Self-assembled nanoscale biosensors based on quantum dot FRET donors

Sensing the Future-Frontiers in Biosensors: Exploring Classifications, Principles, and Recent Advances

Biosensors are transforming healthcare by delivering swift, precise, and economical diagnostic solutions. These analytical instruments combine biological indicators with physical transducers to identify and quantify biomarkers, thereby improving illness detection, management, and patient surveillance. Biosensors are widely utilized in healthcare for the diagnosis of chronic and infectious diseases, tailored treatment, and real-time health monitoring. This thorough overview examines several categories of biosensors and their uses in the detection of numerous biomarkers, including glucose, proteins, nucleic acids, and infections. Biosensors are commonly classified based on the type of transducer employed or the specific biorecognition element utilized. This review introduces a novel classification based on substrate morphology, offering a comprehensive perspective on biosensor categorization. Considerable emphasis is placed on the advancement of point-of-care biosensors, facilitating decentralized diagnostics and alleviating the strain on centralized healthcare systems. Recent advancements in nanotechnology have significantly improved the sensitivity, selectivity, and downsizing of biosensors, rendering them more efficient and accessible. The study examines problems such as stability, reproducibility, and regulatory approval that must be addressed to enable the widespread implementation of biosensors in clinical environments. The study examines the amalgamation of biosensors with wearable devices and smartphones, emphasizing the prospects for ongoing health surveillance and individualized medical care. This viewpoint clarifies the distinct types of biosensors and their particular roles, together with recent developments in the "smart biosensor" sector, facilitated by artificial intelligence and the Internet of Medical Things (IoMT). This novel approach seeks to deliver a comprehensive evaluation of the present condition of biosensor technology in healthcare, recent developments, and prospective paths, emphasizing their significance in influencing the future of medical diagnostics and patient care.

Exploring the landscape of FRET-based molecular sensors: Design strategies and recent advances in emerging applications

Probing biological processes in living organisms that could provide one-of-a-kind insights into real-time alterations of significant physiological parameters is a formidable task that calls for specialized analytic devices. Classical biochemical methods have significantly aided our understanding of the mechanisms that regulate essential biological processes. These methods, however, are typically insufficient for investigating transient molecular events since they focus primarily on the end outcome. Fluorescence resonance energy transfer (FRET) microscopy is a potent tool used for exploring non-invasively real-time dynamic interactions between proteins and a variety of biochemical signaling events using sensors that have been meticulously constructed. Due to their versatility, FRET-based sensors have enabled the rapid and standardized assessment of a large array of biological variables, facilitating both high-throughput research and precise subcellular measurements with exceptional temporal and spatial resolution. This review commences with a brief introduction to FRET theory and a discussion of the fluorescent molecules that can serve as tags in different sensing modalities for studies in chemical biology, followed by an outlining of the imaging techniques currently utilized to quantify FRET highlighting their strengths and shortcomings. The article also discusses the various donor-acceptor combinations that can be utilized to construct FRET scaffolds. Specifically, the review provides insights into the latest real-time bioimaging applications of FRET-based sensors and discusses the common architectures of such devices. There has also been discussion of FRET systems with multiplexing capabilities and multi-step FRET protocols for use in dual/multi-analyte detections. Future research directions in this exciting field are also mentioned, along with the obstacles and opportunities that lie ahead.

Enhancing mycotoxins detection through quantum dots-based optical biosensors

Quantum dot-based optical biosensors represent a significant advancement for detection of mycotoxins that are toxic secondary metabolites produced by fungi and pose serious health risk effects. This review highlights the importance of detection of filamentous fungi such as Aspergillus, Penicillium, Fusarium, Claviceps, and Alternaria in mycotoxin production, leading to contamination of agricultural products and subsequent health issues. Conventional detection methods such as thin-layer chromatography, high-performance liquid chromatography, gas chromatography, and enzyme-linked immunosorbent assay are discussed with their respective advantages and limitations. Then the innovative use of quantum dots (QDs) in fabrication of biosensors is discussed in the present review, emphasizing their unique optical properties, such as size-tunable fluorescence and high photostability. These properties enable the development of highly sensitive and specific biosensors for mycotoxin detection. The application of QD-based biosensors, based on their applied bioreceptors including antibodies, molecularly imprinted polymers and aptamer, is explored through various detection strategies and recent advancements. The review concludes by underscoring the potential of QD-based biosensors in providing portable, cost-effective, and efficient solutions for real-time monitoring of mycotoxin for enhancing food safety and protecting public health.

Catalytic NIR chemiluminescence sensor with enhanced persistence and intensity for in vivo imaging

Chemiluminescence (CL) is a self-illumination phenomenon that involves the emission of light from chemical reactions, and it provides favorable spatial and temporal information on biological processes. However, it is still a great challenge to construct effective CL sensors that equip strong CL intensity, long emission wavelength, and persistent luminescence for deep tissue imaging. Here, we report a liposome encapsulated polymer dots (Pdots)-based system using catalytic CL substrates (L-012) as energy donor and fluorescent polymers and dyes (NIR 695) as energy acceptors for efficient Near-infrared (NIR) CL in vivo imaging. Thanks to the modulation of paired donor and acceptor distance and the slow diffusion of biomarker by liposome, the Pdots show a NIR emission wavelength (λ em, max = 720 nm), long CL duration (>24 h), and a high chemiluminescence resonance energy transfer efficiency (46.5 %). Furthermore, the liposome encapsulated Pdots possess excellent biocompatibility, sensitive response to H2O2, and persistent whole-body NIR CL imaging in the drug-induced inflammation and the peritoneal metastatic tumor mouse model. In a word, this NIR-II CL nanoplatform with long-lasting emission and high spatial-temporal resolution will be a concise strategy in deep tissue imaging and clinical diagnostics.

