PfAgo-based dual signal amplification biosensor for rapid and highly sensitive detection of alkaline phosphatase activity

A Pyrococcus furiosus Argonaute (PfAgo)-based biosensor is presented for alkaline phosphatase (ALP) activity detection in which the ALP-catalyzed hydrolysis of 3'-phosphate-modified functional DNA activates the strand displacement amplification, and the amplicon mediates the fluorescent reporter cleavage as a guide sequence of PfAgo. Under the dual amplification mode of PfAgo-catalyzed multiple-turnover cleavage activity and pre-amplification technology, the developed method was successfully applied to ALP activity determination with a detection limit (LOD) of 0.0013 U L-1 (3σ) and a detection range of 0.0025 to 1 U L-1 within 90 min. The PfAgo-based method exhibits satisfactory analytic performance in the presence of potential interferents and in complex human serum samples. The proposed method shows several advantages, such as rapid analysis, high sensitivity, low-cost, and easy operation, and has great potential in disease evolution fundamental studies and clinical diagnosis applications.

The development of biosensors for alkaline phosphatase activity detection based on a phosphorylated DNA probe

Alkaline phosphatase (ALP) is a zinc-containing metalloprotein that shows very great significance in clinical diagnosis, which can catalyze the hydrolysis of phosphorylated species. ALP has the potential to serve as a valuable biomarker for detecting liver dysfunction and bone diseases. On the other hand, ALP is an efficient biocatalyst to amplify detection signals in the enzyme-linked assay. It has always been a major research focus to develop novel biosensors that can detect ALP activity with high selectivity and sensitivity. There have been numerous reports on the development of biosensors to determine ALP activity using a phosphorylated DNA probe. Among them, various beneficial strategies, such as λ exonuclease-mediated cleavage reaction, terminal deoxynucleotidyl transferase-triggered DNA polymerization, and Klenow fragment polymerase-catalyzed elongation, are employed to generate amplified and more intuitive signal. This review discusses and summarizes the development and advances of biosensors for ALP activity detection that use a well-designed phosphorylated DNA probe, aiming to provide some guidelines for the design of more sophisticated sensing strategies that exhibit improved sensitivity, selectivity, and adaptability in detecting ALP activity.

Demethylation-activated light-up dual-color RNA aptamersensor for label-free detection of multiple demethylases in lung tissues

Methylation is one of the most prevalent epigenetic modifications in natural organisms, and the processes of methylation and demethylation are closely associated with cell growth, differentiation, gene transcription and expression. Abnormal methylation may lead to various human diseases including cancers. Simultaneous analysis of multiple DNA demethylases remains a huge challenge due to the requirement of diverse substrate probes and scarcity of proper signal transduction strategies. Herein, we propose a sensitive and label-free method for simultaneous monitoring of multiple DNA demethylases on the basis of demethylation-activated light-up dual-color RNA aptamers. The presence of targets AlkB homologue-3 (ALKBH3) and fat mass and obesity-associated enzyme (FTO) erases the methyl group in DNA substrate probes, activating the ligation-mediate bidirectional transcription amplification reaction to produce enormous Spinach and Mango aptamers. The resulting RNA aptamers (i.e., Spinach and Mango aptamers) can bind with their cognate nonfluorescent fluorogens (DFHBI and TO1-biotin) to significantly improve the fluorescence signals. This aptamersensor shows high specificity and sensitivity with a limit of detection (LOD) of 8.50 × 10-14 M for ALKBH3 and 6.80 × 10-14 M for FTO, and it can apply to screen DNA demethylase inhibitors, evaluate DNA demethylase kinetic parameters, and simultaneously measure multiple endogenous DNA demethylases in a single cell. Importantly, this aptamersensor can accurately discriminate the expressions of ALKBH3 and FTO between healthy tissues and non-small cell lung cancer (NSCLC) patient tissues, offering a powerful platform for clinical diagnosis and drug discovery.

A Ratiometric Fluorescence Biosensor for Detection of Alkaline Phosphatase Via an Advanced Chemometric Model

In this paper, a ratiometric fluorescence biosensor was introduced for alkaline phosphatase (ALP) detection based on 2-aminopurine (2-Amp) and thioflavin T (ThT)-G-quadruplex system. We designed a special DNA (5'-AGGGTTAGGGTTAGGGTTAGGGAAA/i2-Amp/AAAA-PO4-3', AP) modified with a phosphate moiety at the 3'-end, G-quadruplex at the 5'-end, and a fluorophore (2-Amp) in the middle. In the absence of ALP, the G-rich AP strand could be prone to fold into G-quadruplex structures in the presence of K+. Then, ThT combined with G-quandruplex, resulting in the enhancement of fluorescence emission peak at 485 nm. However, ALP-mediated hydrolysis of the 3'-phosphoryl end promoted the cleavage of AP by the exonuclease I (Exo I), releasing 2-Amp which displayed a strong fluorescence emission peak at 365 nm. Moreover, the quantitative fluorescence model (QFM) was derived for the analysis of the fluorescence measurements obtained by the proposed ratiometric fluorescent biosensor. With the aid of the advanced model, the proposed ratiometric fluorescent biosensor possessed satisfactory results for the detection of ALP in the human serum samples, with accuracy comparable to that of the reference method-the commercial ALP assay kit. Under the optimized experimental conditions, this method exhibited good selectivity and higher sensitivity, and the detection limit was found to be as low as 0.017 U/L. Therefore, it is reasonable to expect that the method had a great potential to detect ALP quantitatively in clinical diagnosis.

