Fluorescent Biosensor Research Articles

DNA‐Templated Gold Nanoclusters for miRNA Diagnostics with Branched Hybridization Chain Reaction

In this study, a novel nonlinear branched hybridization chain reaction (BHCR) strategy is developed for accurate biosensing and bioimaging. Four fuel strands are designed. The first two assist the growth of primary long double‐stranded chain. Meanwhile, branched tails are left, which consist the trigger of downstream HCR with the second group of fuel strands. Branched DNA nanostructures are thus formed, which significantly amplify the information of initial target miRNA. Besides, the output fluorescent signal is originated from DNA‐templated gold nanoclusters (AuNCs). Surface ligands of AuNCs always play important roles in the regulation of optical mechanisms. Herein, peptide/DNA‐stabilized AuNCs are prepared. Phosphorothioate‐modified DNA (psDNA) is used as the template for in situ synthesis. The short peptide (Tyr‐Cys‐Tyr, YCY) is introduced as the protecting ligand, which benefits significant Stokes shift via a two‐step Förster resonance energy transfer. Coupling BHCR and AuNCs, this method performs satisfactory for in vitro fluorescent biosensing and intracellular bioimaging. It exhibits potential application for the investigation of miRNA‐related bioprocesses.

Multicolor Gold Clusterzyme-Enabled Construction of Ratiometric Fluorescent Sensor Array for Visual Biosensing.

The simultaneous detection of multiple bioanalytes with similar structures has been a long-standing challenge for biological research and disease diagnosis. Bioreceptor-inspired sensor arrays provide an attractive and competitive solution for addressing this challenge, but applying this technique to biosensing in practical application scenarios is complicated by many factors such as the lack of robust probes, interference from the biological matrix, and difficulty for on-site analysis. In this work, by taking advantage of the intrinsic fluorescence and enzyme-mimic properties of gold nanoclusters (AuNCs), we report the design of an innovative ratiometric sensor array toward enhanced fluorescent visual biosensing. With biologically important phosphates as an example, we show that the present fluorescent clusterzyme-based ratiometric sensor array could effectively discriminate and detect eight types of phosphates. In particular, AuNCs with three different emission colors (blue, green, and red) and good peroxidase-mimic properties were employed as the sensing units, and the presence of phosphates affected both the intrinsic fluorescence and the enzymatic activity of these AuNCs, yielding distinct optical responses in a ratiometric manner. Moreover, a portable sensor array was established by further integrating these fluorescent clusterzymes into a hydrogel matrix, which could visually identify different phosphates based on their distinct fluorescence color changes. Consequently, the point-of-care diagnosis of urinary tract infections at different levels was achieved by analyzing urinary microbial ATP via the present strategy. This study illustrates the great potential of clusterzyme-based fluorescent sensor arrays as a promising biosensing platform for disease diagnosis.

Enzyme-free and highly sensitive detection of human epidermal growth factor receptor-2 based on MNAzyme signal amplification in breast cancer.

As a common cancer biomarker, human epidermal growth factor receptor-2 (HER2) is highly expressed in breast cancer. Consequently, developing a simple and accurate HER2 sensing platform is of great significance for early diagnosis and treatment of breast cancer. Herein, we developed a rapid enzyme-free fluorescent assay biosensor based on MNAzyme signal amplification for breast cancer biomarker, HER2. The MNAzyme consists of multiple parts, including complementary DNA (cDNA) and two parts of DNAzyme (partzyme A/B). Initially, cDNA is blocked by combining with the HER2 aptamer to form a double-stranded DNA. When HER2 is present, cDNA is released as a result of the binding between HER2 and its aptamer. Due to the complementary sequences among cDNA and partzyme A/B, the MNAzyme is successfully assembled to cleave the substrate, recovering the fluorescence output. The MNAzyme biosensor exhibited a low detection limit of 0.02 ng mL-1 and excellent selectivity. Furthermore, the proposed biosensor can also change the recognition element by changing the aptamer sequence to detect various biomarkers, holding great potential for cancer diagnosis and other related biomedical applications.

Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals.

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.

