A fluorescent amplification strategy for high-sensitive detection of 17 β-estradiol based on EXPAR and HCR

EXPAR for biosensing: recent developments and applications

Emerging as a promising novel amplification technique, the exponential amplification reaction (EXPAR) offers significant advantages due to its potent exponential amplification capability, straightforward reaction design, rapid reaction kinetics, and isothermal operation. The past few years have witnessed swift advancements and refinements in EXPAR-based technologies, with numerous high-performance biosensing systems documented. A deeper understanding of the EXPAR mechanism has facilitated the proposal of novel strategies to overcome limitations inherent to traditional EXPAR. Furthermore, the synergistic integration of EXPAR with diverse amplification methodologies, including the use of a CRISPR/Cas system, metal nanoparticles, aptamers, alternative isothermal amplification techniques, and enzymes, has significantly bolstered analytical efficacy, aiming to enhance specificity, sensitivity, and amplification efficiency. This comprehensive review presents a detailed exposition of the EXPAR mechanism and analyzes its primary challenges. Additionally, we summarize the latest research advancements in the biomedical field concerning the integration of EXPAR with diverse amplification technologies for sensing strategies. Finally, we discuss the challenges and future prospects of EXPAR technology in the realms of biosensing and clinical applications.

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.

Ultrasensitive Detection Strategy of Norovirus Based on a Dual Enhancement Strategy: CRISPR-Responsive Self-Assembled SNA and Isothermal Amplification

Spherical nucleic acids (SNAs) have been used to construct various nanobiosensors with gold nanoparticles (AuNPs) as nuclei. The SNAs play a critical role in biosensing due to their various physical and chemical properties, programmability, and specificity recognition ability. In this study, CRISPR-responsive self-assembled spherical nucleic acid (CRISPR-rsSNA) detection probes were constructed by conjugating fluorescein-labeled probes to the surface of AuNPs to improve the sensing performance. Also, the mechanism of ssDNA and the role of different fluorescent groups in the self-assembly process of CRISPR-rsSNA were explored. Then, CRISPR-rsSNA and reverse transcription-recombinase polymerase amplification (RT-RPA) were combined to develop an ultrasensitive fluorescence-detection strategy for norovirus. In the presence of the virus, the target RNA sequence of the virus was transformed and amplified by RT-RPA. The resulting dsDNA activated the trans-cleavage activity of CRISPR cas12a, resulting in disintegrating the outer nucleic acid structure of the CRISPR-rsSNA at a diffusible rate, which released reporter molecules. Norovirus was quantitated by fluorescence detection. This strategy facilitated the detection of the norovirus at the attomolar level. An RT-RPA kit for norovirus detected would be developed based on this method. The proposed method would be used for the detection of different viruses just by changing the target RNA and crRNA of the CRISPR cas12a system which provided a foundation for high-throughput detection of various substances.

Isothermal nucleic acid amplification and its uses in modern diagnostic technologies

Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.

The development of a fluorescence/colorimetric biosensor based on the cleavage activity of CRISPR-Cas12a for the detection of non-nucleic acid targets

Nano-biosensors are of great significance for the analysis and detection of important biological targets. Surprisingly, the CRISPR-Cas12a system not only provides us with excellent gene editing capabilities, it also plays an important role in biosensing due to its high base resolution and high levels of sensitivity. However, most CRISPR-Cas12a-based sensors are limited by their recognition and output modes, are therefore only utilized for the detection of nucleic acids using fluorescence as an output signal. In the present study, we further explored the potential application of CRISPR-Cas12a and developed a CRISPR-Cas12a-based fluorescence/colorimetric biosensor (UCNPs-Cas12a/hydrogel-MOF-Cas12a) that provides an efficient targeting system for small molecules and protein targets. These two sensors yield multiple types of signal outputs by converting the target molecule into a deoxyribonucleic acid (DNA) signal input system using aptamers, amplifying the DNA signal by catalyzed hairpin assembly (CHA), and then combining CRISPR-Cas12a with various nanomaterials. UCNPs-Cas12a/hydrogel-MOF-Cas12a exhibited prominent sensitivity and stability for the detection of estradiol (E2) and prostate-specific antigen (PSA), and was successfully applied for the detection of these targets in milk and serum samples. A major advantage of the hydrogel-MOF-Cas12a system is that the signal output can be observed directly. When combined with aptamers and nanomaterials, CRISPR-Cas12a can be used to target multiple targets, with a diverse array of signal outputs. Our findings create a foundation for the development of CRISPR-Cas12a-based technologies for application in the fields of food safety, environmental monitoring, and clinical diagnosis.

Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection

Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.

Signal Amplification-Based Biosensors and Application in RNA Tumor Markers

Tumor markers are important substances for assessing cancer development. In recent years, RNA tumor markers have attracted significant attention, and studies have shown that their abnormal expression of post-transcriptional regulatory genes is associated with tumor progression. Therefore, RNA tumor markers are considered as potential targets in clinical diagnosis and prognosis. Many studies show that biosensors have good application prospects in the field of medical diagnosis. The application of biosensors in RNA tumor markers is developing rapidly. These sensors have the advantages of high sensitivity, excellent selectivity, and convenience. However, the detection abundance of RNA tumor markers is low. In order to improve the detection sensitivity, researchers have developed a variety of signal amplification strategies to enhance the detection signal. In this review, after a brief introduction of the sensing principles and designs of different biosensing platforms, we will summarize the latest research progress of electrochemical, photoelectrochemical, and fluorescent biosensors based on signal amplification strategies for detecting RNA tumor markers. This review provides a high sensitivity and good selectivity sensing platform for early-stage cancer research. It provides a new idea for the development of accurate, sensitive, and convenient biological analysis in the future, which can be used for the early diagnosis and monitoring of cancer and contribute to the reduction in the mortality rate.

Ultrasensitive Automatic Detection of Small Molecules by Membrane Imaging of Single Molecule Assays

Determination of trace amounts of targets or even a single molecule target has always been a challenge in the detection field. Digital measurement methods established for single molecule counting of proteins, such as single molecule arrays (Simoa) or dropcast single molecule assays (dSimoa), are not suitable for detecting small molecule, because of the limited category of small molecule antibodies and the weak signal that can be captured. To address this issue, we have developed a strategy for single molecule detection of small molecules, called small molecule detection with single molecule assays (smSimoa). In this strategy, an aptamer is used as a recognition element, and an addressable DNA Nanoflower (DNF) attached on the magnetic beads surface, which exhibit fluorescence imaging, is employed as the output signal. Accompanied by digital imaging and automated counting analysis, E2 at the attomolar level can be measured. The smSimoa breaks the barrier of small molecule detection concentration and provides a basis for high throughput detection of multiple substances with fluorescence encoded magnetic beads.

Dual-Mechanism Quenching of Electrochemiluminescence Immunosensor Based on a Novel ECL Emitter Polyoxomolybdate-Zirconia for 17β-Estradiol Detection

The exploration of novel electrochemiluminescence (ECL) reagents has been a breakthrough work in ECL immunoassay. In this work, the ECL properties of polyoxomolybdate-zirconia (POM-ZrO₂) were discovered for the first time and their luminescence mechanism was initially explored. Virgulate POM-ZrO₂ was synthesized from phosphomolybdic acid hydrate and zirconium oxychloride by solvothermal method, which achieved intense and stabilized cathode ECL emission at a negative potential. Polyaniline@Au nanocrystals (PANI@AuNPs) as the executor of the dual-mechanism quenching strategy were used to reduce the output signal. The quenching efficiency was significantly enhanced by the dual mechanisms of ECL energy transfer and electron transfer. Specifically, PANI@AuNPs can serve as an energy receptor to absorb the energy emitted by POM-ZrO₂ (energy donor), while the appropriate energy level can be regarded as the condition for electron transfer to quench the ECL intensity of POM-ZrO₂. Herein, the proposed dual-mechanism quenching strategy was applied to the immunoassay of 17β-estradiol by constructing a competitive immunosensor. As expected, the immunosensor demonstrated favorable analytical performance and a wide sensing range from 0.01 pg/mL to 200 ng/mL. Hence, it provides a novel method for the sensitive analysis of other biomolecules, such as disease markers and environmental estrogens.