Microwave analogy of Förster resonance energy transfer and effect of finite antenna length

The near-field interaction between quantum emitters, governed by Förster resonance energy transfer (FRET), plays a pivotal role in nanoscale energy transfer mechanisms. However, FRET measurements in the optical regime are challenging as they require nanoscale control of the position and orientation of the emitters. To overcome these challenges, microwave measurements were proposed for enhanced spatial resolution and precise orientation control. However, unlike in optical systems for which the dipole can be taken to be infinitesimal in size, the finite size of microwave antennas can affect energy transfer measurements, especially at short distances. This highlights the necessity to consider the finite antenna length to obtain accurate results. In this study, we advance the understanding of dipole-dipole energy transfer in the microwave regime by developing an analytical model that explicitly considers finite antennas. Unlike previous works, our model calculates the mutual impedance of finite-length thin-wire dipole antennas without assuming a uniform current distribution. We validate our analytical model through experiments investigating energy transfer between antennas placed adjacent to a perfect electric conductor mirror. This allows us to provide clear guidelines for designing microwave experiments, distinguishing conditions where finite-size effects can be neglected and where they must be taken into account. Our study not only contributes to the fundamental physics of energy transfer but also opens avenues for microwave antenna impedance-based measurements to complement optical FRET experiments and quantitatively explore dipole-dipole energy transfer in a wider range of conditions.

Role of transition metals in coinage metal nanoclusters for the remediation of toxic dyes in aqueous systems

A difficult issue in chemistry and materials science is to create metal compounds with well-defined components. Metal nanoclusters, particularly those of coinage groups (Cu, Ag, and Au), have received considerable research interest in recent years owing to the availability of atomic-level precision via joint experimental and theoretical methods, thus revealing the mechanisms in diverse nano-catalysts and functional materials. The textile sector significantly contributes to wastewater containing pollutants such as dyes and chemical substances. Textile and fabric manufacturing account for about 7 × 105 tons of wastewater annually. Approximately one thousand tons of dyes used in textile processing and finishing has been recorded as being discharged into natural streams and water bodies. Owing to the widespread environmental concerns, research has been conducted to develop absorbents that are capable of removing contaminants and heavy metals from water bodies using low-cost technology. Considering this idea, we reviewed coinage metal nanoclusters for azo and cationic dye degradation. Fluorometric and colorimetric techniques are used for dye degradation using coinage metal nanoclusters. Few reports are available on dye degradation using silver nanoclusters; and some of them are discussed in detailed herein to demonstrate the synergistic effect of gold and silver in dye degradation. Mostly, the Rhodamine B dye is degraded using coinage metals. Silver nanoclusters take less time for degradation than gold and copper nanoclusters. Mostly, H2O2 is used for degradation in gold nanoclusters. Still, all coinage metal nanoclusters have been used for the degradation due to suitable HOMO-LUMO gap, and the adsorption of a dye onto the surface of the catalyst results in the exchange of electrons and holes, which leads to the oxidation and reduction of the adsorbed dye molecule. Compared to other coinage metal nanoclusters, Ag/g-C3N4 nanoclusters displayed an excellent degradation rate constant with the dye Rhodamine B (0.0332 min-1). The behavior of doping transition metals in coinage metal nanoclusters is also reviewed herein. In addition, we discuss the mechanistic grounds for degradation, the fate of metal nanoclusters, anti-bacterial activity of nanoclusters, toxicity of dyes, and sensing of dyes.

Leveraging Radiation-triggered Metal Prodrug Activation Through Nanosurface Energy Transfer for Directed Radio-chemo-immunotherapy

Metal-based drugs currently dominate the field of chemotherapeutic agents; however, achieving the controlled activation of metal prodrugs remains a substantial challenge. Here, we propose a universal strategy for the radiation-triggered activation of metal prodrugs via nanosurface energy transfer (NSET). The core-shell nanoplatform (Ru-GNC) is composed of gold nanoclusters (GNC) and ruthenium (Ru)-containing organic-inorganic hybrid coatings. Upon X-ray irradiation, chemotherapeutic Ru (II) complexes were released in a controlled manner through a unique NSET process involving the transfer of photoelectron energy from the radiation-excited Ru-GNCs to the Ru-containing hybrid layer. In contrast to the traditional radiation-triggered activation of prodrugs, such an NSET-based system ensures that the reactive species in the tumor microenvironment are present in sufficient quantity and are not easily quenched. Additionally, ultrasmall Ru-GNCs preferably target mitochondria and profoundly disrupt the respiratory chain upon irradiation, leading to radiosensitization by generating abundant reactive oxygen species. Consequently, Ru-GNC-directed radiochemotherapy induces immunogenic cell death, resulting in significant therapeutic outcomes when combined with the programmed cell death-ligand 1 (PD-L1) checkpoint blockade. This NSET strategy represents a breakthrough in designing radiation-triggered nanoplatforms for metal-prodrug-mediated cancer treatment in an efficient and controllable manner.

Single- and two-photon-induced Förster resonance energy transfer in InP-mCherry bioconjugates

Indium phosphide (InP) quantum dots (QDs) have recently garnered considerable interest in the design of bioprobes due to their non-toxic nature and excellent optical properties. Several attempts for the conjunction of InP QDs with various entities such as organic dyes and dye-labeled proteins have been reported, while that with fluorescent proteins remains largely uncharted. This study reports the development of a Förster resonance energy transfer pair comprising glutathione-capped InP/GaP/ZnS QDs [InP(G)] and the fluorescent protein mCherry. Glutathione on InP(G) undergoes effective bioconjugation with mCherry consisting of a hexahistidine tag, and the nonradiative energy transfer is investigated using steady-state and time-resolved measurements. Selective one-photon excitation of InP(G) in the presence of mCherry shows a decay of the emission of the QDs and a concomitant growth of acceptor emission. Time-resolved investigations prove the nonradiative transfer of energy between InP(G) and mCherry. Furthermore, the scope of two-photon-induced energy transfer between InP(G) and mCherry is investigated by exciting the donor in the optical transparency range. The two-photon absorption is confirmed by the quadratic relationship between the emission intensity and the excitation power. In general, near-infrared excitation provides a path for effective light penetration into the tissues and reduces the photodamage of the sample. The two-photon-induced energy transfer in such assemblies could set the stage for a wide range of biological and optoelectronic applications in the foreseeable future.

