops of oxygen levels, such as ischemic damage in the brain or heart or tissues for transplantation.

Quantum dot conjugated nanobodies for multiplex imaging of protein dynamics at synapses

Neurons communicate with each other through synapses, which show enrichment for specialized receptors. Although many studies have explored spatial enrichment and diffusion of these receptors in dissociated neurons using single particle tracking, much less is known about their dynamic properties at synapses in complex tissue like brain slices. Here we report the use of smaller and highly specific quantum dots conjugated with a recombinant single domain antibody fragment (VHH fragment) against green fluorescent protein to provide information on diffusion of adhesion molecules at the growth cone and neurotransmitter receptors at synapses. Our data reveals that QD-nanobodies can measure neurotransmitter receptor dynamics at both excitatory and inhibitory synapses in primary neuronal cultures as well as in ex vivo rat brain slices. We also demonstrate that this approach can be applied to tagging multiple proteins to simultaneously monitor their behavior. Thus, we provide a strategy for multiplex imaging of tagged membrane proteins to study their clustering, diffusion and transport both in vitro as well as in native tissue environments such as brain slices.

Single quantum dot tracking reveals the impact of nanoparticle surface on intracellular state

Inefficient delivery of macromolecules and nanoparticles to intracellular targets is a major bottleneck in drug delivery, genetic engineering, and molecular imaging. Here we apply live-cell single-quantum-dot imaging and tracking to analyze and classify nanoparticle states after intracellular delivery. By merging trajectory diffusion parameters with brightness measurements, multidimensional analysis reveals distinct and heterogeneous populations that are indistinguishable using single parameters alone. We derive new quantitative metrics of particle loading, cluster distribution, and vesicular release in single cells, and evaluate intracellular nanoparticles with diverse surfaces following osmotic delivery. Surface properties have a major impact on cell uptake, but little impact on the absolute cytoplasmic numbers. A key outcome is that stable zwitterionic surfaces yield uniform cytosolic behavior, ideal for imaging agents. We anticipate that this combination of quantum dots and single-particle tracking can be widely applied to design and optimize next-generation imaging probes, nanoparticle therapeutics, and biologics.

Recent Development of Inorganic Nanoparticles for Biomedical Imaging

Inorganic nanoparticle-based biomedical imaging probes have been studied extensively as a potential alternative to conventional molecular imaging probes. Not only can they provide better imaging performance but they can also offer greater versatility of multimodal, stimuli-responsive, and targeted imaging. However, inorganic nanoparticle-based probes are still far from practical use in clinics due to safety concerns and less-optimized efficiency. In this context, it would be valuable to look over the underlying issues. This outlook highlights the recent advances in the development of inorganic nanoparticle-based probes for MRI, CT, and anti-Stokes shift-based optical imaging. Various issues and possibilities regarding the construction of imaging probes are discussed, and future research directions are suggested.

Structural Contributions to Hydrodynamic Diameter for Quantum Dots Optimized for Live-Cell Single-Molecule Tracking

Quantum dots are fluorescent nanoparticles with narrow-band, size-tunable, and long-lasting emission. Typical formulations used for imaging proteins in cells are hydrodynamically much larger than the protein targets, so it is critical to assess the impact of steric effects deriving from hydrodynamic size. This report analyzes a new class of quantum dots that have been engineered for minimized size specifically for imaging receptors in narrow synaptic junctions between neurons. We use fluorescence correlation spectroscopy and transmission electron microscopy to calculate the contributions of the crystalline core, organic coating, and targeting proteins (streptavidin) to the total hydrodynamic diameter of the probe, using a wide range of core materials with emission spanning 545-705 nm. We find the contributing thickness of standard commercial amphiphilic polymers to be ~8 to ~14 nm, whereas coatings based on the compact ligand HS-(CH₂)₁₁ ^- (OCH₂CH₂)₄-OH contribute ~6 to ~9 nm, reducing the diameter by ~2 to ~5 nm, depending on core size. When the number of streptavidins for protein targeting is minimized, the total diameter can be further reduced by ~5 to ~11 nm, yielding a diameter of 13.8-18.4 nm. These findings explain why access to the narrow synapse derive primarily from the protein functionalization of commercial variants, rather than the organic coating layers. They also explain why those quantum dots with size around 14 nm with only a few streptavidins can access narrow cellular structures for neuronal labeling, whereas those >27 nm and a large number of streptavidins, cannot.

