Fluorescent Biosensor Research Articles

A CRISPR/Cas13a-powered catalytic hairpin assembly evanescent wave fluorescence biosensor for target amplification-free SARS-CoV-2 detection

The end of the coronavirus disease 2019 (COVID-19) pandemic still drives the development of rapid and accurate detection technology to prepare for diverse viral infections and emerging pandemics in the future. Herein, a CRISPR/Cas13a-powered catalytic hairpin assembly evanescent wave fluorescence biosensor (CAPABLE) was developed for amplification-free detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the ingenious design of trigger, the presence of SARS-CoV-2 activated the trans-cleavage activity of Cas13a, followed by the initiation of a catalytic hairpin assembly (CHA) system that exhibited excellent signal amplification efficiency. By integrating the biotin-avidin system, the detection sensitivity of the portable fluorescence platform was greatly improved. Quantitative SARS-CoV-2 detection was realized with a detection limit of 18.6 copies/μL within 50 min based on a fast extraction method. The proposed method exhibited a 100% positive detection rate for environmental water samples spiked with SARS-CoV-2 pseudovirus, which was consistent with standard RTqPCR results. Benefiting from amplification-free performance, the CAPABLE method holds great promise for rapid SARS-CoV-2 detection in field laboratories and primary facilities in resource-limited areas. With the inherent flexibility of the CRISPR/Cas system, the proposed method has the potential to be applied in the diagnosis of various infectious diseases.

Investigating G-protein coupled receptor signalling with light-emitting biosensors.

G protein-coupled receptors (GPCRs) are the most frequent target of currently approved drugs and play a central role in both physiological and pathophysiological processes. Beyond the canonical understanding of GPCR signal transduction, the importance of receptor conformation, beta-arrestin (β-arr) biased signalling, and signalling from intracellular locations other than the plasma membrane is becoming more apparent, along with the tight spatiotemporal compartmentalisation of downstream signals. Fluorescent and bioluminescent biosensors have played a pivotal role in elucidating GPCR signalling events in live cells. To understand the mechanisms of action of the GPCR-targeted drugs currently available, and to develop new and better GPCR-targeted therapeutics, understanding these novel aspects of GPCR signalling is critical. In this review, we present some of the tools available to interrogate each of these features of GPCR signalling, we illustrate some of the key findings which have been made possible by these tools and we discuss their limitations and possible developments.

CRISPR/Cas12a cleavage-mediated isothermal amplification lights up the dimeric G-quadruplex signal unit for ultrasensitive and label-free detection of circulating tumor DNA

Circulating tumor DNA (ctDNA) is a valuable and potential cancer biomarker for real-time monitoring, and plays a vital role in cancer early diagnosis. In this work, we developed an ultrasensitive and label-free fluorescent biosensor for ctDNA detection. A well-designed RNA-DNA chimeric primer (RD) with phosphate groups modified at the 3-terminal was cleaved by target-initiated CRISPR/Cas12a, and then the subsequent exponential amplification reaction (EXPAR) was started to produce numerous G-rich sequences, which could be assembled with Thioflavin T to form a dimeric G-quadruplex (dimer-G4/ThT) and significantly enhance the fluorescence. Due to the innovative combination of the specificity of CRISPR/Cas12a and RD primers, the high amplification efficiency of EXPAR, and the strong fluorescence response of dimer-G4/ThT, this strategy demonstrated excellent sensitivity at the aM level. In addition, the sensing system showed satisfactory anti-interference ability and reliable accuracy in complex serum environment and tumor cell lysate. More importantly, this strategy avoided the complicated and expensive labeling process of traditional signal probes, making the construction of fluorescent biosensor simpler and more practical, offering practical insights for molecular diagnostics and clinical applications.

