Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies

Top-Down Computational Design of Molecule Recognition Peptides (MRPs) for Enzyme-Peptide Self-Assembly and Chemiluminescent Biosensing

The recognition of small molecules plays a crucial role in disease diagnosis, environmental assessment, and food safety. Currently, their recognition elements predominantly rely on antibodies and aptamers while suffering from a limitation of the complex screening process due to the low immunogenicity of small molecules. Herein, we present a top-down computational design strategy for molecule recognition peptides (MRPs) for enzyme-peptide self-assembly and chemiluminescence biosensing. Taking ochratoxin A (OTA) as an illustrative example, human serum albumin (HSA) was selected as the parental protein due to its high affinity for OTA binding. Through iterative computational simulations involving the binding domain of the HSA-OTA complex, our strategy identified a specific 15-mer MRP (RLKCASLKFGERAFK), which possesses excellent binding affinity (38.02 ± 1.24 nM) against OTA. Molecular dynamics simulations revealed that the 15-mer MRP unfolds into a flexible short chain with high affinity for OTA, but exhibits weak or no binding affinity with five structurally similar mycotoxins. Furthermore, we developed a novel enzyme-peptide self-assembly approach mediated by calcium(II) to obtain nanoflowers, which integrates both the recognition element (MRP) and the signal translator (enzyme) for chemiluminescence biosensing. The assembled nanoflowers allow MRPs to be directly utilized as a tracer for OTA biosensing without labeling or secondary antibodies. This computational-to-application approach offers a new route for small-molecule recognition.

Advances in the photon avalanche luminescence of inorganic lanthanide-doped nanomaterials

Photon avalanche (PA)-where the absorption of a single photon initiates a 'chain reaction' of additional absorption and energy transfer events within a material-is a highly nonlinear optical process that results in upconverted light emission with an exceptionally steep dependence on the illumination intensity. Over 40 years following the first demonstration of photon avalanche emission in lanthanide-doped bulk crystals, PA emission has been achieved in nanometer-scale colloidal particles. The scaling of PA to nanomaterials has resulted in significant and rapid advances, such as luminescence imaging beyond the diffraction limit of light, optical thermometry and force sensing with (sub)micron spatial resolution, and all-optical data storage and processing. In this review, we discuss the fundamental principles underpinning PA and survey the studies leading to the development of nanoscale PA. Finally, we offer a perspective on how this knowledge can be used for the development of next-generation PA nanomaterials optimized for a broad range of applications, including mid-IR imaging, luminescence thermometry, (bio)sensing, optical data processing and nanophotonics.

The 4D Camera: An 87 kHz Direct Electron Detector for Scanning/Transmission Electron Microscopy

We describe the development, operation, and application of the 4D Camera-a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at ∼480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10-700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 to 300 kV. Through electron counting, the resulting sparse data sets are reduced in size by 10--300× compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex scanning diffraction experiments to be accomplished with typical scanning transmission electron microscopy scanning parameters.

Short-Wave Infrared Upconverting Nanoparticles

Optical technologies enable real-time, noninvasive analysis of complex systems but are limited to discrete regions of the optical spectrum. While wavelengths in the short-wave infrared (SWIR) window (typically, 1700-3000 nm) should enable deep subsurface penetration and reduced photodamage, there are few luminescent probes that can be excited in this region. Here, we report the discovery of lanthanide-based upconverting nanoparticles (UCNPs) that efficiently convert 1740 or 1950 nm excitation to wavelengths compatible with conventional silicon detectors. Screening of Ln3+ ion combinations by differential rate equation modeling identifies Ho3+/Tm3+ or Tm3+ dopants with strong visible or NIR-I emission following SWIR excitation. Experimental upconverted photoluminescence excitation (U-PLE) spectra find that 10% Tm3+-doped NaYF4 core/shell UCNPs have the strongest 800 nm emission from SWIR wavelengths, while UCNPs with an added 2% or 10% Ho3+ show the strongest red emission when excited at 1740 or 1950 nm. Mechanistic modeling shows that addition of a low percentage of Ho3+ to Tm3+-doped UCNPs shifts their emission from 800 to 652 nm by acting as a hub of efficient SWIR energy acceptance and redistribution up to visible emission manifolds. Parallel experimental and computational analysis shows rate equation models are able to predict compositions for specific wavelengths of both excitation and emission. These SWIR-responsive probes open a new IR bioimaging window, and are responsive at wavelengths important for vision technologies.