A multi-cycle signal amplification-mediated single quantum dot nanosensor for PIWI-interacting RNA detection

We construct a single quantum dot-based nanosensor for piRNA detection based on ligation-mediated multi-cycle signal amplification. This nanosensor is homogenous, selective, and sensitive with a detection limit of 0.104 fM. Moreover, it can detect the endogenous piRNA level in different cell lines, and discriminate cancer tissues from normal tissues.

Photoluminescence switching in quantum dots connected with fluorinated and hydrogenated photochromic molecules

We investigate switching of photoluminescence (PL) from PbS quantum dots (QDs) crosslinked with two different types of photochromic diarylethene molecules, 4,4'-(1-cyclopentene-1,2-diyl)bis[5-methyl-2-thiophenecarboxylic acid] (1H) and 4,4'-(1-perfluorocyclopentene-1,2-diyl)bis[5-methyl-2-thiophenecarboxylic acid] (2F). Our results show that the QDs crosslinked with the hydrogenated molecule (1H) exhibit a greater amount of switching in photoluminescence intensity compared to QDs crosslinked with the fluorinated molecule (2F). With a combination of differential pulse voltammetry and density functional theory, we attribute the different amount of PL switching to the different energy levels between 1H and 2F molecules which result in different potential barrier heights across adjacent QDs. Our findings provide a deeper understanding of how the energy levels of bridge molecules influence charge tunneling and PL switching performance in QD systems and offer deeper insights for the future design and development of QD based photo-switches.

Synergetic Photodynamic-Photothermal-Chemotherapy Dual Targeting Nanoplatform Effective Against Breast Cancer in-Mice Model

Introduction

Combined multimodal therapy for breast cancer is a promising therapeutic approach to increase treatment efficacy and reduce systemic toxicity. The present study aimed to develop a novel multifunctional drug release nanoplatform based on RGD-conjugated hyaluronic acid (HA)-functionalized copper sulfide (CuS) for activatable dual-targeted synergetic therapy against cancer.

Methods

The pH and NIR-responsive dual-targeting nanoplatform CuS:Ce6@HA:DOX@RGD was prepared, characterized, and evaluated for its stability and photodynamic and photothermal properties. The loading and release of the drug were measured at different pH values with or without laser radiation using the dialysis method. The cellular uptake of the platform specifically by the tumor cells treated with different formulations was investigated through fluorescence imaging. The in vitro and in vivo biosafety levels were assessed systematically. Finally, the antitumor efficiencies against breast cancer were assessed via in vitro and in vivo experiments.

Results

The spheroid CuS:Ce6@HA:DOX@RGD exhibited remarkable stability and monodispersity in solution. The photosensitive CuS and Ce6 could simultaneously absorb the near-infrared light efficiently to convert NIR light to fatal heat and to generate reactive oxygen species. The CuS:Ce6@HA:DOX@RGD dissociated under an acid environment, causing the release of DOX into the tumor to accelerate upon laser irradiation. The CuS:Ce6@HA:DOX@RGD exhibited target-specific and strong binding ability via a synergic CD44/αvβ3 receptor-mediated bimodal targeting, which led to improved therapeutic efficacy. The tumor growth was effectively inhibited using synergetic photodynamic/photothermal/chemo therapy. No evident systemic toxicity was noted during treatment.

Conclusion

The newly prepared CuS:Ce6@HA:DOX@RGD has great potential as an activatable theranostic nanoplatform for efficient dual-targeted synergistic therapy against breast cancer.

Progress in quantum dot-based biosensors for microRNA assay: A review

MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.

Influence of Temperature-Guided SAM Growth on Wetting and Its Mass Transfer Models

The formation and growth of self-assembled monolayers (SAMs) composed of amphiphiles have garnered significant attention due to their diverse technical applications. This article reports the findings of molecular dynamics simulations aimed at elucidating the intricate relationship between the wetting behavior of amphiphiles, specifically n-alkanols, and the growth of their SAMs on a mica surface under varying temperature conditions. The investigation quantifies the structural characteristics of the formed SAMs, including density profiles, in-plane radial distribution functions, order parameters, and end-to-end length distributions of n-alkanol molecules within the SAM. Thermodynamic properties, such as the second virial coefficient and excess entropy, are examined in relation to temperature and time. The growth of the SAM is assessed by analyzing characteristic time scales at different temperatures and in-plane diffusion of n-alkanol molecules and utilizing classical theories of mass transfer to quantify the growth rate as a function of temperature. These results are then correlated with changes in the contact angle and spreading coefficient of n-alkanol droplets on the mica surface over time, providing insights into the impact of SAM growth on the wetting behavior and the mass transfer model of such systems.

Zero-Dimensional Carbon Nanomaterials for Fluorescent Sensing and Imaging

Advances in nanotechnology and nanomaterials have attracted considerable interest and play key roles in scientific innovations in diverse fields. In particular, increased attention has been focused on carbon-based nanomaterials exhibiting diverse extended structures and unique properties. Among these materials, zero-dimensional structures, including fullerenes, carbon nano-onions, carbon nanodiamonds, and carbon dots, possess excellent bioaffinities and superior fluorescence properties that make these structures suitable for application to environmental and biological sensing, imaging, and therapeutics. This review provides a systematic overview of the classification and structural properties, design principles and preparation methods, and optical properties and sensing applications of zero-dimensional carbon nanomaterials. Recent interesting breakthroughs in the sensitive and selective sensing and imaging of heavy metal pollutants, hazardous substances, and bioactive molecules as well as applications in information encryption, super-resolution and photoacoustic imaging, and phototherapy and nanomedicine delivery are the main focus of this review. Finally, future challenges and prospects of these materials are highlighted and envisaged. This review presents a comprehensive basis and directions for designing, developing, and applying fascinating fluorescent sensors fabricated based on zero-dimensional carbon nanomaterials for specific requirements in numerous research fields.

Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy

Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM-force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function.

Glycosylated quantum dots as fluorometric nanoprobes for trehalase

Trehalase is an important enzyme in the metabolic cascades of many organisms, catalysing the hydrolysis of the disaccharide trehalose. Herein we describe the first examples of fluorometric nanoprobes for detection of trehalase, based on trehalose-functionalised quantum dots (QDs). QDs cross-linked with trehalose form aggregates, which are released upon enzymatic cleavage of the trehalose glycosidic bond proportionally to the enzyme concentration, offering a unique and efficient approach for specific sensing of this biologically important enzyme.

Nanomaterials for Fluorescence and Multimodal Bioimaging

Bioconjugated nanomaterials replace molecular probes in bioanalysis and bioimaging in vitro and in vivo. Nanoparticles of silica, metals, semiconductors, polymers, and supramolecular systems, conjugated with contrast agents and drugs for image-guided (MRI, fluorescence, PET, Raman, SPECT, photodynamic, photothermal, and photoacoustic) therapy infiltrate into preclinical and clinical settings. Small bioactive molecules like peptides, proteins, or DNA conjugated to the surfaces of drugs or probes help us to interface them with cells and tissues. Nevertheless, the toxicity and pharmacokinetics of nanodrugs, nanoprobes, and their components become the clinical barriers, underscoring the significance of developing biocompatible next-generation drugs and contrast agents. This account provides state-of-the-art advancements in the preparation and biological applications of bioconjugated nanomaterials and their molecular, cell, and in vivo applications. It focuses on the preparation, bioimaging, and bioanalytical applications of monomodal and multimodal nanoprobes composed of quantum dots, quantum clusters, iron oxide nanoparticles, and a few rare earth metal ion complexes.

Fluorescence decay enhancement and FRET inhibition in self-assembled hybrid gold CdSe/CdS/CdZnS colloidal nanocrystal supraparticles

We report on the synthesis of hybrid light emitting particles with a diameter ranging between 100 and 500 nm, consisting in a compact semiconductor CdSe/CdS/CdZnS nanocrystal aggregate encapsulated by a controlled nanometric size silica and gold layers. We first characterize the Purcell decay rate enhancement corresponding to the addition of the gold nanoshell as a function of the particle size and find a good agreement with the predictions of numerical simulations. Then, we show that the contribution corresponding to Förster resonance energy transfer is inhibited.

Quantum Dot-Based Molecular Beacons for Quantitative Detection of Nucleic Acids with CRISPR/Cas(N) Nucleases

Strategies utilizing the CRISPR/Cas nucleases Cas13 and Cas12 have shown great promise in the development of highly sensitive and rapid diagnostic assays for the detection of pathogenic nucleic acids. The most common approaches utilizing fluorophore-quencher molecular beacons require strand amplification strategies or highly sensitive optical setups to overcome the limitations of the readout. Here, we demonstrate a flexible strategy for assembling highly luminescent and colorimetric quantum dot-nucleic acid hairpin (QD-HP) molecular beacons for use in CRISPR/Cas diagnostics. This strategy utilizes a chimeric peptide-peptide nucleic acid (peptide-PNA) to conjugate fluorescently labeled DNA or RNA hairpins to ZnS-coated QDs. QDs are particularly promising alternatives for molecular beacons due to their greater brightness, strong UV absorbance with large emission offset, exceptional photostability, and potential for multiplexing due to their sharp emission peaks. Using Förster resonance energy transfer (FRET), we have developed ratiometric reporters capable of pM target detection (without nucleotide amplification) for both target DNA and RNA, and we further demonstrated their capabilities for multiplexing and camera-phone detection. The flexibility of this system is imparted by the dual functionality of the QD as both a FRET donor and a central nanoscaffold for arranging nucleic acids and fluorescent acceptors on its surface. This method also provides a generalized approach that could be applied for use in other CRISPR/Cas nuclease systems.

Hybrid Nucleic Acid-Quantum Dot Assemblies as Multiplexed Reporter Platforms for Cell-Free Transcription Translation-Based Biosensors

Cell-free synthetic biology has emerged as a valuable tool for the development of rapid, portable biosensors that can be readily transported in the freeze-dried form to the point of need eliminating cold chain requirements. One of the challenges associated with cell-free sensors is the ability to simultaneously detect multiple analytes within a single reaction due to the availability of a limited set of fluorescent and colorimetric reporters. To potentially provide multiplexing capabilities to cell-free biosensors, we designed a modular semiconductor quantum dot (QD)-based reporter platform that is plugged in downstream of the transcription-translation functionality in the cell-free reaction and which converts enzymatic activity in the reaction into distinct optical signals. We demonstrate proof of concept by converting restriction enzyme activity, utilized as our prototypical sensing output, into optical changes across several distinct spectral output channels that all use a common excitation wavelength. These hybrid Förster resonance energy transfer (FRET)-based QD peptide PNA-DNA-Dye reporters (QD-PDDs) are completely self-assembled and consist of differentially emissive QD donors paired to a dye-acceptor displayed on a unique DNA encoding a given enzyme's cleavage site. Three QD-based PDDs, independently activated by the enzymes BamHI, EcoRI, and NcoI, were prototyped in mixed enzyme assays where all three demonstrated the ability to convert enzymatic activity into fluorescent output. Simultaneous monitoring of each of the three paired QD-donor dye-acceptor spectral channels in cell-free biosensing reactions supplemented with added linear genes encoding each enzyme confirmed robust multiplexing capabilities for at least two enzymes when co-expressed. The modular QD-PDDs are easily adapted to respond to other restriction enzymes or even proteases if desired.

