Multiplexed DNA and Protease Detection with Orthogonal Energy Transfer on a Single Quantum Dot Scaffolded Biosensor

Almost all pathogens, whether viral or bacterial, utilize key proteolytic steps in their pathogenesis. The ability to detect a pathogen's genomic material along with its proteolytic activity represents one approach to identifying the pathogen and providing initial evidence of its viability. Here, we report on a prototype biosensor design assembled around a single semiconductor quantum dot (QD) scaffold that is capable of detecting both nucleic acid sequences and proteolytic activity by using orthogonal energy transfer (ET) processes. The sensor consists of a central QD assembled via peptidyl-PNA linkers with multiple DNA sequences that encode complements to genomic sequences originating from the Ebola, Influenza, and COVID-19 viruses, which we use as surrogate targets. These are hybridized to complement strands labeled with a terbium (Tb) chelate, AlexaFluor647 (AF647), and Cy5.5 dyes, giving rise to two potential FRET cascades: the first includes Tb → QD → AF647 → Cy5.5 (→ = ET step), which is detected in a time-gated modality, and QD → AF647 → Cy5.5, which is detected from direct excitation. The labeled DNA-displaying QD construct is then further assembled with a RuII-modified peptide, which quenches QD photoluminescence by charge transfer and is recognized by a protease to yield the full biosensor. Each of the labeled DNAs and peptides can be ratiometrically assembled to the QD in a controllable manner to tune each of the ET pathways. Addition of a given target DNA displaces its labeled complement on the QD, disrupting that FRET channel, while protease addition disrupts charge transfer quenching of the central QD scaffold and boosts its photoluminescence and FRET relay capabilities. Along with characterizing the ET pathways and verifying biosensing in both individual and multiplexed formats, we also demonstrate the ability of this construct to function in molecular logic and perform Boolean operations; this highlights the construct's ability to discriminate and transduce signals between different inputs or pathogens. The potential application space for such a sensor device is discussed.

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.

Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging

Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.

Electron accepting naphthalene bisimide ligand architectures for modulation of π-π stacking in nanocrystal hybrid materials

Investigation of charge transfer in quantum dot (QD) systems is an area of great interest. Specifically, the relationship between capping ligand and rate of charge transfer has been studied as a means to optimize these materials. To investigate the role of ligand interaction on the QD surface for electron transfer, we designed and synthesized a series of ligands containing an electron accepting moiety, naphthalene bisimide (NBI). These ligands differ in their steric bulk: as one allows for π-π stacking between the NBI moieties at high surface coverages, while the other does not, allowing for a direct comparison of these effects. Once grafted onto QDs, these hybrid materials were studied using UV-Vis, fluorescence, and transient absorption spectroscopy. Interestingly, the sample with the fastest electron transfer was not the sample with the most NBI π-π stacking, it was instead where these ligands were mixed amongst oleic acid, breaking up H-aggregates between the NBI groups.

Evaluation of the effects of mild heat in bovine milk by time resolved fluorescence

Heat treatment of milk and dairy products are indispensable for the dairy industry. This thermal processing intends to extend shelf life, improve quality of the milk and minimize the health risks associated with milk and dairy products. The use of time-resolved fluorescence techniques to identify conformation and structure changes ok milk fat and proteins could help understand the temperature effects in bovine milk. This study aimed to use fluorescence lifetimes to evaluate the effects of heating fresh cow milk up to 85 °C. We observed different tendencies for fluorescence lifetimes submitted to different heating temperatures. The longer lifetime values decreased for temperatures higher than room temperature until it reached a minimum value near 40 °C and it slowly increased again for temperatures higher than 40 °C, indicating two distinct processes. These results indicate that time-resolved fluorescence can assist on the analysis of heating effects in fluid milk.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing

Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.