An enzyme-free and label-free ratiometric fluorescence signal amplification biosensor based on DNA-silver nanoclusters and catalytic hairpin assembly for tetracycline detection

Sensitive and accurate in antibiotic detection is crucial for food security, environmental conservation, public health, and environmental protection. In this study, we developed an enzyme-free and label-free ratiometric fluorescence biosensor for highly sensitive detection of tetracycline (TET). This biosensor utilized a combination of target-triggered catalytic hairpin assembly (CHA) and DNA-silver nanocluster (DNA-AgNCs) dual-color fluorescent signal probes. Upon TET binding to the aptamer, it initiated the leakage of CHA initiator, resulting in the formation of numerous double-stranded DNA complexes. This process exposed the foothold sequence of hairpin-structured DNA-AgNCs (H3-AgNCs) that exhibit yellow fluorescence. Subsequently, the conformational changes in H3-AgNCs significantly reduced the yellow fluorescence intensity (FI) and reveal the auxiliary DNA-AgNCs (a-DNA-AgNCs) linkage sequence. The binding of a-DNA-AgNCs brought two dark AgNCs close, forming nanocluster dimers emitting red fluorescence. The results demonstrate that the variation in ratiometric signal is linear with TET concentration between 0.1 and 50 ng/mL, with a detection limit as low as 0.086 ng/mL. Additionally, this approach exhibited good recovery results with spiked milk samples. This enzyme-free and label-free combined signal amplification method with proportional signal output based on DNA-AgNCs provides valuable empirical reference for creating low-cost, stable, and highly-sensitive biosensors.

Recent research progress of selenotungstate-based biomolecular sensing materials.

Polyoxometalates (POMs) have drawn significant attention on account of their structural designability, compositional diversity and great potential applications. As an indispensable branch of POMs, selenotungstates (SeTs) have been synthesized extensively. Some SeTs have been applied as sensing materials for detecting biomarkers (e.g., metabolites, hormones, cancer markers). To gain a comprehensive understanding of advancements in SeT-based sensing materials, we present an overview that encapsulates the sensing performances and mechanisms of SeT-based biosensors. SeT-based biosensors are categorized into electrochemical catalytic biosensors, electrochemical affinity biosensors, "turn-off" fluorescence biosensors and "turn-on" fluorescence biosensors. We anticipate the expansive potential of SeT-based biosensors in wearable and implantable sensing technologies, which promises to catalyze significant breakthroughs in SeT-based biosensors.

Label-free ratiometric fluorescence detection of Pb2+via structure-specific fluorescent dyes and dual signal amplification.

Lead ions (Pb2+) are a widely distributed and highly toxic heavy metal pollutant, which seriously threatens the environment, economy and human safety. Here, a label-free ratiometric fluorescent biosensor was constructed for Pb2+ detection using DNAzyme-driven target cycling and exonuclease III (Exo III)-mediated DNA cycling as a dual signal amplification strategy. The SYBR Green I (SGI) and N-methyl mesoporphyrin IX (NMM) used in this study are characterized by low cost, storage resistance, and short preparation time compared with conventional signaling probes labeled with fluorescent groups. Unlike the single-emission fluorescence strategy, monitoring the fluorescence intensity ratio of SGI and NMM can effectively reduce external interference to achieve accurate detection of Pb2+. DNAzyme structures on the surface of magnetic beads (MBs) can recognize Pb2+ and activate the target circulatory system to cleave single-stranded DNA (ssDNA). The ssDNA further initiated the Exo III-assisted DNA circulatory system to digest double-stranded DNA (dsDNA) and release guanine-rich G1. Finally, the fluorescence signals of SGI and NMM were weakened and enhanced, respectively. The sensing strategy achieved a wide linear range from 0.5 to 500 nM and a low limit of detection (LOD) of 26.4 pM. Furthermore, its anti-interference ability and potential applicability for Pb2+ detection in actual samples were verified. This work ingeniously combines the dual signal amplification strategy with the ratiometric sensing strategy constructed by structure-specific fluorescent dyes, which provides a promising method for constructing sensitive and accurate fluorescent biosensors.

A quadratic isothermal amplification fluorescent biosensor without intermediate purification for ultrasensitive detection of circulating tumor DNA.