Enhanced Solubility and Increased Bioavailability with Engineered Nanocrystals

Abstract:

The exploration of nanocrystal technology is currently receiving significant attention in various fields, including therapeutic formulation, clinical formulation, in-vivo and in-vitro correlation research, and related investigations. The domain of nanocrystals in pharmaceutical delivery has received significant interest as a potential solution for the difficulties associated with medications that have low solubility. The nanocrystals demonstrate promise in improving solubility and bioavailability, presenting a potential resolution to significant challenges. Significantly, nanocrystals have exhibited efficacy in the context of oral administration, showcasing prompt absorption due to their quick breakdown, hence fitting with the requirements of medications that necessitate fast commencement of action. In addition, the adaptability of drug nanocrystals encompasses several methods of administration, including oral, parenteral, ophthalmic, cutaneous, pulmonary, and targeted delivery modalities. The observed consistency can be ascribed to the increased solubility of nanocrystals of the medicine, which effectively counteracts the influence of food on the absorption of the drug. Surface modification tactics have a significant influence on insoluble medicines by enhancing hydrophilicity and reducing plasma protein adsorption on the crystal surface. The surface properties of nanocrystals are modified through the utilization of specific surfactants and polymers, which are subsequently incorporated into polymer solutions via high-pressure homogenization procedures. This article encompasses an examination of the drug distribution mechanism, the nanocrystal formulation technology, the therapeutic applications, the potential future developments, and the challenges associated with the solubility and bioavailability of tailored nanocrystals, as discussed in this article. Consequently, it possesses the capacity to provide guidance for future investigations pertaining to nanocrystal technology.

Upconversion Nanoparticles Based Sensing: From Design to Point-of-Care Testing

Rare earth-doped upconversion nanoparticles (UCNPs) have achieved a wide range of applications in the sensing field due to their unique anti-Stokes luminescence property, minimized background interference, excellent biocompatibility, and stable physicochemical properties. However, UCNPs-based sensing platforms still face several challenges, including inherent limitations from UCNPs such as low quantum yields and narrow absorption cross-sections, as well as constraints related to energy transfer efficiencies in sensing systems. Therefore, the construction of high-performance UCNPs-based sensing platforms is an important cornerstone for conducting relevant research. This work begins by providing a brief overview of the upconversion luminescence mechanism in UCNPs. Subsequently, it offers a comprehensive summary of the sensors' types, design principles, and optimized design strategies for UCNPs sensing platforms. More cost-effective and promising point-of-care testing applications implemented based on UCNPs sensing systems are also summarized. Finally, this work addresses the future challenges and prospects for UCNPs-based sensing platforms.

Quantum Dot-Fab' Conjugates as Compact Immunolabels for Microtubule Imaging and Cell Classification

Antibodies and their conjugates of fluorescent labels are widely applied in life sciences research and clinical pathology. Among diverse label types, compact quantum dots (QDs) provide advantages of multispectral multiplexing, bright signals in the deep red and infrared, and low steric hindrance. However, QD-antibody conjugates have random orientation of the antigen-binding domain which may interfere with labeling and are large (20-30 nm) and heterogeneous, which limits penetration into biospecimens. Here, we develop conjugates of compact QDs and Fab' antibody fragments as primary immunolabels. Fab' fragments are conjugated site-specifically through sulfhydryl groups distal to antigen-binding domains, and the multivalent conjugates have small and homogeneous sizes (∼12 nm) near those of full-sized antibodies. Their performance as immunolabels for intracellular antigens is evaluated quantitatively by metrics of microtubule labeling density and connectivity in fixed cells and for cytological identification in fixed brain specimens, comparing results with probes based on spectrally-matched dyes. QD-Fab' conjugates outperformed QD conjugates of full-sized antibodies and could be imaged with bright signals with 1-photon and 2-photon excitation. The results demonstrate a requirement for smaller bioaffinity agents and site-specific orientation for the success of nanomaterial-based labels to enhance penetration in biospecimens and minimize nonspecific staining.