Quantum Dot-Dye Conjugates for Biosensing, Imaging, and Therapy

Adding value to the intrinsic properties of quantum dots (QDs), a strategy to conjugate dyes on the surface of QDs offers new opportunities, since the coupling between QD and dyes can be designed to allow Förster resonance energy transfer (FRET) and/or electron transfer (eT). These processes are accompanied by the change of QD and/or dye fluorescence and subsequent photochemical reactions (e.g., generation of 1 O2 ). Based on the change of fluorescence signals by the interaction with biomolecules, QD-dye conjugates are exploited as biosensors for the detection of pH, O2 , nicotinamide adenine dinucleotide (phosphate), ions, proteases, glutathione, and microRNA. QD-dye conjugates also can be modulated by the irradiation of external light; this concept is demonstrated for fluorescence super-resolution imaging as photoactivatable or photoswitchable probes. When QDs are conjugated with photosensitizing dyes, the QD-dye conjugates can generate 1 O2 in a repetitive manner for better cancer treatment, and can also be available for approaches using two-photon excitation or bioluminescence resonance energy transfer mechanisms for deep tissue imaging. Here, the recent advances in QD-dye conjugates, where FRET or eT produces fluorescence readouts or photochemical reactions, are reviewed. Various QD-dye conjugate systems and their biosensing/imaging and photodynamic therapeutics are summarized.

Synthesis and characterization of a flexible fluorescent magnetic Fe3O4@SiO2/CdTe-NH2 nanoprobe

In this study, we designed and synthesized two novel fluorescent magnetic nanoparticles. Fe₃O₄@SiO₂-NH-GSH-CdTe (FSGC) (GSH = glutathione) nanoparticles were synthesized using amino-functionalized Fe₃O₄@SiO₂ nanoparticles and GSH-stabilized CdTe quantum dots (CdTe QDs), while flexible Fe₃O₄@SiO₂-NH-GSH-CdTe-NH-NH₂ (FSGCN) nanoparticles were synthesized using the FSGC precursor and 1,6-hexamethylenediamine. These two kinds of nanoprobes exhibited excellent magnetic and fluorescent properties. By comparing the fluorescence quenching effect of folic acid (FA) on FSGC and FSGCN, we found that the quenching effect of FA on FSGC was acute and the process was too fast to determine the FA content. However, the quenching effect of FA on flexible FSGCN was mild and hence it could be used as a nanoprobe to determine FA concentration. At physiological pH, the fluorescence quenching effect of FA on the FSGCN nanoprobes was fitted according to the Stern-Volmer equation with a linear response in the concentration range of 0.14 to 4.20 μg mL^-1 with a detection limit of 15.1 × 10^-9 g mL^-1 (S/N = 3) under optimized experimental conditions. The proposed flexible nanoprobe was successfully used to determine the content of FA in folic acid tablets. Recovery was found to be in the range of 92.7%-105.6% with a relative standard deviation of 1.12%-3.84%. Owing to their good stability, environment-friendly characteristics, high selectivity, and good optical properties and biocompatibility, these nanoprobes have potential for usage in practical applications.

Optical sensing at the nanobiointerface of metal ion-optically-active nanocrystals

Optically-active nanocrystals (such as quantum dots and plasmonic noble metal nanoparticles) have received great attention due to their size-tunable optical properties. The indicator displacement assay (IDA) with optically-active nanocrystals has become a common practice for optical sensor development, since no sophisticated surface functionalization of nanoparticles is required. Among the IDA-based optical sensors, the use of metal ions as receptors seems to be attractive. Therefore, in this review, the research progress of optical sensing at the nanobiointerface of metal ion-optically-active nanocrystals has been summarized. In particular, metal ion-mediated selective recognition has been summarized here based on the classical Hard-Soft-Acid-Base (HSAB) principle, which has been seldom mentioned before. Most of the references were therefore categorized according to their located place based on the HSAB theory. Besides, several metal ion modulation strategies that were not related to the HSAB theory (e.g., redox modulation) were also included. Finally, due to the cross-talk of metal ions in selective recognition, we have also summarized sensor array development based on multiple metal ion receptors in IDA sensing with optically-active nanocrystals. Several interesting applications of the IDA sensing with metal ions as receptors and optically-active nanocrystals as indicators are presented, with specific emphasis on the design principles and photophysical mechanisms of these probes.

Development of quantum dot-based biosensors: principles and applications

We review the recent advances in quantum dot-based biosensors and focus on quantum dot-based fluorescent, bioluminescent, chemiluminescent, and photoelectrochemical biosensors.