Enhanced Detection of Vibrio harveyi Using a Dual-Composite DNAzyme-Based Biosensor

Vibrio harveyi is a serious bacterial pathogen which can infect a wide range of marine organisms, such as marine fish, invertebrates, and shrimp, in aquaculture, causing severe losses. In addition, V. harveyi can be transmitted through food and water, infecting humans and posing a serious threat to public safety. Therefore, rapid and accurate detection of this pathogen is key for the prevention and control of related diseases. In this study, nine rounds of in vitro screening were conducted with Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology using unmodified DNA libraries, targeting the crude extracellular matrix (CEM) of V. harveyi. Two DNAzymes, named DVh1 and DVh3, with high activity and specificity were obtained. Furthermore, a fluorescent biosensor with dual DNAzymes was constructed which exhibited improved detection efficiency. The sensor showed a good fluorescence response to multiple aquatic products (i.e., fish, shrimp, and shellfish) infected with V. harveyi, with a detection limit below 11 CFU/mL. The fluorescence signal was observed within 30 min of reaction after target addition. This simple, inexpensive, highly effective, and easy to operate DNAzymes biosensor can be used for field detection of V. harveyi.

Editorial: Lighting up cellular dynamics with fluorescent biosensors: design and applications in pathophysiology

Editorial: Lighting up cellular dynamics with fluorescent biosensors: design and applications in pathophysiology

Synthesis, Functionalization, and Biomedical Applications of Iron Oxide Nanoparticles (IONPs)

Iron oxide nanoparticles (IONPs) have garnered significant attention in biomedical applications due to their unique magnetic properties, biocompatibility, and versatility. This review comprehensively examines the synthesis methods, surface functionalization techniques, and diverse biomedical applications of IONPs. Various chemical and physical synthesis techniques, including coprecipitation, sol–gel processes, thermal decomposition, hydrothermal synthesis, and sonochemical routes, are discussed in detail, highlighting their advantages and limitations. Surface functionalization strategies, such as ligand exchange, encapsulation, and silanization, are explored to enhance the biocompatibility and functionality of IONPs. Special emphasis is placed on the role of IONPs in biosensing technologies, where their magnetic and optical properties enable significant advancements, including in surface-enhanced Raman scattering (SERS)-based biosensors, fluorescence biosensors, and field-effect transistor (FET) biosensors. The review explores how IONPs enhance sensitivity and selectivity in detecting biomolecules, demonstrating their potential for point-of-care diagnostics. Additionally, biomedical applications such as magnetic resonance imaging (MRI), targeted drug delivery, tissue engineering, and stem cell tracking are discussed. The challenges and future perspectives in the clinical translation of IONPs are also addressed, emphasizing the need for further research to optimize their properties and ensure safety and efficacy in medical applications. This review aims to provide a comprehensive understanding of the current state and future potential of IONPs in both biosensing and broader biomedical fields.

An Upconversion Fluorescent Resonant Energy Transfer Biosensor for the Detection of microRNA through DNA Hybridization

An Upconversion Fluorescent Resonant Energy Transfer Biosensor for the Detection of microRNA through DNA Hybridization

Tetraphenylethene-Based Covalent Organic Polymers with Aggregation-Induced Electrochemiluminescence for Highly Sensitive Bacterial Biosensors.

Tetraphenylethene (TPE), which usually serves as aggregation-induced emission and aggregation-induced electrochemiluminescence fluorophores, has been widely applied in fabricating fluorescent nanomaterials and biosensors. However, it is still a tremendous challenge to prepare well-controlled TPE aggregates with strong fluorescence (FL) and electrochemiluminescence (ECL). In this study, we constructed a bacterial ECL biosensing platform with high sensitivity based on TPE-based covalent organic polymer (COP) nanoparticles synthesized by a simple Menschutkin reaction strategy to employ bromide group-carrying molecules and 1,1,2,2-tetrakis(4-(pyridine-4-yl)phenyl)ethene as the cross-linking agent and the emissive moiety, respectively. The ECL Escherichia coli biosensor had high sensitivity, a low limit of detection (0.19 CFU mL-1), a wide linear range (1 × 102-5 × 106 CFU mL-1), and good selectivity. The excellent properties of the bacterial biosensor could be attributed to the uniform spherical COP nanoparticles with enhanced FL and ECL signals, the maximal ECL efficiency of which was 8.4-fold higher than that of the typical tris(bipyridine) ruthenium(II) emitter. The FL and ECL intensities of the TPE-based COP nanoparticles could be adjusted by varying bromide group-carrying molecules and thus regulating their energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) orbitals. The TPE-based COP nanoparticles with strong FL and ECL intensities pave a promising avenue to construct highly sensitive bacterial ECL biosensors for the large-scale screening of disease-causing bacteria.