Single-Particle Optical Imaging for Ultrasensitive Bioanalysis

The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.

Choosing the Probe for Single-Molecule Fluorescence Microscopy

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.

Polyvalent Glycan Quantum Dots as a Multifunctional Tool for Revealing Thermodynamic, Kinetic, and Structural Details of Multivalent Lectin-Glycan Interactions

Multivalent lectin-glycan interactions (MLGIs) are widespread and vital for biology. Their binding biophysical and structural details are thus highly valuable, not only for the understanding of binding affinity and specificity mechanisms but also for guiding the design of multivalent therapeutics against specific MLGIs. However, effective techniques that can reveal all such details remain unavailable. We have recently developed polyvalent glycan quantum dots (glycan-QDs) as a new probe for MLGIs. Using a pair of closely related tetrameric viral-binding lectins, DC-SIGN and DC-SIGNR, as model examples, we have revealed and quantified their large affinity differences in glycan-QD binding are due to distinct binding modes: with simultaneous binding for DC-SIGN and cross-linking for DC-SIGNR. Herein, we further extend the capacity of the glycan-QD probes by investigating the correlation between binding mode and binding thermodynamics and kinetics and further probing a structural basis of their binding nature. We reveal that while both lectins' binding with glycan-QDs is enthalpy driven with similar binding enthalpy changes, DC-SIGN pays a lower binding entropy penalty, resulting in a higher affinity than DC-SIGNR. We then show that DC-SIGN binding gives a single second-order k_on rate, whereas DC-SIGNR gives a rapid initial binding followed by a much slower secondary interaction. We further identify a structural element in DC-SIGN, absent in DC-SIGNR, that plays an important role in maintaining DC-SIGN's MLGI character. Its removal switches the binding from being enthalpically to entropically driven and gives mixed binding modes containing both simultaneous and cross-linking binding behavior, without markedly affecting the overall binding affinity and kinetics.

The Shell Matters: Self-Organized CdS-ZnS/MnS-Core-Shell—Porphyrin-Polymer Nano-Assemblies for Photocatalysis

A facile synthesis of catalytically tunable core-shell CdS-ZnxMn1-xS-nanoparticles in conjunction with poly(acrylic acid) (PAA) and porphyrin in an aqueous solution is described in the following: The shell composition of the inorganic nanoparticles is varied to tune the optical properties and to optimize the catalytic activity. Further, the tetravalent cationic 5,10,15,20-tetrakis(4-trimethylammoniophenyl) porphyrin (TAPP) fulfills a triple functionality in the catalyst: as a photosensitizer, as an electrostatic linker connecting the nanoparticles and as a probe to investigate the surface composition of the II-VI semiconducting nanoparticles. Different nanoparticles with varying zinc sulfide/manganese sulfide shell ratios are tested with regard to their photocatalytic behavior by crocin bleaching. The results reveal that the shell composition can be a crucial key to optimize the catalytic activity, which can further be important in tuning the reactivity of related systems. Fundamentally, the stepwise multi-component self-assembly in an aqueous solution has been demonstrated to allow the tuning of optic and catalytic properties of core-shell nanoparticles, a general concept that may be widely applicable.

Graphene Nanobeacons with High-Affinity Pockets for Combined, Selective, and Effective Decontamination and Reagentless Detection of Heavy Metals

Access to clean water for drinking, sanitation, and irrigation is a major sustainable development goal of the United Nations. Thus, technologies for cleaning water and quality-monitoring must become widely accessible and of low-cost, while being effective, selective, sustainable, and eco-friendly. To meet this challenge, hetero-bifunctional nanographene fluorescent beacons with high-affinity pockets for heavy metals are developed, offering top-rated and selective adsorption for cadmium and lead, reaching 870 and 450 mg g^-1 , respectively. The heterobifunctional and multidentate pockets also operate as selective gates for fluorescence signal regulation with sub-nanomolar sensitivity (0.1 and 0.2 nm for Pb²⁺ and Cd²⁺ , respectively), due to binding affinities as low as those of antigen-antibody interactions. Importantly, the acid-proof nanographenes can be fully regenerated and reused. Their broad visible-light absorption offers an additional mode for water-quality monitoring based on ultra-low cost and user-friendly reagentless paper detection with the naked-eye at a limit of detection of 1 and 10 ppb for Pb²⁺ and Cd²⁺ ions, respectively. This work shows that photoactive nanomaterials, densely-functionalized with strong, yet selective ligands for targeted contaminants, can successfully combine features such as excellent adsorption, reusability, and sensing capabilities, in a way to extend the material's applicability, its life-cycle, and value-for-money.

Targeting Cancer Stem Cells: Therapeutic and diagnostic strategies by the virtue of nanoparticles

Cancer stem cells (CSCs) are the subpopulation of cells present within a tumor with the properties of self-renewing, differentiating, and proliferating. Owing to the presence of ATP-binding cassette drug pumps and increased expression of anti-apoptotic proteins, the conventional chemotherapeutic agents have failed to eliminate CSCs resulting in relapse and resistance of cancer. Therefore, to obtain long-lasting clinical responses and avoid the recurrence of cancer, it is crucial to develop an efficient strategy targeting CSCs by either employing a differentiation therapy or specifically delivering drugs to CSCs. Several intracellular and extracellular cancer specific biomarkers are overexpressed by CSCs and are utilized as targets for the development of new approaches in the diagnosis and treatment of CSCs. Moreover, several nanostructured particles, alone or in combination with current treatment approaches, have been used to improve the detection, imaging, and targeting of CSCs, thus addressing the limitations of cancer therapies. Targeting CSC surface markers, stemness-related signaling pathways, and tumor microenvironmental signals has improved the detection and eradication of CSCs and, therefore, tumor diagnosis and treatment. This review summarizes a variety of promising nanoparticles targeting the surface biomarkers of CSCs for the detection and eradication of tumor-initiating stem cells, used in combination with other treatment regimens.