Super-resolution imaging of synaptic and Extra-synaptic AMPA receptors with different-sized fluorescent probes

Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, post-synaptic densities (PSDs) from rats. Organic fluorescent dyes (≈4 nm), quantum dots, either small (≈10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.

Covalent Protein Labeling and Improved Single-Molecule Optical Properties of Aqueous CdSe/CdS Quantum Dots

Semiconductor quantum dots (QDs) have proven to be superior probes for single-molecule imaging compared to organic or genetically encoded fluorophores, but they are limited by difficulties in protein targeting, their larger size, and on-off blinking. Here, we report compact aqueous CdSe/CdS QDs with significantly improved bioconjugation efficiency and superior single-molecule optical properties. We have synthesized covalent protein labeling ligands (i.e., SNAP tags) that are optimized for nanoparticle use, and QDs functionalized with these ligands label SNAP-tagged proteins ∼10-fold more efficiently than existing SNAP ligands. Single-molecule analysis of these QDs shows 99% of time spent in the fluorescent on-state, ∼4-fold higher quantum efficiency than standard CdSe/ZnS QDs, and 350 million photons detected before photobleaching. Bright signals of these QDs enable us to track the stepping movement of a kinesin motor in vitro, and the improved labeling efficiency enables tracking of single kinesins in live cells.

Selective Targeting of Neurons with Inorganic Nanoparticles: Revealing the Crucial Role of Nanoparticle Surface Charge

Nanoparticles (NPs) are increasingly used in biomedical applications, but the factors that influence their interactions with living cells need to be elucidated. Here, we reveal the role of NP surface charge in determining their neuronal interactions and electrical responses. We discovered that negatively charged NPs administered at low concentration (10 nM) interact with the neuronal membrane and at the synaptic cleft, whereas positively and neutrally charged NPs never localize on neurons. This effect is shape and material independent. The presence of negatively charged NPs on neuronal cell membranes influences the excitability of neurons by causing an increase in the amplitude and frequency of spontaneous postsynaptic currents at the single cell level and an increase of both the spiking activity and synchronous firing at neural network level. The negatively charged NPs exclusively bind to excitable neuronal cells, and never to nonexcitable glial cells. This specific interaction was also confirmed by manipulating the electrophysiological activity of neuronal cells. Indeed, the interaction of negatively charged NPs with neurons is either promoted or hindered by pharmacological suppression or enhancement of the neuronal activity with tetrodotoxin or bicuculline, respectively. We further support our main experimental conclusions by using numerical simulations. This study demonstrates that negatively charged NPs modulate the excitability of neurons, revealing the potential use of NPs for controlling neuron activity.

Segmentation of 3D Trajectories Acquired by TSUNAMI Microscope: An Application to EGFR Trafficking

Whereas important discoveries made by single-particle tracking have changed our view of the plasma membrane organization and motor protein dynamics in the past three decades, experimental studies of intracellular processes using single-particle tracking are rather scarce because of the lack of three-dimensional (3D) tracking capacity. In this study we use a newly developed 3D single-particle tracking method termed TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) to investigate epidermal growth factor receptor (EGFR) trafficking dynamics in live cells at 16/43 nm (xy/z) spatial resolution, with track duration ranging from 2 to 10 min and vertical tracking depth up to tens of microns. To analyze the long 3D trajectories generated by the TSUNAMI microscope, we developed a trajectory analysis algorithm, which reaches 81% segment classification accuracy in control experiments (termed simulated movement experiments). When analyzing 95 EGF-stimulated EGFR trajectories acquired in live skin cancer cells, we find that these trajectories can be separated into three groups-immobilization (24.2%), membrane diffusion only (51.6%), and transport from membrane to cytoplasm (24.2%). When EGFRs are membrane-bound, they show an interchange of Brownian diffusion and confined diffusion. When EGFRs are internalized, transitions from confined diffusion to directed diffusion and from directed diffusion back to confined diffusion are clearly seen. This observation agrees well with the model of clathrin-mediated endocytosis.