Circulating tumor DNA (ctDNA) is an auspicious tumor biomarker released into the bloodstream by tumor cells, offering abundant information concerning cancer genes. It plays a crucial role in the early diagnosis of cancer. However, due to extremely low levels in body fluids, achieving a simple, sensitive, and highly specific detection of ctDNA remains challenging. Here, we constructed a purification-free fluorescence biosensor based on quadratic amplification of ctDNA by combining nicking enzyme mediated amplification (NEMA) and catalytic hairpin assembly (CHA) reactions. After double isothermal amplification, this biosensor achieved an impressive signal amplification of nearly 107-fold, enabling it to detect ctDNA with ultra-sensitivity. And the detection limit of this biosensor is as low as 2 aM. In addition, we explored the influence of human serum on the performance of the biosensor and found that it showed favorable sensitivity in the presence of serum. This biosensor eliminates the need for an intermediate purification step, resulting in enhanced sensitivity and convenience. Thus, our purification-free fluorescent biosensor exhibits ultra-high sensitivity when compared to other biosensors and has the potential to serve as an effective diagnostic tool for early detection of cancer.

Analysis of Guard Cell Readouts Using Arabidopsis thaliana Isolated Epidermal Peels.

Stomata are pores surrounded by a pair of specialized cells, called guard cells, that play a central role in plant physiology through the regulation of gas exchange between plants and the environment. Guard cells have features like cell-autonomous responses and easily measurable readouts that have turned them into a model system to study signal transduction mechanisms in plants. Here, we provide a detailed protocol to analyze different physiological responses specifically in guard cells. We describe, in detail, the steps and conditions to isolate epidermal peels with tweezers and to analyze i) stomatal aperture in response to different stimuli, ii) cytosolic parameters such as hydrogen peroxide (H2O2), glutathione redox potential (E GSH), and MgATP-2 in vivo dynamics using fluorescent biosensors, and iii) gene expression in guard cell-enriched samples. The importance of this protocol lies in the fact that most living cells on epidermal peels are guard cells, enabling the preparation of guard cell-enriched samples. Key features • Isolation of epidermal peels as a monolayer enriched in guard cells • Measurement of cytosolic guard cell signaling component dynamics in isolated epidermal peels through fluorescent biosensor analysis • Gene expression analysis of guard cell-enriched isolated tissue.

A label free fluorescent aptamer sensor based on the combined action of Graphene oxide and SYBR Green I for the detection of Aflatoxin B1.

Here, based on the characteristics of Graphene oxide(GO) and SYBR Green I(SGI) dye, an enzyme-free and label-free fluorescent biosensor with signal amplification through DNA strand reaction is proposed for the detection of Aflatoxin B1(AFB1) in food safety. Firstly, without the addition of AFB1, the substrate in the system includes a double stranded Apt-S with a long sticky end and two hairpins H1 and H2. Although the complementary pairing of bases may exhibit fluorescence due to the insertion of SGI dyes, the use of GO, which is highly capable of adsorbing single stranded parts and quenching fluorescence, cleverly reduces the background fluorescence. Adding the target AFB1 triggers DNA inter chain reactions, generating a large amount of long double stranded DNA H1-H2, thereby generating strong fluorescence signals under the action of SGI. More importantly, logical theory verification and computer simulation were conducted before biological experiments, providing a theoretical basis for the implementation of the biosensor. After analysis, the fluorescence biosensor exhibits a good linear relationship with AFB1 concentration in the range of 5-50nM, with a detection limit of 0.76nM. It also has good specificity, anti-interference ability, and practical application ability, and has broad application prospects in the field of food safety.

Application of CRISPR/Cas13a-based biosensors in serum marker detection.

The detection of serum markers is important for the early diagnosis and monitoring of diseases, but conventional detection methods have the problem of low specificity or sensitivity. CRISPR/Cas13a-based biosensors have the characteristics of simple detection methods and high sensitivity, which have a certain potential to solve the problems of conventional detection. This paper focuses on the research progress of CRISPR/Cas13a-based biosensors in serum marker detection, introduces the principles and applications of fluorescence, electrochemistry, colorimetric, and other biosensors based on CRISPR/Cas13a in the detection of serum markers, compares and analyzes the differences between the above CRISPR/Cas13a-based biosensors, and looks forward to the future development direction of CRISPR/Cas13a-based biosensors.