DNA sequencing by Förster resonant energy transfer

We propose a new DNA sequencing concept based on nonradiative Förster resonant energy transfer (FRET) from a donor quantum dot (QD) to an acceptor molecule. The FRET mechanism combined with the nanopore-based DNA translocation is suggested as a novel concept for sequencing DNA molecules. A recently-developed hybrid quantum/classical method is employed, which uses time-dependent density functional theory and quasistatic finite difference time domain calculations. Due to the significant absorbance of DNA bases for photon energies higher than 4 eV, biocompatibility, and stability, we use Zinc-Oxide (ZnO) QD as a donor in the FRET mechanism. The most sensitivity for the proposed method to DNA is achieved for the Hoechst fluorescent-dye acceptor and 1 nm ZnO-QD. Results show that the insertion of each type of DNA nucleobases between the donor and acceptor changes the frequency of the emitted light from the acceptor molecule between 0.25 to 1.6 eV. The noise analysis shows that the method can determine any unknown DNA nucleobases if the signal-to-noise ratio is larger than 5 dB. The proposed concept and excellent results shed light on a new promising class of DNA sequencers.

The Rise and Future of Discrete Organic-Inorganic Hybrid Nanomaterials

Hybrid nanomaterials (HNs), the combination of organic semiconductor ligands attached to nanocrystal semiconductor quantum dots, have applications that span a range of practical fields, including biology, chemistry, medical imaging, and optoelectronics. Specifically, HNs operate as discrete, tunable systems that can perform prompt fluorescence, energy transfer, singlet fission, upconversion, and/or thermally activated delayed fluorescence. Interest in HNs has naturally grown over the years due to their tunability and broad spectrum of applications. This Review presents a brief introduction to the components of HNs, before expanding on the characterization and applications of HNs. Finally, the future of HN applications is discussed.

Current and Future Perspectives on Microfluidic Tear Analytic Devices

Most current invasive analytic devices for disease diagnosis and monitoring require the collection of blood, which causes great discomfort for patients and may potentially cause infection. This explains the great need for noninvasive devices that utilize other bodily fluids like sweat, saliva, tears, or urine. Among them, eye tears are easily accessible, less complex in composition, and less susceptible to dilution. Tears also contain valuable clinical information for the diagnosis of ocular and systemic diseases as the tear analyte level shows great correlation with the blood analyte level. These unique advantages make tears a promising platform for use in clinical settings. As the volume of tear film and the rate of tear flow are only microliters in size, the use of microfluidic technology in analytic devices allows minimal sample consumption. Hence, more and more microfluidic tear analytic devices have been proposed, and their working mechanisms can be broadly categorized into four main types: (a) electrochemical, (b) photonic crystals, (c) fluorescence, and (d) colorimetry. These devices are being developed toward the application of point-of-care tests with rapid yet accurate results. This review aims to provide a general overview of the recent developmental trend of microfluidic devices for tear analysis. Moreover, the fundamental principle behind each type of device along with their strengths and weaknesses will be discussed, especially in terms of their abilities and potential in being used in point-of-care settings.

Designing the Surface Chemistry of Inorganic Nanocrystals for Cancer Imaging and Therapy

Inorganic nanocrystals, such as gold, iron oxide and semiconductor quantum dots, offer promising prospects for cancer diagnostics, imaging and therapy, due to their specific plasmonic, magnetic or fluorescent properties. The organic coating, or surface ligands, of these nanoparticles ensures their colloidal stability in complex biological fluids and enables their functionalization with targeting functions. It also controls the interactions of the nanoparticle with biomolecules in their environment. It therefore plays a crucial role in determining nanoparticle biodistribution and, ultimately, the imaging or therapeutic efficiency. This review summarizes the various strategies used to develop optimal surface chemistries for the in vivo preclinical and clinical application of inorganic nanocrystals. It discusses the current understanding of the influence of the nanoparticle surface chemistry on its colloidal stability, interaction with proteins, biodistribution and tumor uptake, and the requirements to develop an optimal surface chemistry.

Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers

We report the peptide-programmed fractal assembly of silver nanoparticles (AgNPs) in a diffusion-limited aggregation (DLA) mode, and this change in morphology generates a significant color change. We show that peptides with specific repetitions of defined amino acids (i.e., arginine, histidine, or phenylalanine) can induce assembly and coalescence of the AgNPs (20 nm) into a hyperbranched structure (AgFSs) (∼2 μm). The dynamic process of this assembly was systematically investigated, and the extinction of the nanostructures can be modulated from 400 to 600 nm by varying the peptide sequences and molar ratio. According to this rationale, two strategies of SARS-CoV-2 detection were investigated. The activity of the main protease (Mpro) involved in SARS-CoV-2 was validated with a peptide substrate that can bridge the AgNPs after the proteolytic cleavage. A sub-nanomolar limit of detection (0.5 nM) and the capacity to distinguish by the naked eye in a wide concentration range (1.25-30 nM) were achieved. Next, a multichannel sensor-array based on multiplex peptides that can visually distinguish SARS-CoV-2 proteases from influenza proteases in doped human samples was investigated.