Dynamic imaging of AMPA receptor trafficking in vitro and in vivo

Modulation of synaptic strength through trafficking of AMPA receptors is a fundamental mechanism underlying synaptic plasticity and has been shown to be an important process in higher brain functions such as learning and memory. Many studies have used live time-lapse imaging of fluorescently tagged AMPA receptors to directly monitor their membrane trafficking in the basal state as well as during synaptic plasticity. While most of these studies are performed in vitro using neuronal cell cultures, in the past years technological advances have enabled the imaging of synaptic proteins in vivo in intact organisms. This has allowed for visualization of synaptic plasticity on a molecular level in living and behaving animals. Here, we discuss key studies and approaches using dynamic imaging to visualize AMPA receptor trafficking in vitro as well as imaging synaptic proteins, including AMPA receptors, in vivo.

Drive the Car(go)s-New Modalities to Control Cargo Trafficking in Live Cells

Synaptic transmission is a fundamental molecular process underlying learning and memory. Successful synaptic transmission involves coupled interaction between electrical signals (action potentials) and chemical signals (neurotransmitters). Defective synaptic transmission has been reported in a variety of neurological disorders such as Autism and Alzheimer’s disease. A large variety of macromolecules and organelles are enriched near functional synapses. Although a portion of macromolecules can be produced locally at the synapse, a large number of synaptic components especially the membrane-bound receptors and peptide neurotransmitters require active transport machinery to reach their sites of action. This spatial relocation is mediated by energy-consuming, motor protein-driven cargo trafficking. Properly regulated cargo trafficking is of fundamental importance to neuronal functions, including synaptic transmission. In this review, we discuss the molecular machinery of cargo trafficking with emphasis on new experimental strategies that enable direct modulation of cargo trafficking in live cells. These strategies promise to provide insights into a quantitative understanding of cargo trafficking, which could lead to new intervention strategies for the treatment of neurological diseases.

Multifunctional and High Affinity Polymer Ligand that Provides Bio-Orthogonal Coating of Quantum Dots

We detail the design of hydrophilic metal-coordinating ligands and their use for the effective coating of luminescent quantum dots (QDs). The ligand design exploits the specific, reagent-free nucleophilic addition reaction of amine-modified molecules toward maleic anhydride to introduce several lipoic acid metal anchors, hydrophilic zwitterion moieties, and specific reactive groups along a poly(isobutylene-alt-maleic anhydride) (PIMA) chain. Tunable reactive groups tested in this study include azide, biotin, carboxyl, and amine. Cap exchange with these multilipoic acid ligands via a photochemical ligation strategy yields homogeneous QD dispersions that are colloidally stable over several biologically relevant conditions and for extended periods of time. The zwitterionic coating yields compact nanoparticle size and imparts nonsticky surface properties onto the QDs, preventing protein absorption. The introduction of a controllable number of reactive groups allows conjugation of the QDs to biomolecules via bio-orthogonal coupling chemistries including (1) attachment of the neurotransmitter dopamine to QDs via amine-isothiocyanate reaction to produce a platform capable of probing interactions with cysteine in proteins, based on charge transfer interactions; (2) self-assembly of biotinylated QDs with streptavidin-dye; and (3) ligation of azide-functionalized QDs to cyclooctyne-modified transferrin via copper-free click chemistry, used for intracellular delivery. This ligand design strategy can be used to prepare an array of metal-coordinating ligands adapted for coating other inorganic nanoparticles, including magnetic and plasmonic nanomaterials.

Quantum Dot Surface Engineering: Toward Inert Fluorophores with Compact Size and Bright, Stable Emission

The surfaces of colloidal nanocrystals are complex interfaces between solid crystals, coordinating ligands, and liquid solutions. For fluorescent quantum dots, the properties of the surface vastly influence the efficiency of light emission, stability, and physical interactions, and thus determine their sensitivity and specificity when they are used to detect and image biological molecules. But after more than 30 years of study, the surfaces of quantum dots remain poorly understood and continue to be an important subject of both experimental and theoretical research. In this article, we review the physics and chemistry of quantum dot surfaces and describe approaches to engineer optimal fluorescent probes for applications in biomolecular imaging and sensing. We describe the structure and electronic properties of crystalline facets, the chemistry of ligand coordination, and the impact of ligands on optical properties. We further describe recent advances in compact coatings that have significantly improved their properties by providing small hydrodynamic size, high stability and fluorescence efficiency, and minimal nonspecific interactions with cells and biological molecules. While major progress has been made in both basic and applied research, many questions remain in the chemistry and physics of quantum dot surfaces that have hindered key breakthroughs to fully optimize their properties.