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.

Hairpin Switches-Based Isothermal Transcription Amplification for Simple, Sensitivity Detection of MicroRNA

The ability to simply, selectively, and sensitively detect low numbers of miRNAs in clinical samples is highly valuable but remains a challenge. In this work, we present a novel miRNA detection system by using the elaborately designed hairpin switch, where the T7 primer, template, target recognize sequence, and light-up RNA aptamer template are edited and embedded in one single-stranded DNA hairpin structure. In the beginning, the hairpin switch maintained the hairpin structure 1, in which the ds promoter of T7 polymerase was disrupted, thus the transcription reaction of T7 polymerase was inhibited. After binding to the target, the hairpin switch 1 was unfolded and turned to the hairpin structure 2. This switch initiates the in vitro T7 transcription reaction, producing plenty of RNA transcripts containing RNA aptamers. Consequently, transcribed tremendous RNA aptamers lighted up the fluorophore for quantitative analysis. Compared with the existing T7 polymerase-based amplification system, this strategy exhibits several advantages, including simplicity, convenience, and high selectivity and sensitivity. The experimental results demonstrated that we could achieve the quantification of miRNA in buffer and complex biological samples.

Methylation-sensitive transcription-enhanced single-molecule biosensing of DNA methylation in cancer cells and tissues

As a major epigenetic modification, DNA methylation participates in diverse cellular functions and emerges as a promising biomarker for disease diagnosis and monitoring. Herein, we developed a methylation-sensitive transcription-enhanced single-molecule biosensor to detect DNA methylation in human cells and tissues. In this biosensor, a rationally designed transcription machine is split into two parts including a promoter sequence (probe-P) for initiating transcription and a template sequence (probe-T) for RNA synthesis. The presence of specific DNA methylation leads to the formation of full-length transcription machine through sequence-specific ligation of probe-P and probe-T, initiating the synthesis of abundant ssRNA transcripts. The resultant ssRNAs can activate CRISPR/Cas12a to catalyze cyclic cleavage of fluorophore- and quencher-dual labeled signal probes, resulting in the recovery of the fluorophore signal that can be quantified by single-molecule detection. Taking advantages of the high-fidelity ligation of split transcription machine and the high efficiency of transcription- and CRISPR/Cas12a cleavage-mediated dual signal amplification, this single-molecule biosensor achieves a low detection limit of 337 aM and high selectivity. Moreover, it can distinguish 0.01% methylation level, and even accurately detect genomic DNA methylation in single cell and clinical samples, providing a powerful tool for epigenetic researches and clinical diagnostics.

Transcriptionally amplified synthesis of fluorogenic RNA aptamers for label-free DNA glycosylase assay

We demonstrate for the first time the utilization of fluorogenic RNA aptamers for label-free uracil-DNA glycosylase (UDG) assay. Through rationally engineering the transcription machine with dU substitution, this assay requires only a single probe to simultaneously sense and amplify the UDG signal, achieving a low detection limit of 6.3 × 10^-6 U mL^-1. Moreover, it can be applied for screening UDG inhibitors and measuring endogenous UDG activity in different cells.

Programmable Ligation-Transcription Circuit-Driven Cascade Amplification Machinery for Multiple Long Noncoding RNAs Detection in Lung Tissues

The measurement of long noncoding RNAs (lncRNAs) is essential to diagnosis and treatment of various diseases such as cancers. Herein, we develop a simple method to simultaneously detect multiple lncRNAs using programmable ligation-transcription circuit-driven cascade amplification and single-molecule counting. The presence of targets lncRNA HOTAIR and lncRNA MALAT1 activates the ligation-transcription circuits to produce two corresponding functional RNAs. The functional RNAs then cyclically initiate the digestion of signal probes by duplex-specific nuclease to liberate Cy5 and Cy3 molecules. After magnetic separation, the liberated Cy5 and Cy3 molecules are measured by single-molecule counting. In this assay, a single lncRNA can activate ligation-transcription circuit to generate abundant functional RNAs, endowing this assay with high sensitivity. Integration of single-molecule counting ensures the high sensitivity. This method shows extremely high sensitivity with a limit of detection (LOD) of 0.043 aM for HOX gene antisense intergenic RNA (lncRNA HOTAIR) and 0.126 aM for mammalian metastasis-related lung adenocarcinoma transcript 1 (lncRNA MALAT1). Importantly, this method enables simultaneous measurement of multiple endogenous lncRNAs at the single-cell level, and it may discriminate the expressions of various lncRNA in lung tumor tissues of nonsmall cell lung cancer (NSCLC) patients and their corresponding healthy adjacent tissues, offering a promising platform for clinical diagnosis and biomedical research.

A simple and rapid mix-and-read assay for sensitive detection of O6-methylguanine DNA methyltransferase

We have developed a simple and rapid mix-and-read assay for the sensitive detection of O⁶-methylguanine DNA methyltransferase (MGMT) activity based on exonuclease III-assisted signal amplification under completely isothermal conditions (37 °C). This method is very simple and rapid (60 min) with ultrahigh sensitivity and good specificity, and it can detect MGMT activity at the single-cell level. Moreover, this method can be applied for the screening of MGMT inhibitors and the discrimination of MGMT in different cancer cells.