Quenching Efficiency of Quantum Dots Conjugated to Lipid Bilayers on Graphene Oxide Evaluated by Fluorescence Single Particle Tracking

A single particle observation of quantum dots (QDs) was performed on lipid bilayers formed on graphene oxide (GO). The long-range fluorescence quenching of GO has been applied to biosensing for various biomolecules. We demonstrated the single particle observation of a QD on supported lipid bilayers in this study, aiming to detect the quenching efficiency of lipid and protein molecules in a lipid bilayer by fluorescence single particle tacking (SPT). A single lipid bilayer or double lipid bilayers were formed on GO flakes deposited on a thermally oxidized silicon substrate by the vesicle fusion method. The QDs were conjugated on the lipid bilayers, and single particle images of the QDs were obtained under the quenching effect of GO. The quenching efficiency of a single QD was evaluated from the fluorescence intensities on the regions with and without GO. The quenching efficiency reflecting the layer numbers of the lipid bilayers was obtained.

Optical cytosensors for the detection of circulating tumour cells

Blood analysis is an established approach to monitor various diseases, ranging from heart defects and diabetes to cancer. Among various tumor markers in the blood, circulating tumor cells (CTCs) have received increasing attention due to the fact that they originate directly from the tumors. Capturing and detecting CTCs represents a promising approach in cancer diagnostics and clinical management of cancers. CTCs in blood progress to self-seeding a tumour or initiating a new lesion mass. Cytosensors are biosensors intended to identify CTCs in a blood sample of cancer patients and provide information about the cancer status. Herein, we firstly discuss different detection methods of state-of-the-art optical cytosensors, including colorimetry, fluorescence, surface plasmon resonance, photoelectrochemistry and electrochemiluminescence. Then we review the significant advances made in implementing biorecognition elements and nanomaterials for the detection of cancer cells. Despite great progress in optical cytosensors, and their integration with smartphones, they have still only been explored to prototype stages. Much more effort is needed to fulfil their potential in modern cancer diagnostics and in monitoring the state of disease for cancer patients.

Advances in Nanomaterial-based Biosensors for Determination of Glycated Hemoglobin

Diabetes is a major public health burden whose prevalence has been steadily increasing over the past decades. Glycated hemoglobin (HbA1c) is currently the gold standard for diagnostics and monitoring of glycemic control in diabetes patients. HbA1c biosensors are often considered to be cost-effective alternatives for smaller testing laboratories or clinics unable to access other reference methods. Many of these sensors deploy nanomaterials as recognition elements, detection labels, and/or transducers for achieving sensitive and selective detection of HbA1c. Nanomaterials have emerged as important sensor components due to their excellent optical and electrical properties, tunable morphologies, and easy integration into multiple sensing platforms. In this review, we discuss the advantages of using nanomaterials to construct HbA1c sensors and various sensing strategies for HbA1c measurements. Key gaps between the current technologies with what is needed moving forward are also summarized.

Nucleic acid amplification-integrated single-molecule fluorescence imaging for in vitro and in vivo biosensing

Single-molecule fluorescence imaging is among the most advanced analytical technologies and has been widely adopted for biosensing due to its distinct advantages of simplicity, rapidity, high sensitivity, low sample consumption, and visualization capability. Recently, a variety of nucleic acid amplification approaches have been developed to provide a straightforward and highly efficient way for amplifying low abundance target signals. The integration of single-molecule fluorescence imaging with nucleic acid amplification has greatly facilitated the construction of various fluorescent biosensors for in vitro and in vivo detection of DNAs, RNAs, enzymes, and live cells with high sensitivity and good selectivity. Herein, we review the advances in the development of fluorescent biosensors by integrating single-molecule fluorescence imaging with nucleic acid amplification based on enzyme (e.g., DNA polymerase, RNA polymerase, exonuclease, and endonuclease)-assisted and enzyme-free (e.g., catalytic hairpin assembly, entropy-driven DNA amplification, ligation chain reaction, and hybridization chain reaction) strategies, and summarize the principles, features, and in vitro and in vivo applications of the emerging biosensors. Moreover, we discuss the remaining challenges and future directions in this area. This review may inspire the development of new signal-amplified single-molecule biosensors and promote their practical applications in fundamental and clinical research.

Fluorescent quantum dots enable SARS-CoV-2 antiviral drug discovery and development

INTRODUCTION

SARS-CoV-2 is a highly infectious and deadly coronavirus whose study requires the use of a biosafety level 3 (BSL-3) containment facility to investigate viral biology and pathogenesis, which limits the study of live virus and slows progress toward finding suitable treatments for infection. While vaccines from several companies have proven very effective in combating the virus, few treatments exist for those who do succumb to the viral-induced systemic disease called COVID-19.

AREAS COVERED

This short review focuses on fluorescent quantum dot-based modeling of SARS-CoV-2. New BSL-2 viral models are essential for finding small molecules and biologics that may be effective in stopping viral infection, as well as treating already infected individuals. Nanoparticles are invaluable tools for biological research as they can be used to both model pathogens and serve as a platform for developing vaccines.

EXPERT OPINION

Visualizing viral activity with fluorescent quantum dots enables both biochemical and cell-based assays to detect virus-host receptor interactions, cellular activity after binding to the cell plasma membrane, screening for interventions using small-molecule drug repurposing, and testing of novel biologics. Quantum dots can also be used for diagnostic assays, vaccine development, and importantly, pan-antiviral drugs to address variants that may escape the immune response.

Bio-Conjugated Quantum Dots for Cancer Research: Detection and Imaging

Ultrasound, computed tomography, magnetic resonance, and gamma scintigraphy-based detection and bio-imaging technologies have achieved outstanding breakthroughs in recent years. However, these technologies still encounter several limitations such as insufficient sensitivity, specificity and security that limit their applications in cancer detection and bio-imaging. The semiconductor quantum dots (QDs) are a kind of newly developed fluorescent nanoparticles that have superior fluorescence intensity, strong resistance to photo-bleaching, size-tunable light emission and could produce multiple fluorescent colors under single-source excitation. Furthermore, QDs have optimal surface to link with multiple targets such as antibodies, peptides, and several other small molecules. Thus, QDs might serve as potential, more sensitive and specific methods of detection than conventional methods applied in cancer molecular targeting and bio-imaging. However, many challenges such as cytotoxicity and nonspecific uptake still exist limiting their wider applications. In the present review, we aim to summarize the current applications and challenges of QDs in cancer research mainly focusing on tumor detection, bio-imaging, and provides opinions on how to address these challenges.