A fluorescent DNAzyme-based biosensor for the detection of lead ions using carbon quantum dots prepared from grapefruit peel

The key design strategy lies in hemin/G-CQDs. The fluorescence of G-CQDs was quenched after binding with hemin and recovered after removing hemin by combining with a G-quadruplex.

Fluorescent and electrochemical detection of nuclease activity associated with Streptococcus pneumoniae using specific oligonucleotide probes.

Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 102 CFU mL-1, whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 106 CFU mL-1. Moreover, the specificity studies have demonstrated the biosensors' remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.

Dual-mode colorimetric and fluorescence detection of BRCA1 based on a CRISPR-Cas12a system.

Breast cancer, the most common malignant tumor in the world, seriously threatens human life and health. Early diagnosis of breast cancer may help enhance the survival rate. In this work, a colorimetric and fluorescent dual-mode biosensor based on the CRISPR-Cas12a system was constructed to detect the breast cancer biomarker BRCA1. The intact G4 DNA, with the assistance of K+ and hemin, catalyses the oxidation of o-phenylenediamine (OPD) with the assistance of hydrogen peroxide (H2O2), generating the oxidation product 2,3-diaminophenazine (DAP), which has distinct absorption and fluorescence peaks. The presence of the target BRCA1 activates the trans-cleavage activity of CRISPR-Cas12a, leading to the cleavage of G4 DNA and inhibiting the catalytic oxidation of OPD. Target BRCA1 was quantitatively determined by measuring both the absorbance and fluorescence intensity of DAP. The detection limits were calculated to be 0.615 nM for the colorimetric method and 0.289 nM for the fluorescence method. The dual-mode biosensor showed good selectivity and reliability for BRCA1 and can resist interference from complex substrates, and it has great potential in biomedical detection.

Recent advances in biosensors for screening plant pathogens.

Worldwide, plant pathogens have been a considerably important cause of economic loss in agriculture especially in the decades of agricultural intensification. The increasing losses in agriculture due to biotic plant diseases have drawn attention towards the development of plant disease analyzing methods. In this context, biosensors have emerged as significantly important tools which help farmers in on-field diagnosis of plant diseases. Compared to traditional methods, biosensors have outstanding features such as being highly sensitive and selective, cost-effective, portable, fast and user-friendly operation, and so on. There are three common types of biosensors including electrochemical, fluorescent, and colorimetric biosensors. In this review, some common biotic plant diseases caused by fungi, bacteria, and viruses are first summarized. Then, current advances in developing biosensors are discussed.

Mitochondria-derived reactive oxygen species are the likely primary trigger of mitochondrial retrograde signaling in Arabidopsis

Besides their central function in respiration, plant mitochondria play a crucial role in maintaining cellular homeostasis during stress by providing "retrograde" feedback to the nucleus. Despite the growing understanding of this signaling network, the nature of the signals that initiate mitochondrial retrograde regulation (MRR) in plants remains unknown. Here, we investigated the dynamics and causative relationship of a wide range of mitochondria-related parameters for MRR, using a combination of Arabidopsis fluorescent protein biosensor lines, invitro assays, and genetic and pharmacological approaches. We show that previously linked physiological parameters, including changes in cytosolic ATP, NADH/NAD+ ratio, cytosolic reactive oxygen species (ROS), pH, free Ca2+, and mitochondrial membrane potential, may often be correlated with-but are not the primary drivers of-MRR induction in plants. However, we demonstrate that the induced production of mitochondrial ROS is the likely primary trigger for MRR induction in Arabidopsis. Furthermore, we demonstrate that mitochondrial ROS-mediated signaling uses the ER-localized ANAC017-pathway to induce MRR response. Finally, our data suggest that mitochondrially generated ROS can induce MRR without substantially leaking into other cellular compartments such as the cytosol or ER lumen, as previously proposed. Overall, our results offer compelling evidence that mitochondrial ROS elevation is the likely trigger of MRR.

Polyhedral oligomeric silsesquioxane (POSS)-silicon/carbon quantum dots nanocomposites for cell imaging.