Redox-Responsive Breakup of a Nucleic Acids@CoOOH Nanocomplex Triggering Cascade Recycling Amplification for Sensitive Sensing of Alkaline Phosphatase

Alkaline phosphatase (ALP), an essential hydrolase with crucial roles in living organisms, has widely been regarded as a biomarker for various human diseases in clinical diagnoses. Herein, taking advantage of cobalt oxyhydroxide (CoOOH) nanoflakes and nonenzymatic cascade recycling amplification (CRA), a highly sensitive and label-free fluorescence biosensing strategy for the determination of ALP activity is introduced. In our design, ALP can promote the dephosphorylation of l-ascorbic acid 2-phosphate (AAP) to reduce ascorbic acid (AA), which is then able to decompose CoOOH in a nucleic acids@CoOOH nanocomplex into Co²⁺ cofactors. Further, enzyme-free CRA was rapidly initiated by integrating DNAzyme recycling amplification and catalytic hairpin assembly, resulting in the generation of an abundance of G-quadruplex structure-contained DNA duplexes. In the presence of thioflavin T (ThT), analytical target ALP was converted in an amplified and activatable fluorescence signal. The experimental results show that this method can be applied for the quantitative analysis of ALP activity with a low detection limit of 0.027 mU/mL. Moreover, this developed biosensing approach exhibits excellent specificity, and the evaluation of ALP activity in the complex human serum samples was successfully realized, indicating that it can afford a reliable, robust, and cost-effective nanoplatform for an ALP-based clinical diagnosis and for biomedical research.

Single-Molecule Biosensing of Alkaline Phosphatase in Cells and Serum Based on Dephosphorylation-Triggered Catalytic Assembly and Disassembly of the Fluorescent DNA Chain

Alkaline phosphatase (ALP) is a valuable biomarker and effective therapeutic target for the diagnosis and treatment of diverse human diseases, including bone disorder, cardiovascular disease, and cancers. The reported ALP assays often suffer from laborious procedures, costly reagents, inadequate sensitivity, and large sample consumption. Herein, we report a new single-molecule fluorescent biosensor for the simple and ultrasensitive detection of ALP. In this assay, the ALP-catalyzed dephosphorylation of detection probe can protect the detection probe against lambda exonuclease-mediated digestion, and the remaining detection probes can trigger ceaseless hybridization between two Cy5-labeled hairpin probes through toehold-mediated DNA strand displacement, generating a long fluorescent DNA chain, which can be subsequently separated from unhybridized hairpin probes and disassembled into dispersed Cy5 moieties upon NaOH treatment. The free Cy5 moieties indicate the presence of ALP and can be directly quantified via single-molecule counting. This biosensor enables efficient amplification and transduction of the target ALP signal through enzyme-free assembly and disassembly processes, significantly simplifying the experimental procedure and improving the assay accuracy. The proposed biosensor allows specific and ultrasensitive detection of ALP activity with a detection limit down to 2.61 × 10^-6 U mL^-1 and is suitable for ALP inhibition assay and kinetic analysis. Moreover, this biosensor can be applied for endogenous ALP detection in human cells and clinical human serum, holding the potential in the ALP biological function study and clinical diagnosis.

Systems biomarker characteristics of circulating alkaline phosphatase activities for 48 types of human diseases

BACKGROUND

Most human diseases are accompanied by systems changes. Systems biomarkers should reflect such changes. The phosphorylation and dephosphorylation of biomolecules maintain human homeostasis. However, the systems biomarker characteristics of circulating alkaline phosphatase, a routine blood test conducted for many human diseases, have never been investigated.

METHOD

This study retrieved the circulating alkaline phosphatase (ALP) activities from patients with 48 clinically confirmed diseases and healthy individuals from the database of our hospital during the past five years. A detailed analysis of the statistical characteristics of ALP was conducted, including quantiles, receiving operator curve (ROC), and principal component analysis.

RESULTS

Among the 48 diseases, 45 had increased, and three had decreased median levels of ALP activities compared to the healthy control. Preeclampsia, hepatic encephalopathy, pancreatic cancer, and liver cancer had the highest median values, whereas nephrotic syndrome, lupus erythematosus, and nephritis had decreased median values compared to the healthy control. Further, area under curve (AUC) values were ranged between 0.61 and 0.87 for 19 diseases, and the ALP activities were the best systems biomarker for preeclampsia (AUC 0.87), hepatic encephalopathy (AUC 0.87), liver cancer (AUC 0.81), and pancreatic cancer (AUC 0.81).

CONCLUSIONS

Alkaline phosphatase was a decent systems biomarker for 19 different types of human diseases. Understanding the molecular mechanisms of over-up-and-down-regulation of ALP activities might be the key to understanding the whole-body systems' reactions during specific disease progression.

Label-free and sensitive detection of RNA demethylase FTO with primer generation rolling circle amplification

We develop for the first time a label-free fluorescent method for sensitive detection of fat mass and obesity-associated protein (FTO) activity using MazF-mediated primer generation rolling circle amplification. This method is very simple with ultrahigh sensitivity and good specificity, and it can detect FTO activity at the single-cell level. Moreover, this method can be applied for the measurement of kinetic parameters and the screening of FTO inhibitors.

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

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

Target-induced transcription of a light-up RNA aptamer to construct a novel method for alkaline phosphatase assay

We herein developed a novel method for alkaline phosphatase (ALP) assay based on the target-induced transcription of a light-up RNA aptamer, consequently producing a highly enhanced fluorescence signal upon specifically binding to the corresponding dye. Using this strategy, we successfully determined the ALP activity down to 0.018 U L-1 (dynamic linear range of 0.04-4 U L-1) with excellent selectivity.