Highly-sensitive and simple fluorescent aptasensor for 17 b-estradiol detection coupled with HCR-HRP structure

As an important kind of environmental endocrine disruptors, 17 β -Estradiol (E2) plays a major role in affecting the growth of human including sexual characters, pregnancy system, etc. In the modern society, with the threat of abuse in breeding, it is imperative to design sensitive methods for detecting low concentration of E2 in environment. In this work, we constructed a highly sensitive and simple fluorescent aptasenor for detecting E2 via amplification of hybridization chain reaction (HCR) and horseradish peroxidase (HRP). Through the competitions between complementary strand (cmDNA) and E2 to E2 aptamer modified on magnetic beads, the unbound cmDNA would be collected and captured by polystyrene microspheres to induce HCR which brought abundant biotin sites. Subsequently, benefit from the excellent catalytic performance of streptavidin-horseradish peroxidase (SA-HRP), the highly sensitive fluorescence signals could be obtained in low concentration of E2. Under the optimal conditions, the prospered method for E2 detection was shown a good liner range from 1 to 100 pg/mL, with the lower detecting limit of 0.2 pg/mL compared with previous work. In addition, the recovery rates tested in the real samples of milk and water were 99.20%-108.06% and 91.07%-106.13%. In all, the assay may provide a perspective way for highly sensitive detection for various contaminants in the real samples.

NIR persistent luminescence nanoparticles based turn-on aptasensor for autofluorescence-free determination of 17β-estradiol in milk

Consistent exposure to 17β-estradiol through drinking water and food can cause health problems. Although many simple and sensitive fluorescence sensors of 17β-estradiol have been reported, most of them are based on fluorescence quenching test mode working in visible light range, which are inferior in anti-interference ability and quantitative range. Here, we developed a near-infrared (NIR) phosphorescence aptasensor for the detection of 17β-estradiol that has no background fluorescence. The aptasensor was based on Foster resonance energy transfer (FRET) between aptamer conjugated NIR persistent luminescence nanoparticles (PLNPs-Apt) and MoS₂ nanosheets. The 17β-estradiol was quantified by the recovery of PLNPs' phosphorescence. This assay can detect 17β-estradiol in 0.5 mL samples with the LOD of 0.29 ng mL^-1 and in concentrations of more than three orders of magnitude (from 0.5 ng mL^-1 to 1.2 μg mL^-1). This aptasensor exhibited selectivity for 17β-estradiol and was applicable in complex milk samples.

A Polydopamine-Coated Gold Nanoparticles Quenching Quantum Dots-Based Dual-Readout Lateral Flow Immunoassay for Sensitive Detection of Carbendazim in Agriproducts

In this study, a fluorometric and colorimetric dual-readout lateral flow immunoassay (LFIA) using antibody functionalized polydopamine-coated gold nanoparticles (Au@PDAs) as a probe was developed for the detection of carbendazim (CBD). Colloidal gold nanoparticles (AuNPs) were coated with polydopamines (PDA) by the oxidation of dopamine to synthesize Au@PDA nanoparticles. The Au@PDA nanoparticles mediated ZnCdSe/ZnS quantum dots (QDs) fluorescence quenching and recovery, resulting in a reverse fluorescence enhancement detection format of CBD. The CBD detection was obtained by the competition between the CBD and the immobilized antigen for Au@PDAs labelled antibody binding, resulting in a significant fluorescence increase and colorimetry decrease corresponded to the concentration of CBD. Dual readout modes were incorporated into the LFIA using the colorimetry signal under natural light and the fluorescence signal under UV light. The cut-off value in the mode of the colorimetric signal and fluorometric signal for CBD detection was 0.5 μg/mL and 0.0156 μg/mL, respectively. The sensitivity of LFIA of the fluorescence mode was 32 times higher than that of the colorimetry mode. There was negligible cross reactivity obtained by using LFIA for the determination of thiabendazole, benomyl, thiophanate-methyl, and thiophanate-ethyl. Consistent and satisfactory results have been achieved by comparing the results of Au@PDAs-QDs-LFIA and liquid chromatography-tandem mass spectrometry (LC-MS/MS) testing spiked cucumber and strawberry samples, indicating good reliability of the Au@PDAs-QDs-LFIA.