Long-term optical imaging of the spinal cord in awake behaving mice.

Advances in optical imaging and fluorescent biosensors enable study of the spatiotemporal and long-term neural dynamics in the brain of awake animals. However, methodological difficulties and fibrosis limit similar advances in the spinal cord. Here, to overcome these obstacles, we combined in vivo application of fluoropolymer membranes that inhibit fibrosis, a redesigned implantable spinal imaging chamber and improved motion correction methods that together permit imaging of the spinal cord in awake behaving mice, for months to over a year. We demonstrated a robust ability to monitor axons, identified a spinal cord somatotopic map, performed months-long imaging in freely moving mice, conducted Ca2+ imaging of neural dynamics in behaving mice responding to pain-provoking stimuli and observed persistent microglial changes after nerve injury. The ability to couple in vivo imaging and behavior at the spinal cord level will drive insights not previously possible at a key location for somatosensory transmission to the brain.

Reversible addition-fragmentation chain transfer enhanced aggregation signal-on fluorescence detection of alkaline phosphatase.

The instability of the signal intensity of fluorescent biosensors and the false signals have been significant factors affecting the performance of biosensors. Herein, a novel signaling system is devised through the application of reversible addition-fragmentation chain transfer (RAFT) polymerization with monomers containing the tetraphenylethylene (TPE) groups. TPE exhibits an aggregation-induced emission (AIE) phenomenon in certain solvents, mainly due to the blockage of the rotation of its four benzene rings, which also exist in the aggregated state. With this property, a series of molecules are modified based on click chemistry for RAFT polymerization using Fe3O4 magnetic beads as the carriers, and stable aggregated luminescent TPE polymers are formed on the surface of magnetic beads to realize the transformation of fluorescence signal from "0" to "1". In addition, the fluorescence signal demonstrates a positive correlation with alkaline phosphatase (ALP) activity, which can be quantified by measuring the fluorescence intensity. The biosensor exhibits high sensitivity and good linearity in the range of 0.1-5 U/L, with a LOD of 0.079 U/L. Furthermore, the designed strategy demonstrated satisfactory performance in the quantitative determination of ALP activity in serum samples, indicating that the signaling system developed by combining RAFT polymerization and AIE molecules has an important application in the field of fluorescent biosensors.

Locking-Fluorescence Signals Regulated CRISPR/Cas12a Biosensor Based on Metal-Organic Framework for Sensitive Detection of Salmonella typhimurium.

The efficient, sensitive, and rapid detection of Salmonella typhimurium (S. typhimurium) in food and food products is important to ensure food safety and health. This study developed a fluorescence biosensing assay that integrated recombinase-aided amplification (RAA) and CRISPR/Cas12a with a zeolitic imidazolate framework-8@fluorescein sodium (ZIF-8@FLS) nanocomposite for the sensitive detection of S. typhimurium. In this approach, using RAA as a preamplification module, CRISPR/Cas12a-AChE as a target recognition and dual-enzyme cascade amplification module, and the prepared ZIF-8@FLS with high porosity and rapid pH responsiveness as a fluorescence signal explosive amplification module, the RAA-CRISPR/Cas12a-ZIF-8@FLS biosensor was constructed. Under optimal conditions, it exhibited an excellent linear relationship for S. Typhimurium, with a sensitive detection limit as low as 1.3 × 102 CFU/mL and could complete sample detection within 2 h relying on the RAA and ZIF-8@FLS explosive fluorescence rapid response, demonstrating its significant advantages in specificity, sensitivity, and reliability in food-borne pathogens detection.

Self-Assembly of Microstructured Protein Coatings with Programmable Functionality for Fluorescent Biosensors.

Proteins, as genetically programmable functional macromolecules, hold immense potential as biocompatible self-assembling building blocks, owing to their versatility in building coating materials and programming their functionality genetically. In this study, we demonstrate a modular self-assembly of protein coatings that are genetically programmable for a biosensor application. We designed and produced recombinant fusion protein building blocks to form microstructured coatings on diverse substrates, such as glass or polymers, through thermally triggered liquid-liquid phase separation and an orthogonal high-affinity coiled-coil interaction. We incorporated fluorescence proteins into coatings and controlled the protein density to enable fluorescence imaging and quantification in a low-resource setting. Then, we created a coating for a calcium biosensor using a genetically engineered calcium indicator protein. This protein coating served as the foundation for our smartphone-based fluorescent biosensor, which successfully measured free calcium concentrations in the millimolar range at which extracellular calcium homeostasis is maintained. Using this fluorescent biosensor, we were able to detect abnormal physiological conditions, such as mild or moderate hypercalcemia. We envision that this modular and genetically programmable functional protein coating platform could be extended to the development of highly accessible, low-cost fluorescent biosensors for a variety of targets.