Self-Assembly of Superquenched Gold Nanoparticle Nanosensors for Lighting up BACE-1 in Live Cells

The β-site amyloid precursor protein-cleaving enzyme 1 (BACE-1) plays a key role in Alzheimer's disease (AD) pathogenesis and is regarded as a valuable biomarker for AD diagnosis and treatment. The reported BACE-1 assay often suffers from laborious procedures, large sample consumption, and unsatisfactory sensitivity with high background signals. Herein, we report the self-assembly of superquenched gold nanoparticle (AuNP) nanosensors for lighting up the BACE-1 in live cells. Through the self-assembly of both fluorophore-labeled peptide probes and quencher-labeled assistant DNAs on the surface of a single AuNP, a superquenched AuNP nanoprobe is obtained with a high quenching efficiency of 98.37% and a near-zero background fluorescence. The presence of target BACE-1 induces a distinct fluorescence signal as a result of the BACE-1-catalyzed cleavage of peptide probe and the subsequent release of abundant fluorophore moieties from the AuNP nanoprobe. The fluorescence signal can be directly visualized by single-molecule imaging and easily quantified by single-molecule counting. This nanosensor involves only a single nanoprobe for the one-step homogeneous detection of the BACE-1 activity without the requirements of any antibodies and separation steps, and it possesses good selectivity and high sensitivity with a low detection limit of 26.48 pM. Moreover, it can be employed to screen BACE-1 inhibitors and analyze kinetic parameters. Especially, this nanoprobe possesses good stability and can be easily transferred into live cells for the real-time imaging of cellular BACE-1 activity, providing a new platform for BACE-1-associated research and early diagnosis of Alzheimer's disease.

A novel ratiometric MALDI-MS quantitation strategy for alkaline phosphatase activity with a homogeneous reaction and a tunable dynamic range

A unique ratiometric MALDI-MS strategy is proposed for the convenient and reliable quantitation of alkaline phosphatase based on the homogeneous enzymatic cleavage of a coded phosphopeptide (CPP)-triggered double-signal output. The dynamic range can be tuned by simply adjusting the primary concentration of CPP. The proposed strategy is also capable of being challenged by real human serum, and thus it may offer a wonderful approach for the convenient identification and quantitation of various enzyme activities in clinical diagnosis.

3'-Terminal Repair-Powered Dendritic Nanoassembly of Polyadenine Molecular Beacons for One-Step Quantification of Alkaline Phosphatase in Human Serum

Alkaline phosphatase (ALP) is an important hydrolase with crucial roles in biological processes, and the dysregulation of ALP may cause various human diseases. The conventional ALP assays usually involve cumbersome procedures with poor sensitivity. Herein, taking advantage of intrinsic superiorities of molecular beacons (MBs) and unique features of terminal deoxynucleotidyl transferase (TdT), we demonstrate for the first time the 3'-terminal repair-powered dendritic nanoassembly of polyadenine (A) MBs for one-step quantification of ALP in human serum. When ALP is present, it catalyzes 3'-terminal dephosphorylation of poly-A MBs to induce TdT-mediated template-free polymerization, generating long chains of polythymidine (T) sequences. The long poly-T chains can function as the anchoring templates to hybridize with many poly-A MBs, leading to the unfolding of loop structures and the dissociation of FAM/BHQ1 pairs (the 1st amplification stage). Subsequently, all 3'-hydroxylated poly-A MBs can be extended with the assistance of TdT to generate the branched long poly-T chains, leading to the hybridization of more poly-A MBs and the dissociation of more FAM/BHQ1 pairs (the 2nd amplification stage). Through multiple rounds of extension, assembly, and activation of poly-A MBs, dendritic DNA nanostructures are automatically formed, resulting in the dissociation of abundant fluorophores from the FAM/BHQ1 pairs to generate an exponentially amplified fluorescence signal (the nth amplification stage). This strategy possesses high sensitivity and excellent specificity, and the detection limit can reach 1 cell. Moreover, it can evaluate kinetic parameters, screen inhibitors, estimate cellular inhibition effects, and measure ALP in human serums.

Digital counting of single semiconducting polymer nanoparticles for the detection of alkaline phosphatase

Alkaline phosphatase (ALP) as a necessary hydrolase in phosphate metabolism is closely related to various diseases. Ultrasensitive detection of ALP with a convenient and sensitive method is of fundamental importance. In this work, a fluorescence resonance energy transfer (FRET)-based single-particle enumeration (SPE) method is proposed for the quantitative analysis of ALP. This strategy is based on the effective fluorescence suppression by a polydopamine (PDA) shell on the surface of semiconducting polymer nanoparticles (SPNs). PDA with broadband absorption in the UV-vis region can serve as an excellent quencher for SPNs. However, ascorbic acid (AA), the product of the hydrolysis of 2-phosphate-l-ascorbic acid trisodium salt (AAP) in the presence of ALP, can effectively inhibit the self-polymerization of dopamine (DA) to form a PDA layer. Therefore, ALP can be accurately quantified by counting the concentration-related fluorescent particles in the fluorescence image. A linear range from 0.031 to 12.4 μU mL-1 and a limit-of-detection (LOD) of 0.01 μU mL-1 for ALP determination are achieved. The spiked recoveries for ALP determination in a human serum sample are between 90% and 108% with RSD less than 3.1%. In summary, this convenient and sensitive approach proposed here provides promising prospects for ALP detection in a complex biological matrix.