The fluorescent biosensor for detecting N6 methyladenine FzD5 mRNA and MazF activity

N⁶ methyladenine (m⁶A) modification of the FzD5 mRNA, an important post-transcriptional regulation in eukaryotes, is closely related to the occurrence and development of breast cancer. Here, we developed an ultra-sensitive biosensor based on MazF combining with cascaded strand displacement amplification (C-SDA) and CRISPR/Cas12a to detect m⁶A FzD5 mRNA. MazF toxin protein is a vital component of the bacterial mazEF toxin-antitoxin system that is sensitive to m⁶A RNA. Take advantage of it, the biosensor achieved antibody-independent and gene-specific detection for m⁶A RNA. Moreover, compared with traditional amplification methods, the more efficient C-SDA and the CRISPR/Cas12a system with trans-cleavage activity gave the fluorescent biosensor an excellent sensitivity with the detection limit of 0.64 fM. In addition, MazF, as a new antibacterial target, was detected by the biosensor based on C-SDA and CRISPR/Cas12a with the detection limit of 1.127 × 10^-4 U mL^-1. More importantly, the biosensor has good performance in complex samples. Therefore, the biosensor is a potential tool in detecting m⁶A FzD5 mRNA and MazF activity.

Proximity-Induced Hybridization Chain Reaction-Based Photoacoustic Imaging System for Amplified Visualization Protein-Specific Glycosylation in Mice

Glycosylation is a key cellular mechanism that regulates several physiological and pathological functions. Therefore, identification and characterization of specific-protein glycosylation in vivo are highly desirable for studying glycosylation-related pathology and developing personalized theranostic modalities. Herein, we demonstrated a photoacoustic (PA) nanoprobe based on the proximity-induced hybridization chain reaction (HCR) for amplified visual detection of protein-specific glycosylation in vivo. Two kinds of functional DNA probes were designed. A glycan probe (DBCO-GP) was attached to glycans through metabolic oligosaccharide engineering (MOE) and protein probe (PP)-targeted proteins by aptamer recognition. Proximity-induced hybridization of the complementary domain between the two kinds of probes promoted conformational changes in the protein probes and in situ release of the HCR initiator domain. Gold nanoparticles (AuNPs) modified by complementary sequences (Au-H1 and Au-H2) self-assembled into Au aggregates via the HCR, thereby converting DNA signals to photoacoustic signals. Due to the high contrast and deep penetration of photoacoustic imaging, this strategy enabled in situ detection of Mucin 1 (MUC1)-specific glycosylation in mice with breast cancer and successfully monitored its dynamic states during tunicamycin treatment. This imaging technique provides a powerful platform for studying the effects of glycosylation on the protein structure and function, which helps to elucidate its role in disease processes.

Visual-afterglow dual-mode immunochromatographic strip for 17β-estradiol detection in milk

The continuous intake of 17β-estradiol (E2) residue from animal-derived food may pose a threat to the health of consumers, so the rapid screen and detection of E2 is very necessary. Although visual immunochromatographic strip (ICS) has played a great role in food safety control such as the screen of many food contaminants, it cannot meet the requirements for E2 detection due to the insufficient sensitivity of traditional visual ICS and the low concentration range of estrogen in food. Here, we developed a dual-mode ICS strategy to achieve rapid and highly sensitive detection of E2. Based on the visual detection mode of a competitive ICS, the afterglow detection mode working in fluorescence resonance energy transfer mechanism was introduced by using the afterglow particles (APs) as energy donor and gold nanoparticles (AuNPs) as energy acceptor. In this method, large APs of micron size with superior afterglow were applied as the test zone-fixed fluorescence signal source, thus the contradiction between migration and afterglow characteristics was skillfully resolved. In addition, a 6 W UV lamp was used as the light source to excite APs, and a smartphone was used to capture an image of 0.5 s after the UV light was turned off to effectively remove the autofluorescence from the strips and improve the signal-to-noise ratio. The limit of detection of this afterglow mode was 0.5 ng/mL, twenty times more sensitive than that of visual mode (10 ng/mL). The strategy has been successfully applied to the detection of estradiol in milk and verified by HPLC-FLD.

Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification

17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA-RCA-MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836-183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8-107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.