Definition of phosphatidylinositol 4,5-bisphosphate distribution by freeze-fracture replica labeling.

Phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] is a phospholipid essential for plasma membrane functions, but its two-dimensional distribution is not clear. Here, we compared the result of sodium dodecyl sulfate-treated freeze-fracture replica labeling (SDS-FRL) of quick-frozen cells with the actual PtdIns(4,5)P2 content and the results obtained by fluorescence biosensor and by labeling of chemically-fixed membranes. In yeast, enrichment of PtdIns(4,5)P2 in the membrane compartment of Can1 (MCC)/eisosome, especially in the curved MCC/eisosome, was evident by SDS-FRL, but not by fluorescence biosensor, GFP-PLC1δ-PH. PtdIns(4,5)P2 remaining after acute ATP depletion and in the stationary phase, 30.0% and 56.6% of the control level, respectively, was not detectable by fluorescence biosensor, whereas the label intensity by SDS-FRL reflected the PtdIns(4,5)P2 amount. In PC12 cells, PtdIns(4,5)P2 was observed in a punctate pattern in the formaldehyde-fixed plasma membrane, whereas it was distributed randomly by SDS-FRL and showed clustering after formaldehyde fixation. The results indicate that the distribution of PtdIns(4,5)P2 can be defined most reliably by SDS-FRL of quick-frozen cells.

Development and Optimization of a Redox Enzyme-Based Fluorescence Biosensor for the Identification of MsrB1 Inhibitors

MsrB1 is a thiol-dependent enzyme that reduces protein methionine-R-sulfoxide and regulates inflammatory response in macrophages. Therefore, MsrB1 could be a promising therapeutic target for the control of inflammation. To identify MsrB1 inhibitors, we construct a redox protein-based fluorescence biosensor composed of MsrB1, a circularly permutated fluorescent protein, and the thioredoxin1 in a single polypeptide chain. This protein-based biosensor, named RIYsense, efficiently measures protein methionine sulfoxide reduction by ratiometric fluorescence increase. We used it for high-throughput screening of potential MsrB1 inhibitors among 6868 compounds. A total of 192 compounds were selected based on their ability to reduce relative fluorescence intensity by more than 50% compared to the control. Then, we used molecular docking simulations of the compound on MsrB1, affinity assays, and MsrB1 activity measurement to identify compounds with reliable and strong inhibitory effects. Two compounds were selected as MsrB1 inhibitors: 4-[5-(4-ethylphenyl)-3-(4-hydroxyphenyl)-3,4-dihydropyrazol-2-yl]benzenesulfonamide and 6-chloro-10-(4-ethylphenyl)pyrimido[4,5-b]quinoline-2,4-dione. They are heterocyclic, polyaromatic compounds with a substituted phenyl moiety interacting with the MsrB1 active site, as revealed by docking simulation. These compounds were found to decrease the expression of anti-inflammatory cytokines such as IL-10 and IL-1rn, leading to auricular skin swelling and increased thickness in an ear edema model, effectively mimicking the effects observed in MsrB1 knockout mice. In summary, using a novel redox protein-based fluorescence biosensor, we identified potential MsrB1 inhibitors that can regulate the inflammatory response, particularly by influencing the expression of anti-inflammatory cytokines. These compounds are promising tools for understanding MsrB1’s role during inflammation and eventually controlling inflammation in therapeutic approaches.