Ligand-Assisted Direct Lithography of Upconverting and Avalanching Nanoparticles for Nonlinear Photonics

Upconverting nanoparticles (UCNPs) exhibit unique nonlinear optical properties that can be harnessed in microscopy, sensing, and photonics. However, forming high-resolution nano- and micropatterns of UCNPs with large packing fractions is still challenging. Additionally, there is limited understanding of how nanoparticle patterning chemistries are affected by the particle size. Here, we explore direct patterning chemistries for 6-18 nm Tm3+-, Yb3+/Tm3+-, and Yb3+/Er3+-based UCNPs using ligands that form either new ionic linkages or covalent bonds between UCNPs under ultraviolet (UV), electron-beam (e-beam), and near-infrared (NIR) exposure. We study the effect of UCNP size on these patterning approaches and find that 6 nm UCNPs can be patterned with compact ionic-based ligands. In contrast, patterning larger UCNPs requires long-chain, cross-linkable ligands that provide sufficient interparticle spacing to prevent irreversible aggregation upon film casting. Compared to approaches that use a cross-linkable liquid monomer, our patterning method limits the cross-linking reaction to the ligands bound on UCNPs deposited as a thin film. This highly localized photo-/electron-initiated chemistry enables the fabrication of densely packed UCNP patterns with high resolutions (∼1 μm with UV and NIR exposure; <100 nm with e-beam). Our upconversion NIR lithography approach demonstrates the potential to use inexpensive continuous-wave lasers for high-resolution 2D and 3D lithography of colloidal materials. The deposited UCNP patterns retain their upconverting, avalanching, and photoswitching behaviors, which can be exploited in patterned optical devices for next-generation UCNP applications.

Quantum Dot Fluorescent Imaging: Using Atomic Structure Correlation Studies to Improve Photophysical Properties

Efforts to study intricate, higher-order cellular functions have called for fluorescence imaging under physiologically relevant conditions such as tissue systems in simulated native buffers. This endeavor has presented novel challenges for fluorescent probes initially designed for use in simple buffers and monolayer cell culture. Among current fluorescent probes, semiconductor nanocrystals, or quantum dots (QDs), offer superior photophysical properties that are the products of their nanoscale architectures and chemical formulations. While their high brightness and photostability are ideal for these biological environments, even state of the art QDs can struggle under certain physiological conditions. A recent method correlating electron microscopy ultrastructure with single-QD fluorescence has begun to highlight subtle structural defects in QDs once believed to have no significant impact on photoluminescence (PL). Specific defects, such as exposed core facets, have been shown to quench QD PL in physiologically accurate conditions. For QD-based imaging in complex cellular systems to be fully realized, mechanistic insight and structural optimization of size and PL should be established. Insight from single QD resolution atomic structure and photophysical correlative studies provides a direct course to synthetically tune QDs to match these challenging environments.