Activatable MRI probes for the specific detection of bacteria

Activatable fluorescent probes have been successfully used as molecular tools for biomedical research in the last decades. Fluorescent probes allow the detection of molecular events, providing an extraordinary platform for protein and cellular research. Nevertheless, most of the fluorescent probes reported are susceptible to interferences from endogenous fluorescence (background signal) and limited tissue penetration is expected. These drawbacks prevent the use of fluorescent tracers in the clinical setting. To overcome the limitation of fluorescent probes, we and others have developed activatable magnetic resonance probes. Herein, we report for the first time, an oligonucleotide-based probe with the capability to detect bacteria using magnetic resonance imaging (MRI). The activatable MRI probe consists of a specific oligonucleotide that targets micrococcal nuclease (MN), a nuclease derived from Staphylococcus aureus. The oligonucleotide is flanked by a superparamagnetic iron oxide nanoparticle (SPION) at one end, and by a dendron functionalized with several gadolinium complexes as enhancers, at the other end. Therefore, only upon recognition of the MRI probe by the specific bacteria is the probe activated and the MRI signal can be detected. This approach may be widely applied to detect bacterial infections or other human conditions with the potential to be translated into the clinic as an activatable contrast agent.

Surface-Modified Colloid CdTe/CdS Quantum Dots by a Biocompatible Thiazolidine Derivative as Promising Platform for Immobilization of Glucose Oxidase: Application to Fluorescence Sensing of Glucose

This work focuses on the synthesis of novel modified core-shell CdTe/CdS quantum dots (QDs) and develops as a fluorescence sensor for glucose determination. The (E)-2,2'-(4,4'-dioxo-2,2'-dithioxo-2H,2'H-[5,5'-bithiazolylidene]-3,3'(4H,4'H)-diyl)bis(3- mercaptopropanoic acid) (DTM) as a new derivative of thiazolidine was synthesized and characterized and used to surface-modification of CdTe/CdS QDs. DTM-capped CdTe/CdS QDs used to immobilization of glucose oxidase (GOD). The intensity fluorescence emission of the CdSe/CdS-DTM/GOD is highly sensitive to the concentration of H₂O₂ as a byproduct of the catalytic oxidation of glucose. The experimental results showed that the quenched fluorescence was proportional to the glucose concentration within the range of 10 nM-0.32 μM under optimized experimental conditions. The limit of detection of this system was found to be 4.3 nM. Compared with most of the existing methods, this newly developed system possesses many advantages, including simplicity, low cost, and good sensitivity.

Ir(III) Complex Dimer Nanoparticles for Photodynamic Therapy

Iridium compounds are versatile in catalysis and photodynamic therapy. We present two Ir(III) complex dimers that can self-assemble into nanoparticles in the absence of adjuvant or surfactants. The formed nanoparticles possess a spherical morphology and robust colloidal stability and could be internalized by cancer cells. The Ir(III) complex nanoparticles have relatively strong photodynamic activity upon irradiation, which includes type I and type II reactive oxygen species. The generated reactive oxygen species could effectively induce cell death upon irradiation. This work highlights the potential of metal complexes and their nanoparticles in cancer treatment.

Bottom-Up Assembled Photonic Crystals for Structure-Enabled Label-Free Sensing

Photonic crystals (PhCs) display photonic stop bands (PSBs) and at the edges of these PSBs transport light with reduced velocity, enabling the PhCs to confine and manipulate incident light with enhanced light-matter interaction. Intense research has been devoted to leveraging the optical properties of PhCs for the development of optical sensors for bioassays, diagnosis, and environmental monitoring. These applications have furthermore benefited from the inherently large surface area of PhCs, giving rise to high analyte adsorption and the wide range of options for structural variations of the PhCs leading to enhanced light-matter interaction. Here, we focus on bottom-up assembled PhCs and review the significant advances that have been made in their use as label-free sensors. We describe their potential for point-of-care devices and in the review include their structural design, constituent materials, fabrication strategy, and sensing working principles. We thereby classify them according to five sensing principles: sensing of refractive index variations, sensing by lattice spacing variations, enhanced fluorescence spectroscopy, surface-enhanced Raman spectroscopy, and configuration transitions.

Real-Time In Vivo Detection and Monitoring of Bacterial Infection Based on NIR-II Imaging

Treatment according to the dynamic changes of bacterial load in vivo is critical for preventing progression of bacterial infections. Here, we present a lead sulfide quantum dots (PbS QDs) based second near-infrared (NIR-II) fluorescence imaging strategy for bacteria detection and real-time in vivo monitoring. Four strains of bacteria were labeled with synthesized PbS QDs which showed high bacteria labeling efficiency in vitro. Then bacteria at different concentrations were injected subcutaneously on the back of male nude mice for in vivo imaging. A series of NIR-II images taken at a predetermined time manner demonstrated changing patterns of photoluminescence (PL) intensity of infected sites, dynamically imaging a changing bacterial load in real-time. A detection limit around 10²–10⁴ CFU/ml was also achieved in vivo. Furthermore, analysis of pathology of infected sites were performed, which showed high biocompatibility of PbS QDs. Therefore, under the guidance of our developed NIR-II imaging system, real-time detection and spatiotemporal monitoring of bacterial infection in vivo can be achieved, thus facilitating anti-infection treatment under the guidance of the dynamic imaging of bacterial load in future.