Enzyme-Assisted Fluorescence Biosensor Based on Circular Single-Stranded DNA Without Group Modification for MicroRNA Detection

Fluorescent biosensor, which has the characteristics of high sensitivity, specificity, and low cost, can be directly detected in physiological fluids such as blood and serum. Therefore, the development of fluorescence sensor platforms for miRNA detection has a positive effect on the prevention and treatment of various diseases. In this paper, miR-34a was selected as a biological indicator of Alzheimer’s disease (AD). We designed a circular single-stranded DNA (CSSD) biosensor, which uses two unmodified single-stranded DNA (ssDNA) with complementary ends, DNAa and DNAb, to form CSSD by DNA sequence pairing to improve thermal stability and achieve signal amplification. At the same time, CSSD can react with miR-34a, and then the DNA of the DNA–RNA chain is hydrolyzed by duplex-specific nuclease (DSN enzyme). Finally, miR-34a is released to partake in the subsequent step, thus realizing cycle amplification. By evaluating the change in fluorescence signal under the optimized conditions, we discovered that this approach exhibits impressive sensitivity, with a detection threshold reaching as low as 0.36 nM. This surpasses the performance of numerous preceding miRNA detection biosensors. Furthermore, the system displays excellent detection capabilities even in intricate settings like serum, showcasing a strong ability to differentiate and choose effectively. In summary, this is a signal-off fluorescent biosensor, which realizes the purpose of double amplification of biosensor signal by using CSSD and enzyme assistance so that it can be used as a valuable tool for early diagnosis of diseases.

A fluorescent biosensor based on surface cell imprinting film for Salmonella typhimurium detection

Salmonella typhimurium (S. typhimurium) is a major foodborne pathogen that poses a potentialrisk to public health. The development of biosensors that are specific, sensitive, and easy to manipulate can greatly reduce the potential risk posed by S. typhimurium. A robust, highly sensitive and specific fluorescent biosensor was proposed by combining N-succinyl-chitosan-doped surface bacterial cell imprinted film (SCIF) with typical aggregation induced emission (AIE) fluorescent substance Au(I)-disulfide nanoparticles. The proposed fluorescent sensor can achieve linear detection of S. typhimurium in the concentration range from 10 to 106 CFU/mL with a detection limit of 4 CFU/mL. In addition, the modification of the SCIF on the surface enables specific abiotic recognition of the target bacteria. This fluorescence sensing strategy can be used for the detection of S. typhimurium in chicken meat samples. The platform can be replicated for the detection of other bacteria or cells via making different SCIFs, which is promising for the detection of practical samples for clinical and biological applications.

Graphene oxide-based fluorescent biosensors for pathogenic bacteria detection: a review

Graphene oxide-based fluorescent biosensors for pathogenic bacteria detection: a review

Elucidating the spatiotemporal dynamics of glucose metabolism with genetically encoded fluorescent biosensors.

Glucose metabolism has been well understood for many years, but some intriguing questions remain regarding the subcellular distribution, transport, and functions of glycolytic metabolites. To address these issues, a living cell metabolic monitoring technology with high spatiotemporal resolution is needed. Genetically encoded fluorescent sensors can achieve specific, sensitive, and spatiotemporally resolved metabolic monitoring in living cells and invivo, and dozens of glucose metabolite sensors have been developed recently. Here, we highlight the importance of tracking specific intermediate metabolites of glycolysis and glycolytic flux measurements, monitoring the spatiotemporal dynamics, and quantifying metabolite abundance. We then describe the working principles of fluorescent protein sensors and summarize the existing biosensors and their application in understanding glucose metabolism. Finally, we analyze the remaining challenges in developing high-quality biosensors and the huge potential of biosensor-based metabolic monitoring at multiple spatiotemporal scales.

Peptide-Based Rapid and Selective Detection of Mercury in Aqueous Samples with Micro-Volume Glass Capillary Fluorometer

Mercury, a toxic heavy metal produced through both natural and anthropogenic processes, is found in all of Earth’s major systems. Mercury’s bioaccumulation characteristics in the human body have a significant impact on the liver, kidneys, brain, and muscles. In order to detect Hg2+ ions, a highly sensitive and specific fluorescent biosensor has been developed using a novel, modified seven amino acid peptide, FY7. The tyrosine ring in the FY7 peptide sequence forms a 2:1 complex with Hg2+ ions that are present in the water-based sample. As a result, the peptide’s fluorescence emission decreases with higher concentrations of Hg2+. The FY7 peptide’s performance was tested in the presence of Hg2+ ions and other metal ions, revealing its sensitivity and stability despite high concentrations. Conformational changes to the FY7 structure were confirmed by FTIR studies. Simultaneously, we designed a miniaturized setup to support an in-house-developed micro-volume capillary container for volume fluorometry measurements. We compared and verified the results from the micro-volume system with those from the commercial setup. The micro-volume capillary system accommodated only 2.9 µL of sample volume, allowing for rapid, sensitive, and selective detection of toxic mercury (II) ions as low as 0.02 µM.