Targeted Single Particle Tracking with Upconverting Nanoparticles

Single particle tracking (SPT) is a powerful technique for real-time microscopic visualization of the movement of individual biomolecules within or on the surface of living cells. However, SPT often suffers from the suboptimal performance of the photon-emitting labels used to tag the biomolecules of interest. For example, fluorescent dyes have poor photostability, while quantum dots suffer from blinking that hampers track acquisition and interpretation. Upconverting nanoparticles (UCNPs) have recently emerged as a promising anti-Stokes luminescent label for SPT. In this work, we demonstrated targeted SPT using UCNPs. For this, we synthesized 30 nm diameter doped UCNPs and coated them with amphiphilic polymers decorated with polyethylene glycol chains to make them water-dispersible and minimize their nonspecific interactions with cells. Coated UCNPs highly homogeneous in brightness (as confirmed by a single particle investigation) were functionalized by immunoglobulin E (IgE) using a biotin-streptavidin strategy. Using these IgE-UCNP SPT labels, we tracked high-affinity IgE receptors (FcεRI) on the membrane of living RBL-2H3 mast cells at 37 °C in the presence and absence of antigen and obtained good agreement with the literature. Moreover, we used the FcεRI-IgE receptor-antibody system to directly compare the performance of UCNP-based SPT labels to organic dyes (AlexaFluor647) and quantum dots (QD655). Due to their photostability as well as their backgroundless and continuous luminescence, SPT trajectories obtained with UCNP labels are no longer limited by the photophysics of the label but only by the dynamics of the system and, in particular, the movement of the label out of the field of view and/or focal plane.

Compact and modular bioprobe: Integrating SpyCatcher/SpyTag recombinant proteins with zwitterionic polymer-coated quantum dots

The development of quantum dot (QD)-based modular bioprobe that has a compact size and enable a facile conjugation of various biofunctional groups is in high demand. To address this, we surface engineered QDs with zwitterion polymer ligands to have an inherent compact size and derivatized them sequentially with the recombinant proteins SpyCatcher/SpyTag (SC/ST) to use their protein ligation system. SC/ST spontaneously form one complex through the isopeptide bond between them. SC-conjugated QDs (QD-SC) were used as base building blocks. Then, ST-biomolecules were added for modular biofunctionalization. We synthesized compact sized (∼15 nm) QD-SC-ST-affibody (antibody-mimicking small protein for tumor detection) conjugates, which showed successful cell-receptor targeting. The target cell-receptor could be easily tuned by changing the type of ST-affibody. We also demonstrated that anti-human-chorionic-gonadotropin mouse IgG1 antibodies can be labeled on the QD surface by mixing QD-SC with the ST-MG1Nb (mouse-IgG1-specific protein). The immunoassay performance of the antibody-labeled QDs was evaluated using a pregnancy test kit, displaying equivalent detection sensitivity to a commercially available kit. This study proposed an innovative strategy for QD biofunctionalization in a modular manner, which can be expanded to a diverse range of colloidal particle derivatization.

Advanced techniques in automated high-resolution scanning transmission electron microscopy

Scanning transmission electron microscopy is a common tool used to study the atomic structure of materials. It is an inherently multimodal tool allowing for the simultaneous acquisition of multiple information channels. Despite its versatility, however, experimental workflows currently rely heavily on experienced human operators and can only acquire data from small regions of a sample at a time. Here, we demonstrate a flexible pipeline-based system for high-throughput acquisition of atomic-resolution structural data using an all-piezo sample stage applied to large-scale imaging of nanoparticles and multimodal data acquisition. The system is available as part of the user program of the Molecular Foundry at Lawrence Berkeley National Laboratory.

A Generalized Approach to Photon Avalanche Upconversion in Luminescent Nanocrystals

Photon avalanching nanoparticles (ANPs) exhibit extremely nonlinear upconverted emission valuable for subdiffraction imaging, nanoscale sensing, and optical computing. Avalanching has been demonstrated with Tm3+-, Pr3+-, or Nd3+-doped nanocrystals, but their emission is limited to a few wavelengths and materials. Here, we utilize Gd3+-assisted energy migration to tune the emission wavelengths of Tm3+-sensitized ANPs and generate highly nonlinear emission from Eu3+, Tb3+, Ho3+, and Er3+ ions. The upconversion intensities of these spectrally discrete ANPs scale with nonlinearity factor s = 10-17 under 1064 nm excitation at power densities as low as 7 kW cm-2. This strategy for imprinting avalanche behavior on remote emitters can be extended to fluorophores adjacent to ANPs, as we demonstrate with CdS/CdSe/CdS core/shell/shell quantum dots. ANPs with rationally designed energy transfer networks provide the means to transform conventional linear emitters into a highly nonlinear ones, expanding the use of photon avalanching in biological, chemical, and photonic applications.