A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases

Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10-8 U μL-1 for hOGG1 and 3.55 × 10-7 U μL-1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.

Barcode signal amplifying strategy for sensitive and accurate protein detection on LC-MS/MS

Protein drugs showing strong pharmaceutical activity, high specificity, and low toxicity and side effects have drawn extensive attention in the field of life sciences and medicine. Precise evaluation of the function of these drugs requires accurate and sensitive detection methods. Here, we report a novel chromatography-tandem mass spectrometry (LC-MS/MS) method for sensitive and selective detection of protein drugs. Magnetic nanoparticles (Apt29@MNPs) were functionalized by thrombin aptamers, and quantum dots (Apt15@ss@QDs) were dual-functionalized with quantitative thrombin aptamers and small molecules with high ionization efficiency as the mass barcode. After Apt29@MNPs specifically purify and enrich thrombin from biological samples, they can form a nano "sandwich structure" when Apt15@ss@QDs are added, resulting in the release of the mass barcode for LC-MS/MS analysis via the cutting of the disulfide bond. Since there is a higher quantitative molecular ratio of mass barcode to thrombin in the nano-"sandwich structure", quantitative detection of thrombin with high sensitivity and selectivity can be achieved via the LC-MS/MS detection of the mass barcode with high ionization efficiency rather than thrombin, which effectively avoids the disadvantages of direct protein detection by mass spectrometry. The established method for thrombin detection shows a good linear relationship in a concentration range of 0.00115-1.15 nM with a limit of detection (LOD) of 0.0007 nM. The present work provides a new approach for the effective and sensitive quantitative analysis of protein drugs and would be of great significance in promoting the development of protein drugs and clinical applications.

3D NiO nanoflakes/carbon fiber meshwork: Facile preparation and utilization as general platform for photocathodic bioanalysis

Herein, we describe a customized approach for facile preparation of three-dimensional (3D) NiO nanoflakes (NFs)/carbon fiber meshwork (CFM) and its validation as a common photocathode matrix for photoelectrochemical (PEC) bioanalysis, which to our knowledge has not been reported. Specifically, 3D NiO NFs/CFM was fabricated by a sequential liquid phase deposition and annealing process, which was then characterized by scanning electron microscopy, X-ray photoelectron spectrum, UV-vis absorption spectra and N₂ adsorption-desorption measurement. Sensitized by BiOI and incorporated with an alkaline phosphatase (ALP)/tyrosinase (TYR) bi-enzyme cascade system, a sensitive split-type cathodic PEC bioanalysis for the determination of ALP was achieved. This method can detect ALP concentrations down to 3 × 10^-5 U L^-1 with a linear response range of 0.001-10 U L^-1. Moreover, this proposed system exhibited good selectivity, stability and excellent performance for real sample analysis. This research features the facile preparation of 3D NiO NFs/CFM that could acts as a universal matrix for photocathodic analysis, and is envisioned to stimulate more effort for advanced 3D photocathode for PEC bioanalysis and beyond.

Homogeneous assay based on the pre-reduction and selective cation exchange for detection of multiple targets by atomic spectrometry

In view of the high sensitivity and good selectivity, chemical vapor generation atomic spectrometry (CVG-AS) and inductively coupled plasma mass spectrometer (ICP-MS), especially low-cost atomic fluorescence spectrometry (AFS) have been widely used in bioassay. However, the existing AS method is mostly based on heterogeneous strategies, and can't detect multiple targets in one system. In this study, we present the discovery and mechanism study of a phenomenon of Hg²⁺ pre-reduction that the concentration of Hg²⁺ decreased when it was mixed with the reductants (ascorbic acid (AA), SnCl₂, or NaBH₄/KBH₄) over long-time reaction (hours) by CVG-AFS and ICP-MS. A homogeneous Cu²⁺ assay method was developed based on the competition reaction of Cu²⁺ and Hg²⁺ for consuming AA, and its application in the detection of pyrophosphate (PPi) and alkaline phosphatase (ALP) was investigated based on the PPi complexation with Cu²⁺, and ALP hydrolyzation of PPi using CVG-AFS as a representative detector. Subsequently, in order to further verify the applicability of the system, cation exchange reaction (CER) was utilized here based on the selectively recognize Ag⁺ and C-Ag⁺-C by CuS nanoparticles (NPs). As the exchanged Cu²⁺ from CuS NPs can be sensitively and selectively detected via above-mentioned Cu²⁺ assay method, this strategy can be extended for the Ag⁺, DNA and prostate specific antigen (PSA) detection based on base complementary pairing and the specific recognition of aptamer. Under the optimal experimental conditions, the system showed high sensitivity for the detection of Cu²⁺, PPi, ALP, Ag⁺, DNA, and PSA, with limit of detections (LODs) of 0.12 nmol L^-1, 25 μmol L^-1, 0.025 U/L, 0.2 nmol L^-1, 0.05 nmol L^-1, and 0.03 ng/mL, respectively. The method was successfully used to determination Cu²⁺, ALP, and PSA in human serums, showing similar results with those of ICP-MS and kits methods.