Silicon quantum dots (SiQDs) and carbon quantum dots (CQDs) are renowned for their outstanding applications in fluorescence imaging and biosensing. However, their small size poses significant challenges in terms of preparation, collection, and purification. Polyhedral oligomeric silsesquioxanes (POSS), an organic-inorganic nanohybrid with a cage-like structure, has recently attracted considerable attention due to its excellent biocompatibility. In this research, we utilize the encapsulating properties of POSS to improve the optical property of SiQDs/CQDs through an in situ synthesis strategy, resulting in the production of blue-emitting POSS-SiQDs, green-emitting POSS-G-CNDs, and red-emitting POSS-R-CNDs. By examining their structural and optical characteristics, it is found that these hybrid materials exhibit excellent luminescent properties, biocompatibility and cell membrane permeability. This facilitates multicolor intracellular imaging and underscores their successful application in biological imaging. Our study presents a novel approach to synthesize POSS-QDs composite nanomaterials with new perspectives in biological imaging and medical diagnostics.

Expanding the scope of self-assembled supramolecular biosensors: a highly selective and sensitive enzyme-responsive AIE-based fluorescent biosensor for trypsin detection and inhibitor screening.

Trypsin, a pancreatic enzyme associated with diseases like pancreatic cancer and cystic fibrosis, requires effective diagnostic tools. Current detection systems seldom utilize macrocyclic molecules and tetraphenyl ethylene (TPE) derivative-based supramolecular assemblies, known for their biocompatibility and aggregation-induced emission (AIE) properties, for trypsin detection. This study presents an enzyme-responsive, AIE-based fluorescence 'Turn-On' sensing platform for trypsin detection, employing sulfated-β-cyclodextrin (S-βCD), an imidazolium derivative of TPE (TPE-IM), and protamine sulfate (PrS). The anionic S-βCD and cationic TPE-IM formed a strongly fluorescent supramolecular aggregation complex in an aqueous buffer. However, PrS suppresses fluorescence because of its strong binding affinity with S-βCD. The non-fluorescent TPE-IM/S-βCD/PrS supramolecular assembly system exhibits trypsin-responsive properties, as PrS is a known trypsin substrate. Trypsin restores fluorescence in the TPE-IM/S-βCD system through the enzymatic cleavage of PrS, correlating linearly with trypsin catalytic activity in the 0-10 nM concentration range. The limit of detection is 10 pM. This work contributes to the development of self-assembled supramolecular biosensors using charged TPE derivatives and β-cyclodextrin-based host-guest chemistry, offering an innovative fluorescence 'Turn-On' trypsin sensing platform. The sensing system is highly stable under various conditions, selective for trypsin, and demonstrates potential for biological analysis and disease diagnosis in human serum. Additionally, it shows promise for the screening of trypsin inhibitors.

A cascade signal-amplified fluorescent biosensor combining APE1 enzyme cleavage-assisted target cycling with rolling circle amplification.

A cascade signal-amplified fluorescent biosensor was developed for miRNA-21 detection by combining APE1 enzyme-assisted target recycling and rolling circle amplification strategy. A key feature of this biosensor is its dual-trigger mechanism, utilizing both tumor-endogenous miRNA-21 and the APE1 enzyme in the initial amplification step, followed by a second rolling circle amplification reaction. This dual signal amplification cascade significantly enhanced sensitivity, achieving a detection limit of 3.33 pM. Furthermore, this biosensor exhibited excellent specificity and resistance to interference, allowing it to effectively distinguish and detect the target miRNA-21 in the presence of multiple interfering miRNAs. Moreover, the biosensor maintained its robust detection capabilities in a 10% serum environment, demonstrating its potential for clinical disease diagnosis applications.

Highly efficient WS2 QD-based non-enzymatic fluorescent biosensor for ofloxacin and ciprofloxacin monitoring in aquatic media

We demonstrated a WS2 QDs-induced fluorescence probe for monitoring ofloxacin (OFL) and ciprofloxacin (CIP) in water in the range of 0–3 μM, showing enhanced fluorescence, high sensitivity and anti-interference ability.

A Nitroreductase-Sensitive Near-IR Fluorescent Biosensor for Detecting Tumor Hypoxia in Vivo

Tumor cells have high metabolic demands, leading to increased oxygen consumption and further exacerbating hypoxia, which has been regarded as a characteristic feature of solid tumors and plays a significant...