Catalyst-free thiazolidine formation chemistry enables the facile construction of peptide/protein-cell conjugates (PCCs) at physiological pH

Although numerous genetic, chemical, and physical strategies have been developed to remodel the cell surface landscape for basic research and the development of live cell-based therapeutics, new chemical modification strategies capable of decorating cells with various genetically/non-genetically encodable molecules are still urgently needed. Herein, we describe a remarkably simple and robust chemical strategy for cell surface modifications by revisiting the classical thiazolidine formation chemistry. Cell surfaces harbouring aldehydes can be chemoselectively conjugated with molecules containing a 1,2-aminothiol moiety at physiological pH without the need to use any toxic catalysts and complicated chemical synthesis. Through the combined use of thiazolidine formation and the SpyCatcher-SpyTag system, we have further developed a SpyCatcher-SpyTag Chemistry Assisted Cell Surface Engineering (SpyCASE) platform, providing a modular approach for the construction of large protein-cell conjugates (PCCs) in their native state. Thiazolidine-bridged molecules can also be detached from the surface again through a biocompatible Pd-catalyzed bond scission reaction, enabling reversible modification of living cell surfaces. In addition, this approach allows us to modulate specific cell-cell interactions and generate NK cell-based PCCs to selectively target/kill several EGFR-positive cancer cells in vitro. Overall, this study provides an underappreciated but useful chemical tool to decorate cells with tailor-made functionalities.

Indefinite and bidirectional near-infrared nanocrystal photoswitching

Materials whose luminescence can be switched by optical stimulation drive technologies ranging from superresolution imaging^1-4, nanophotonics⁵, and optical data storage^6,7, to targeted pharmacology, optogenetics, and chemical reactivity⁸. These photoswitchable probes, including organic fluorophores and proteins, can be prone to photodegradation and often operate in the ultraviolet or visible spectral regions. Colloidal inorganic nanoparticles^6,9 can offer improved stability, but the ability to switch emission bidirectionally, particularly with near-infrared (NIR) light, has not, to our knowledge, been reported in such systems. Here, we present two-way, NIR photoswitching of avalanching nanoparticles (ANPs), showing full optical control of upconverted emission using phototriggers in the NIR-I and NIR-II spectral regions useful for subsurface imaging. Employing single-step photodarkening^10-13 and photobrightening^12,14-16, we demonstrate indefinite photoswitching of individual nanoparticles (more than 1,000 cycles over 7 h) in ambient or aqueous conditions without measurable photodegradation. Critical steps of the photoswitching mechanism are elucidated by modelling and by measuring the photon avalanche properties of single ANPs in both bright and dark states. Unlimited, reversible photoswitching of ANPs enables indefinitely rewritable two-dimensional and three-dimensional multilevel optical patterning of ANPs, as well as optical nanoscopy with sub-Å localization superresolution that allows us to distinguish individual ANPs within tightly packed clusters.

Photodarkening, Photobrightening, and the Role of Color Centers in Emerging Applications of Lanthanide-Based Upconverting Nanomaterials

Upconverting nanoparticles (UCNPs) compose a class of luminescent materials that utilize the unique wavelength-converting properties of lanthanide (Ln) ions for light-harvesting applications, photonics technologies, and biological imaging and sensing experiments. Recent advances in UCNP design have shed light on the properties of local color centers, both intrinsic and controllably induced, within these materials and their potential influence on UCNP photophysics. In this review, we describe fundamental studies of color centers in Ln-based materials, including research into their origins and their roles in observed photodarkening and photobrightening mechanisms. We place particular focus on the new functionalities that are enabled by harnessing the properties of color centers within Ln-doped nanocrystals, illustrated through applications in afterglow-based bioimaging, X-ray detection, all-inorganic nanocrystal photoswitching, and fully rewritable optical patterning and memory.