A dual-mode strategy for sensing and bio-imaging of endogenous alkaline phosphatase based on the combination of photoinduced electron transfer and hyperchromic effect

Benefit from the additional correction of the output signal in dual-mode detection, traditional dual signal readout strategies are performed by constructing the ratiometric fluorescent probe through excitation energy transfer (EET) or fluorescence resonance energy transfer (FRET). To avoid the complicated modification process and obtain the results rapidly, a simple dual-mode sensing strategy based on the electronic effects of p-nitrophenol (PNP) is described to monitor the activities of alkaline phosphatase (ALP). In the sensing platform, p-nitrophenylphosphate was used as a substrate to produce the PNP using ALP as the catalyst. Due to the PNP possesses negative effect of induction and conjugation, photoinduced electron transfer and hyperchromic effect have been achieved between PNP and polyethyleneimine-protected copper nanoclusters (PEI-Cu NCs), which caused the changes of the fluorescence intensity and UV-visible absorption. The dual-mode signal sensing system showed the satisfactory linear results of ALP from 1 to 100 U/L for fluorescent sensing strategy and 1-70 U/L for the absorption method with a competitive LOD of 0.27 and 0.87 U/L (signal-to-noise ratio of 3). This strategy detected biological ALP in human serum and bio-imaging of endogenous ALP in A549 cells successfully, which verifies a certain potential of the strategy for the practical applications.

A path-choice-based biosensor to detect the activity of the alkaline phosphatase as the switch

Alkaline phosphatase (ALP), which converts the phosphate group (-PO₄) in the substrate to the hydroxyl group (-OH), is a useful tool in the biological analysis, a good indicator of dissolved inorganic phosphorus levels and an important biomarker for several diseases. In conventional designs for ALP detection, both the interferent with a -PO₄ and the target with a -OH will go into the sensing path and give out the undesired background and the desired signal respectively. This limited the sensitivity of the method and required the complicated design to achieve a satisfying limit of detection (LOD) of ALP. Here, we provided a new sensing strategy for ALP detection design. We designed a path-choice-based biosensor with two DNA tracks in which ALP works as the switch to guide the reaction path of lambda exonuclease (λ exo). The path-choice character enlarged the difference between signal and background by separating the interferent removing path and the target sensing path. The substrate preference of ALP and λ exo was studied to optimize the structure of DNA tracks. The path-choice-based biosensor achieved simple, fast (30 min), sensitive (LOD 0.014 U L^-1) and selective detection of the activity of ALP. The method has been applied to detect the activity of ALP in cell lysates, which shows the potential application in ALP-related biological research.

High-sensitive sensing of plant microRNA by integrating click chemistry with an unusual on-bead poly(T)-promoted transcription amplification

MicroRNAs (miRNAs) act as pivotal regulators in plants. Therefore, sensing strategies with high specificity and high sensitivity are desired for plant miRNA analysis in order to unveil the exact biofunctions of miRNAs. Toward this goal, a fluorescent assay is developed based on a two-step signal amplification strategy. In the first step, target miRNA-templated cycling click nucleic acid ligation is employed for target recognition and amplification, the product of which can bind to magnetic microbeads (MBs) and introduce the T7 promoter sequence to the surface. In the second step, the poly(T) containing transcription template partially hybridizes with the T7 promoter sequence on the ligated strand and then regulates the on-bead transcription in a cycling manner with the participation of T7 RNA polymerase. Surprisingly, different from other reported templates, the poly(T) template improves the transcription efficiency to an unexpectedly high level by releasing ultra-long RNA chains in the reaction system. Finally, the RNA intercalating dye, RiboGreen, is utilized to specifically light up the as-produced RNA chains for low-background signal readout. Benefiting from the elaborate design, the detection limit of plant miRNA is down to ∼0.1 amol. This strategy provides a highly specific and highly sensitive platform for plant miRNA detection, which promises potential in the practical applications of miRNA-related biofunctions.

A signal amplification strategy for prostate specific antigen detection via releasing oxidase-mimics from coordination nanoparticles by alkaline phosphatase

A novel signal amplification method for prostate specific antigen (PSA) is developed by freeing fluorescein with photoinduced oxidase-like activity from coordination nanoparticles (CNPs) in the presence of alkaline phosphatase (ALP). CNPs loaded with fluorescein (F@CNPs) are obtained in aqueous solution by self-assembly using Tb³⁺ as metal ion, guanosine monophosphate (5'-GMP) as ligand, and fluorescein as signal molecule. The F@CNPs display outstanding properties of simple synthesis, low cost, good water solubility, negligible leakage and satisfactory load capacity. Fluorescein is quantitatively encapsulated in CNPs with a binding ratio of 92.72%. Meanwhile, ALP can specifically hydrolyze the phosphate group of 5'-GMP ligand, triggering the destruction of F@CNPs and leakage of fluorescein. Fluorescein, a photoinduced oxidase mimic, can catalyze the oxidation of non-fluorescent Amplex UltraRed (AUR) into fluorescent resorufin under LED lamp. This strategy exhibits good sensitivity for ALP detection. In addition, a new immunoassay for PSA is validated by labelling ALP on PSA antibody. The low detection limit of 0.04 ng mL^-1 in detecting PSA is appropriate for PSA detection in real samples. Therefore, the work not only establishes a new strategy for ALP and PSA determination, but also provides a new conception for putting photoinduced oxidase-like fluorescein in practical application.