Cancer-Microenvironment-Sensitive Activatable Quantum Dot Probe in the Second Near-Infrared Window

Recent technological advances have expanded fluorescence (FL) imaging into the second near-infrared region (NIR-II; wavelength = 1000-1700 nm), providing high spatial resolution through deep tissues. However, bright and compact fluorophores are rare in this region, and sophisticated control over NIR-II probes has not been fully achieved yet. Herein, we report an enzyme-activatable NIR-II probe that exhibits FL upon matrix metalloprotease activity in tumor microenvironment. Bright and stable PbS/CdS/ZnS core/shell/shell quantum dots (QDs) were synthesized as a model NIR-II fluorophore, and activatable modulators were attached to exploit photoexcited electron transfer (PET) quenching. The quasi type-II QD band alignment allowed rapid and effective FL modulations with the compact surface ligand modulator that contains methylene blue PET quencher. The modulator was optimized to afford full enzyme accessibility and high activation signal surge upon the enzyme activity. Using a colon cancer mouse model, the probe demonstrated selective FL activation at tumor sites with 3-fold signal enhancement in 10 min. Optical phantom experiments confirmed the advantages of the NIR-II probe over conventional dyes in the first near-infrared region.

Synthetic strategies and biomedical applications of I–III–VI ternary quantum dots

In this review, we discuss recent advances of I–III–VI QDs with a major focus on synthesis and biomedical applications; advantages include low toxicity and fluorescent tuning in the biological window.

Ratiometric fluorescence, electrochemiluminescence, and photoelectrochemical chemo/biosensing based on semiconductor quantum dots

Ratiometric fluorescent sensors, which can provide built-in self-calibration for correction of a variety of analyte-independent factors, have attracted particular attention for analytical sensing and optical imaging with the potential to provide a precise and quantitative analysis. A wide variety of ratiometric sensing probes using small fluorescent molecules have been developed. Compared with organic dyes, exploiting semiconductor quantum dots (QDs) in ratiometric fluorescence sensing is even more intriguing, owing to their unique optical and photophysical properties that offer significant advantages over organic dyes. In this review, the main photophysical mechanism for generating dual-emission from QDs for ratiometry is discussed and categorized in detail. Typically, dual-emission can be obtained either with energy transfer from QDs to dyes or with independent dual fluorophores of QDs and dye/QDs. The recent discovery of intrinsic dual-emission from Mn-doped QDs offers new opportunities for ratiometric sensing. Particularly, the signal transduction of QDs is not restricted to fluorescence, and electrochemiluminescence and photoelectrochemistry from QDs are also promising for sensing, which can be made ratiometric for correction of interferences typically encountered in electrochemistry. All these unique photophysical properties of QDs lead to a new avenue of ratiometry, and the recent progress in this area is addressed and summarized here. Several interesting applications of QD-based ratiometry are presented for the determination of metal ions, temperature, and biomolecules, with specific emphasis on the design principles and photophysical mechanisms of these probes.

Combining semiconductor quantum dots and bioscaffolds into nanoscale energy transfer devices

Significant advances have been made in the development of nanoscale devices capable of exciton transport via Förster resonance energy transfer. Several requirements must be met for effective operation, including a reliable energy-harvesting source along with highly organized, precisely placed energy relay elements. For the latter, biological scaffolds such as DNA provide a customizable, symmetric, and stable structure that can be site-specifically modified with organic fluorophores. Here, advancements in nanoscale energy transfer devices incorporating semiconductor nanocrystals and bioscaffolds are reviewed with discussion of biofunctionalization, linker chemistries, design considerations, and concluding with applications in light harvesting, multiplexed biosensing, and optical logic.

Graphene Quantum Dots-based Photoluminescent Sensor: A Multifunctional Composite for Pesticide Detection

Due to their size and difficulty to obtain, cost/effective biological or synthetic receptors (e.g., antibodies or aptamers, respectively), organic toxic compounds (e.g., less than 1 kDa) are generally challenging to detect using simple platforms such as biosensors. This study reports on the synthesis and characterization of a novel multifunctional composite material, magnetic silica beads/graphene quantum dots/molecularly imprinted polypyrrole (mSGP). mSGP is engineered to specifically and effectively capture and signal small molecules due to the synergy among chemical, magnetic, and optical properties combined with molecular imprinting of tributyltin (291 Da), a hazardous compound, selected as a model analyte. Magnetic and selective properties of the mSGP composite can be exploited to capture and preconcentrate the analyte onto its surface, and its photoluminescent graphene quantum dots, which are quenched upon analyte recognition, are used to interrogate the presence of the contaminant. This multifunctional material enables a rapid, simple and sensitive platform for small molecule detection, even in complex mediums such as seawater, without any sample treatment.