Fully Integrated Ultra-thin Intraoperative Micro-imager for Cancer Detection Using Upconverting Nanoparticles

PURPOSE

Intraoperative detection and removal of microscopic residual disease (MRD) remain critical to the outcome of cancer surgeries. Today's minimally invasive surgical procedures require miniaturization and surgical integration of highly sensitive imagers to seamlessly integrate into the modern clinical workflow. However, current intraoperative imagers remain cumbersome and still heavily dependent on large lenses and rigid filters, precluding further miniaturization and integration into surgical tools.

PROCEDURES

We have successfully engineered a chip-scale intraoperative micro-imager array-without optical filters or lenses-integrated with lanthanide-based alloyed upconverting nanoparticles (aUCNPs) to achieve tissue imaging using a single micro-chip. This imaging platform is able to leverage the unique optical properties of aUCNPs (long luminescent lifetime, high-efficiency upconversion, no photobleaching) by utilizing a time-resolved imaging method to acquire images using a 36-by-80-pixel, 2.3 mm [Formula: see text] 4.8 mm silicon-based electronic imager micro-chip, that is, less than 100-µm thin. Each pixel incorporates a novel architecture enabling automated background measurement and cancellation. We have validated the performance, spatial resolution, and the background cancellation scheme of the imaging platform, using resolution test targets and mouse prostate tumor sample intratumorally injected with aUCNPs. To demonstrate the ability to image MRD, or tumor margins, we evaluated the imaging platform in visualizing a single-cell thin section of the injected prostate tumor sample.

RESULTS

Tested on USAF resolution targets, the imager is able to achieve a resolution of 71 µm. We have also demonstrated successful background cancellation, achieving a signal-to-background ratio of 8 when performing ex vivo imaging on aUCNP-injected prostate tumor sample, improved from originally 0.4. The performance of the imaging platform on single-cell layer sections was also evaluated and the sensor achieved a signal-to-background ratio of 4.3 in resolving cell clusters with sizes as low as 200 cells.

CONCLUSION

The imaging system proposed here is a scalable chip-scale ultra-thin alternative for bulky conventional intraoperative imagers. Its novel pixel architecture and background correction scheme enable visualization of microscopic-scale residual disease while remaining completely free of lenses and filters, achieving an ultra-miniaturized form factor-critical for intraoperative settings.

The Coming of Age of Neodymium: Redefining Its Role in Rare Earth Doped Nanoparticles

Among luminescent nanostructures actively investigated in the last couple of decades, rare earth (RE³⁺) doped nanoparticles (RENPs) are some of the most reported family of materials. The development of RENPs in the biomedical framework is quickly making its transition to the ∼800 nm excitation pathway, beneficial for both in vitro and in vivo applications to eliminate heating and facilitate higher penetration in tissues. Therefore, reports and investigations on RENPs containing the neodymium ion (Nd³⁺) greatly increased in number as the focus on ∼800 nm radiation absorbing Nd³⁺ ion gained traction. In this review, we cover the basics behind the RE³⁺ luminescence, the most successful Nd³⁺-RENP architectures, and highlight application areas. Nd³⁺-RENPs, particularly Nd³⁺-sensitized RENPs, have been scrutinized by considering the division between their upconversion and downshifting emissions. Aside from their distinctive optical properties, significant attention is paid to the diverse applications of Nd³⁺-RENPs, notwithstanding the pitfalls that are still to be addressed. Overall, we aim to provide a comprehensive overview on Nd³⁺-RENPs, discussing their developmental and applicative successes as well as challenges. We also assess future research pathways and foreseeable obstacles ahead, in a field, which we believe will continue witnessing an effervescent progress in the years to come.

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

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