Peptide-templated gold nanoparticle nanosensor for simultaneous detection of multiple posttranslational modification enzymes

We developed a peptide-templated gold nanoparticle (AuNP) nanosensor for simultaneous detection of multiple posttranslational modification (PTM) enzymes with a detection limit of 28 pM for histone deacetylase (HDAC) and 0.8 pM for protein tyrosine phosphatase 1B (PTP1B), and it can be further applied for the screening of PTM enzyme inhibitors and the measurement of PTM enzymes in cancer cells.

Nanomaterial-based biosensors for DNA methyltransferase assay

We review the recent advances in the development of nanomaterial-based biosensors for DNA methyltransferase assay.

Responsive methylene blue release from lanthanide coordination polymer for label-free, immobilization-free and sensitive electrochemical alkaline phosphatase activity assay

Alkaline phosphatase (ALP) is an important enzyme related to many clinical diseases and also widely used as a labeling enzyme for immunoassay. Herein, a new electrochemical sensing strategy for ALP activity was proposed, which was based on the ALP-triggered methylene blue (MB) release from a lanthanide coordination polymer and successive penetration through a self-assembled dodecanethiol monolayer for electrochemical response. The supramolecular lanthanide coordination polymer was constructed by using guanine monophosphate (GMP) and Tb³⁺ as the ligand and the metal ion, respectively, and the encapsulated MB as the signal molecule. ALP catalyzed the cleavage of the phosphate group from the GMP ligand and disrupted the coordination polymer network to release abundant MB molecules for electrochemical responses related to ALP activity. The obtained lanthanide coordination polymers were well characterized by various techniques. The fabricated electrochemical sensor for ALP activity assay shows distinct advantages such as being one-step, label-free, immobilization-free and highly sensitive. The detection limit toward ALP activity was down to 0.5 U L^-1. With the aid of a MB enrichment process on the modified electrode before measurement, the detection limit could be further improved to 0.1 U L^-1. Moreover, the assay method could be applied for ALP detection in complex matrixes such as human serum and also for efficient inhibitor evaluation. Thus, the current study provides a new pathway to the fabrication of a coordination polymer-based electrochemical sensing platform for applications in disease diagnosis and drug discovery.

Fluorometric and Colorimetric Dual-Readout Immunoassay Based on an Alkaline Phosphatase-Triggered Reaction

Alkaline phosphatase (ALP) usually acts as a signal transmitter in enzyme-linked immunosorbent assay (ELISA); therefore, developing an attractive ALP activity assay, especially using a preferable substrate, would help improve the efficiency and convenience of ELISA in practical applications. Herein we have first prepared an original and creative substrate, named m-hydroxyphenyl phosphate sodium salt ( m-HPP), with a desirable dephosphorylation site for ALP. On the basis of the ALP-catalyzed hydrolysis of m-HPP to resorcinol and its subsequent specific nucleophilic reaction with dopamine, we have exploited a fluorometric and colorimetric dual-readout ALP activity assay and ALP-based ELISA system. Under the employed experimental conditions, highly sensitive and specific assay of ALP and cardiac troponin I (cTnI) has been accomplished in a straightforward way. Furthermore, the commendable sensing performance of our proposed ELISA in the determination of the cTnI level in diluted human serum unambiguously illustrates great potential in the early diagnosis of acute myocardial infarction.

CdTe QD-CeO2 Complex as a Strong Photoelectrochemical Signal Indicator for the Ultrasensitive microRNA Assay

The photoelectrochemical (PEC) signal can be enhanced by constructing sensitization structures containing photoactive materials and appropriate sensitizers. However, usually, the photoactive materials and sensitizers were separated in independent nanostructures, thereby producing long electron-transfer path and large energy loss, which could further result in limited photoelectric conversion efficiency and PEC signals. Herein, we designed a novel sensitization nanostructure simultaneously containing the photoactive material cerium dioxide (CeO₂) and its sensitizer CdTe quantum dots (QDs) as the strong PEC signal indicator (CdTe QD-CeO₂ complex), which prominently enhanced photoelectric conversion efficiency because of the shortened electron-transfer path and reduced energy loss. The proposed CdTe QD-CeO₂ complex was used to construct a PEC biosensor for achieving ultrasensitive determination of microRNA-141 (miRNA-141) coupling with target converting amplification and DNA supersandwich structure amplification. The designed PEC biosensor demonstrated a wide linear range from 0.5 fM to 5 nM with a detection limit of 0.17 fM for miRNA-141. Impressively, this work provided a new and strong PEC signal indicator for the construction of  PEC sensing platform and would extend the application of PEC sensors in bioanalysis and early disease diagnosis.

Enzyme-free amplified DNA assay: five orders of linearity provided by metal stable isotope detection

For the quantification of mutated genes at greatly varied concentrations in body fluids, nucleic acid amplification strategies are often challenged by limited dynamic linear ranges. The proposed metal stable isotope detection strategy demonstrates five orders of linear range and a lower attomol detection limit, showing promising potential in clinical diagnosis.

