Recent advances in nucleic acid signal amplification-based aptasensors for sensing mycotoxins.

Mycotoxin contamination in food products may cause serious health hazards and economic losses. The effective control and accurate detection of mycotoxins have become a global concern. Even though a variety of methods have been developed for mycotoxin detection, most conventional methods suffer from complicated operation procedures, low sensitivity, high cost, and long assay time. Therefore, the development of simple and sensitive methods for mycotoxin assay is highly needed. The introduction of nucleic acid signal amplification technology (NASAT) into aptasensors significantly improves the sensitivity and facilitates the detection of mycotoxins. Herein, we give a comprehensive review of the recent advances in NASAT-based aptasensors for assaying mycotoxins and summarize the principles, features, and applications of NASAT-based aptasensors. Moreover, we highlight the challenges and prospects in the field, including the simultaneous detection of multiple mycotoxins and the development of portable devices for field detection.

Elongation and Ligation-Mediated Differential Coding for Label-Free and Locus-Specific Analysis of 8-Oxo-7,8-dihydroguanine in DNA.

Oxidative DNA damage is closely associated with the occurrence of numerous human diseases and cancers. 8-Oxo-7,8-dihydroguanine (8-oxoG) is the most prevalent form of DNA damage, and it has become not only an oxidative stress biomarker but also a new epigenetic-like biomarker. However, few approaches are available for the locus-specific detection of 8-oxoG because of the low abundance of 8-oxoG damage in DNA and the limited sensitivity of existing assays. Herein, we demonstrate the elongation and ligation-mediated differential coding for label-free and locus-specific analysis of 8-oxoG in DNA. This assay is very simple without the involvement of any specific labeled probes, complicated steps, and large sample consumption. The utilization of Bsu DNA polymerase can specifically initiate a single-base extension reaction to incorporate dATP into the opposite position of 8-oxoG, endowing this assay with excellent selectivity. The introduction of cascade amplification reaction significantly enhances the sensitivity. The proposed method can monitor 8-oxoG with a limit of detection of 8.21 × 10-19 M (0.82 aM), and it can identify as low as 0.001% 8-oxoG damage from a complex mixture with excessive undamaged DNAs. This method can be further applied to measure 8-oxoG levels in the genomic DNA of human cells under diverse oxidative stress, holding prospect potential in the dynamic monitoring of critical 8-oxoG sites, early clinical diagnosis, and gene damage-related biomedical research.

Ligase detection reaction amplification-activated CRISPR-Cas12a for single-molecule counting of FEN1 in breast cancer tissues.

We construct a simple fluorescent biosensor for single-molecule counting of flap endonuclease 1 (FEN1) based on ligase detection reaction (LDR) amplification-activated CRISPR-Cas12a. This biosensor exhibits excellent selectivity and high sensitivity with a detection limit (LOD) of 1.31 × 10-8 U. Moreover, it can be employed to screen the FEN1 inhibitors and quantitatively measure the FEN1 activity in human cells and breast cancer tissues, holding great promise in clinical diagnosis and drug discovery.

Construction of a label-free fluorescent biosensor for homogeneous detection of m6A eraser FTO in breast cancer tissues.

Fat mass and obesity-associated protein (FTO) is a crucial eraser of RNA N6- methyladenosine (m6A) modification, and abnormal FTO expression level is implicated in pathogenesis of numerous cancers. Herein, we demonstrate the construction of a label-free fluorescent biosensor for homogeneous detection of m6A eraser FTO in breast cancer tissues. When FTO is present, it specifically erases the methyl group in m6A, inducing the cleavage of demethylated DNA by endonuclease DpnII and the generation of a single-stranded DNA (ssDNA) with a 3'-hydroxyl group. Subsequently, terminal deoxynucleotidyl transferase (TdT) promotes the incorporation of dTTPs into the ssDNA to obtain a long polythymidine (T) DNA sequence. The resultant long poly (T) DNA sequence can act as a template to trigger hyperbranched strand displacement amplification (HSDA), yielding numerous DNA fragments that may be stained by SYBR Gold to produce an enhanced fluorescence signal. This biosensor processes ultrahigh sensitivity with a detection limit of 1.65 × 10-10 mg/mL (2.6 fM), and it can detect the FTO activity in a single MCF-7 cell. Moreover, this biosensor can screen the FTO inhibitors, evaluate enzyme kinetic parameters, and discriminate the FTO expression levels in the tissues of breast cancer patients and healthy persons.

Near-room temperature ferromagnetism and a tunable anomalous Hall effect in atomically thin Fe4CoGeTe2.