Control of Transmembrane Protein Diffusion within the Postsynaptic Density Assessed by Simultaneous Single-Molecule Tracking and Localization Microscopy

Postsynaptic transmembrane proteins are critical elements of synapses, mediating trans-cellular contact, sensitivity to neurotransmitters and other signaling molecules, and flux of Ca and other ions. Positioning and mobility of each member of this large class of proteins is critical to their individual function at the synapse. One critical example is that the position of glutamate receptors within the postsynaptic density (PSD) strongly modulates their function by aligning or misaligning them with sites of presynaptic vesicle fusion. In addition, the regulated ability of receptors to move in or out of the synapse is critical for activity-dependent plasticity. However, factors that control receptor mobility within the boundaries of the synapse are not well understood. Notably, PSD scaffold molecules accumulate in domains much smaller than the synapse. Within these nanodomains, the density of proteins is considerably higher than that of the synapse as a whole, so high that steric hindrance is expected to reduce receptor mobility substantially. However, while numerical modeling has demonstrated several features of how the varying protein density across the face of a single PSD may modulate receptor motion, there is little experimental information about the extent of this influence. To address this critical aspect of synaptic organizational dynamics, we performed single-molecule tracking of transmembrane proteins using universal point accumulation-for-imaging-in-nanoscale-topography (uPAINT) over PSDs whose internal structure was simultaneously resolved using photoactivated localization microscopy (PALM). The results provide important experimental confirmation that PSD scaffold protein density strongly influences the mobility of transmembrane proteins. A protein with a cytosolic domain that does not bind PSD-95 was still slowed in regions of high PSD-95 density, suggesting that crowding by scaffold molecules and perhaps other proteins is sufficient to stabilize receptors even in the absence of binding. Because numerous proteins thought to be involved in establishing PSD structure are linked to disorders including autism and depression, this motivates further exploration of how PSD nanostructure is created. The combined application PALM and uPAINT should be invaluable for distinguishing the interactions of mobile proteins with their nano-environment both in synapses and other cellular compartments.

From single-molecule spectroscopy to super-resolution imaging of the neuron: a review

For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.

Super resolution microscopy is poised to reveal new insights into the formation and maturation of dendritic spines

Dendritic spines and synapses are critical for neuronal communication, and they are perturbed in many neurological disorders; however, the study of these structures in living cells has been hindered by their small size. Super resolution microscopy, unlike conventional light microscopy, is diffraction unlimited and thus is well suited for imaging small structures, such as dendritic spines and synapses. Super resolution microscopy has already revealed important new information about spine and synapse morphology, actin remodeling, and nanodomain composition in both healthy cells and diseased states. In this review, we highlight the advancements in probes that make super resolution more amenable to live-cell imaging of spines and synapses. We also discuss recent data obtained by super resolution microscopy that has advanced our knowledge of dendritic spine and synapse structure, organization, and dynamics in both healthy and diseased contexts. Finally, we propose a series of critical questions for understanding spine and synapse formation and maturation that super resolution microscopy is poised to answer.

Multidentate Polymer Coatings for Compact and Homogeneous Quantum Dots with Efficient Bioconjugation

Quantum dots are fluorescent nanoparticles used to detect and image proteins and nucleic acids. Compared with organic dyes and fluorescent proteins, these nanocrystals have enhanced brightness, photostability, and wavelength tunability, but their larger size limits their use. Recently, multidentate polymer coatings have yielded stable quantum dots with small hydrodynamic dimensions (≤10 nm) due to high-affinity, compact wrapping around the nanocrystal. However, this coating technology has not been widely adopted because the resulting particles are frequently heterogeneous and clustered, and conjugation to biological molecules is difficult to control. In this article we develop new polymeric ligands and optimize coating and bioconjugation methodologies for core/shell CdSe/Cd(x)Zn(1-x)S quantum dots to generate homogeneous and compact products. We demonstrate that "ligand stripping" to rapidly displace nonpolar ligands with hydroxide ions allows homogeneous assembly with multidentate polymers at high temperature. The resulting aqueous nanocrystals are 7-12 nm in hydrodynamic diameter, have quantum yields similar to those in organic solvents, and strongly resist nonspecific interactions due to short oligoethylene glycol surfaces. Compared with a host of other methods, this technique is superior for eliminating small aggregates identified through chromatographic and single-molecule analysis. We also demonstrate high-efficiency bioconjugation through azide-alkyne click chemistry and self-assembly with hexa-histidine-tagged proteins that eliminate the need for product purification. The conjugates retain specificity of the attached biomolecules and are exceptional probes for immunofluorescence and single-molecule dynamic imaging. These results are expected to enable broad utilization of compact, biofunctional quantum dots for studying crowded macromolecular environments such as the neuronal synapse and cellular cytoplasm.