Spectrophotometric, fluorimetric and electrochemical selective pyrophosphate/ATP sensing based on the dimethyltin(IV)-tiron system

Sensing of pyrophosphate anion (PPi) in the presence of nucleotide triphosphates allows the real time monitoring of the polymerase chain reaction. To get a deeper understanding of the factors involved in PPi/nucleotide triphosphate discrimination, a detailed study on the performance of a dimethyltin (IV)-catecholate complex capable of both separate fluorimetric or electrochemical detection of PPi in the presence of adenosine triphosphate (ATP) has been undertaken. Dimethyltin (IV) tightly binds PPi or ATP, and forms a stable 1:1 complex with tiron (4,5-dihydroxy-1,3-benzenedisulfonic acid) in water. The complexation equilibria with all components are characterized quantitatively by potentiometric and spectroscopic titrations. Pyrophosphate anion can be detected owing to its ability to release free tiron from the complex by measuring either a fluorimetric or an electrochemical signal. On the contrary, ATP does not displace tiron but causes an interference with PPi in the fluorimetric detection method due to the formation of a ternary Me₂Sn(IV)-tiron-ATP complex with optical properties intermediate between those of free and bound tiron. In the electrochemical (square wave voltammetry) method, the ternary ATP complex shows a separate peak which does not coincide with the peaks of neither free nor bound tiron, thus making possible the simultaneous detection of ATP in addition to PPi.

Colorimetric sensing of alkaline phosphatase and α-fetoprotein based on the photoinduced oxidase activity of fluorescein

A simple and inexpensive colorimetric assay for alkaline phosphatase (ALP) and α-fetoprotein (AFP) has been established by the hydrolysis of fluorescein diphosphate (FDP).

Ligase amplification reaction-catalyzed assembly of a single quantum dot-based nanosensor for sensitive detection of alkaline phosphatase

We demonstrate the ligase amplification reaction-catalyzed assembly of a single quantum dot-based nanosensor for sensitive detection of alkaline phosphatase.

iPhone-imaged and cell-powered electrophoresis titration chip for the alkaline phosphatase assay in serum by the moving reaction boundary

As a vital enzyme, alkaline phosphatase (ALP) has great clinical significance in diagnoses of bone or liver cancer, bone metastases, rickets, and extrahepatic biliary obstruction. However, there is still no really portable chip for the ALP assay in blood. Herein, a simple electrophoresis titration (ET) model was developed for ALP detection via a moving reaction boundary (MRB). In the model, ALP catalyzed the dephosphorylation of a 4-methylumbelliferyl phosphate disodium salt (4-MUP) substrate in the cathode well to 4-methylumbelliferone ([4-MU]-) with a negative charge and blue fluorescence under UV excitation. After the catalysis, an electric field was used between the cathode and the anode. Under the electric field, [4-MU]- moved into the channel and neutralized the acidic Tris-HCl buffer, resulting in the quenching of [4-MU]- and creating a MRB. The ET system just had an ET chip, a lithium cell, a UV LED and an iPhone used as a recorder, having no traditional expensive power supply and fluorescence detector. The relevant method was developed, and a series of experiments were conducted via the ET chip. The experiments showed: (i) a MRB could be formed between the [4-MU]- base and the acidic buffer, and the MRB motion had a linear relationship with the ALP activity, validating the ET model; (ii) the ET run was not impacted by many interferences, implying good selectivity; and (iii) the ET chip could be used for portable detection within 10 min, implying an on-site and rapid analysis. In addition, the ET method had a relatively good sensitivity (0.1 U L-1), linearity (V = 0.033A + 3.87, R2 = 0.9980), stability (RSD 2.4-6.8%) and recoveries (101-105%). Finally, the ET method was successfully used for ALP assays in real serum samples. All the results implied that the developed method was simple, rapid and low-cost, and had potential for POCT clinical ALP assays.

Sensitive and accurate detection of ALP activity using a fluorescence on–off–on switch and mass barcode signal amplification

Alkaline phosphatase (ALP) is an important biomarker for many diseases. Therefore, the sensitive and accurate detection of ALP activity is essential for fundamental biochemical processes and clinic diagnosis. Herein, we design a fluorescent on–off–on switch for sensitive and visual detection of ALP activity. Meanwhile, mass barcode-modified quantum dots (QDs) amplified the LC-MS/MS detection signal in complex biological samples. Firstly, the QDs were modified with phosphorylated Gly-Gly-Phe-Phe-Tyr (OPO₃H₂) peptide (GGFFYp) and the mass barcode. The fluorescence of QDs-SS-Yp was quenched by fluorescence resonance energy transfer (FRET) between QDs-SS-Yp and dansyl chloride (DNS). ALP can hydrolyze the phosphorylated peptide to form peptide self-assemblies on the QDs-SS-Yp surfaces. The effective separation distance between the QDs-SS-Yp donor and DNS acceptor becomes larger, restricting FRET between the QDs-SS-Yp and DNS. At this point, the obvious QDs-SS-Yp fluorescence signal can be restored. However, the absence of ALP results in no peptide self-assembly on the QDs-SS-Yp surface and no obvious QDs-SS-Yp fluorescence signal was detected. Therefore, the ALP activity can be analyzed according to the degree of fluorescence restoration by the fluorescence on–off–on switch. Finally, the small tag molecules obtained by cleaving the disulfide bond of the QDs-SS-Yp as a mass barcode were used to amplify the LC-MS/MS detection signal. The proposed approach shows a good linear relationship (from 0.01 to 2.4 U L⁻¹) and has the significant advantage of a low detection limit of 0.001 U L⁻¹.

The sensitive and accurate detection of ALP activity using a fluorescence on–off–on switch and mass barcode signal amplification.

A dual signal amplification-assisted DNAzyme biosensor for ultrasensitive detection of Argonaute 2 activity

We develop a new dual-signal amplification-assisted DNAzyme biosensor for sensitive detection of Argonaute 2 (Ago2) activity.

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.