A multifunctional polymer combining the imidazole and zwitterion motifs as a biocompatible compact coating for quantum dots

We introduce a set of multicoordinating imidazole- and zwitterion-based ligands suited for surface functionalization of quantum dots (QDs). The polymeric ligands are built using a one-step nucleophilic addition reaction between poly(isobutylene-alt-maleic anhydride) and distinct amine-containing functionalities. This has allowed us to introduce several imidazole anchoring groups along the polymer chain for tight coordination to the QD surface and a controllable number of zwitterion moieties for water solubilization. It has also permitted the introduction of reactive and biomolecular groups for further conjugation and targeting. The QDs capped with these new ligands exhibit excellent long-term colloidal stability over a broad range of pH, toward excess electrolyte, in cell-growth media, and in the presence of natural reducing agents such as glutathione. These QDs are also resistant to the oxidizing agent H2O2. More importantly, by the use of zwitterion moieties as the hydrophilic block, this polymer design provides QDs with a thin coating and compact overall dimensions. These QDs are easily self-assembled with full size proteins expressed with a polyhistidine tag via metal-histidine coordination. Additionally, the incorporation of amine groups allows covalent coupling of the QDs to the neurotransmitter dopamine. This yields redox-active QD platforms that can be used to track pH changes and detect Fe ions and cysteine through charge-transfer interactions. Finally, we found that QDs cap-exchanged with folic acid-functionalized ligands could effectively target cancer cells, where folate-receptor-mediated endocytosis of QDs into living cells was time- and concentration-dependent.

Probability-based particle detection that enables threshold-free and robust in vivo single-molecule tracking

Any single-molecule study starts with finding those single-molecule signals in recorded images. Currently, parameters such as filter and thresholds are user set, and errors are unknown and not observed or controlled. A framework is presented in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test.

Single-molecule detection in fluorescence nanoscopy has become a powerful tool in cell biology but can present vexing issues in image analysis, such as limited signal, unspecific background, empirically set thresholds, image filtering, and false-positive detection limiting overall detection efficiency. Here we present a framework in which expert knowledge and parameter tweaking are replaced with a probability-based hypothesis test. Our method delivers robust and threshold-free signal detection with a defined error estimate and improved detection of weaker signals. The probability value has consequences for downstream data analysis, such as weighing a series of detections and corresponding probabilities, Bayesian propagation of probability, or defining metrics in tracking applications. We show that the method outperforms all current approaches, yielding a detection efficiency of >70% and a false-positive detection rate of <5% under conditions down to 17 photons/pixel background and 180 photons/molecule signal, which is beneficial for any kind of photon-limited application. Examples include limited brightness and photostability, phototoxicity in live-cell single-molecule imaging, and use of new labels for nanoscopy. We present simulations, experimental data, and tracking of low-signal mRNAs in yeast cells.

Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy

Immunofluorescence, a powerful technique to detect specific targets using fluorescently labeled antibodies, has been widely used in both scientific research and clinical diagnostics. The probes should be made with small antibodies and high brightness. We conjugated GFP binding protein (GBP) nanobodies, small single-chain antibodies from llamas, with new ∼7 nm quantum dots. These provide simple and versatile immunofluorescence nanoprobes with nanometer accuracy and resolution. Using the new probes we tracked the walking of individual kinesin motors and measured their 8 nm step sizes; we tracked Piezo1 channels, which are eukaryotic mechanosensitive channels; we also tracked AMPA receptors on living neurons. Finally, we used a new super-resolution algorithm based on blinking of (small) quantum dots that allowed ∼2 nm precision.