Itinerant ferromagnetism at room temperature is a key factor for spin transport and manipulation. Here, we report the realization of near-room temperature itinerant ferromagnetism in Co doped Fe5GeTe2 thin flakes. The ferromagnetic transition temperature TC (∼323 K-337 K) is almost unchanged when the thickness is as low as 12 nm and is still about 284 K at 2 nm (bilayer thickness). Theoretical calculations further indicate that the ferromagnetism persists in monolayer Fe4CoGeTe2. In addition to the robust ferromagnetism down to the ultrathin limit, Fe4CoGeTe2 exhibits an unusual temperature- and thickness-dependent intrinsic anomalous Hall effect. We propose that it could be ascribed to the dependence of the band structure on thickness that changes the Berry curvature near the Fermi energy level subtly. The near-room temperature ferromagnetism and tunable anomalous Hall effect in atomically thin Fe4CoGeTe2 provide opportunities to understand the exotic transport properties of two-dimensional van der Waals magnetic materials and explore their potential applications in spintronics.

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.

Construction of a Dual-Mode Biosensor with Ferrocene as Both a Signal Enhancer and a Signal Tracer for Electrochemiluminescent and Electrochemical Enantioselective Recognition.

We demonstrate for the first time the construction of a dual-mode biosensor for electrochemiluminescent (ECL) and electrochemical chiral recognition of l- and d-isomers of amino acids, with ferrocene (Fc) as both a signal enhancer and a signal tracer. With the dissolved oxygen as a coreactant, ZnIn2S4 acts as the ECL emitter to generate a weak cathodic ECL signal. Fc can enter into the ß-cyclodextrin (ß-CD) cavity on ZnIn2S4-modified electrode as a result of host-guest interaction. Since Fc can promote H2O and O2 to produce abundant reactive oxygen species (ROS) (e.g., O2·- and ·OH), the ECL signal of ZnIn2S4 can be further amplified with Fc as a coreaction accelerator. Meanwhile, Fc molecules on the ß-CD/ZnIn2S4-modified electrode can be electrochemically oxidized to Fc+ to produce a remarkable oxidation peak current. When l-histidine (l-His) is present, the matching of the l-His configuration with the ß-CD cavity leads to the entrance of more l-His into the cavity of ß-CD than d-histidine (d-His), and the subsequent competence of l-His with Fc on the Fc/ß-CD/ZnIn2S4-modified electrode induces the decrease in both Fc peak current and ZnIn2S4-induced ECL intensity. This dual-mode biosensor can efficiently discriminate l-His from d-His, and it can sensitively monitor l-His with a detection limit of 7.60 pM for ECL mode and 3.70 pM for electrochemical mode. Moreover, this dual-mode biosensor can selectively discriminate l-His from other l- and d-isomers (e.g., threonine, phenylalanine, and glutamic acid), with potential applications in the chiral recognition of nonelectroactive chiral compounds, bioanalysis, and disease diagnosis.

Development of a N6-methyladenosine-directed single quantum dot-based biosensor for sensitive detection of METTL3/14 complex activity in breast cancer tissues.

The METTL3/14 complex is an important RNA N6-Methyladenosine (m6A) methyltransferase in organisms, and the abnormal METTL3/14 complex activity is associated with the pathogenesis and various cancers. Sensitive detection of METTL3/14 complex is essential to tumor pathogenesis study, cancer diagnosis, and anti-cancer drug discovery. However, traditional methods for METTL3/14 complex assay suffer from poor specificity, costly antibodies, unstable RNA substrates, and low sensitivity. Herein, we construct a single quantum dot (QD)-based förster resonance energy transfer (FRET) biosensor for sensitive detection of METTL3/14 complex activity. In the presence of METTL3/14 complex, it catalyzes the methylation of adenine in the substrate probe, leading to the formation of m6A that protects the substrate probes from MazF-mediated cleavage. The hybridization of methylated DNA substrate with biotinylated capture probe initiates polymerization reaction to obtain a biotinylated double-stranded DNA (dsDNA) with the incorporation of numerous Cy5 fluorophores. Subsequently, the Cy5-incorporated dsDNA can self-assembly onto the 605QD surface to form the 605QD-dsDNA-Cy5 nanostructure, causing FRET between 605QD donor and Cy5 acceptor. This biosensor has excellent sensitivity with a limit of detection (LOD) of 3.11 × 10-17 M, and it can measure the METTL3/14 complex activity in a single cell. Moreover, this biosensor can be used to evaluate the METTL3/14 complex kinetic parameters and screen potential inhibitors. Furthermore, it can differentiate the METTL3/14 complex expression in healthy human tissues and breast cancer patient tissues, providing a powerful tool for cancer pathogenesis study, clinical diagnosis, prognosis monitoring, and drug discovery.

Construction of Multiple DNAzymes Driven by Single Base Elongation and Ligation for Single-Molecule Monitoring of FTO in Cancer Tissues.

Fat mass and obesity-associated proteins (FTO) play an essential role in the reversible regulation of N6-methyladenosine (m6A) epigenetic modification, and the overexpression of FTO is closely associated with the occurrence of diverse human diseases (e.g., obesity and cancers). Herein, we demonstrate the construction of multiple DNAzymes driven by single base elongation and ligation for the single-molecule monitoring of FTO in cancer tissues. When target FTO is present, the m6A-RNA is specifically demethylated and subsequently acts as a primer to combine with the padlock probe, initiating single-base elongation and ligation reaction to generate a closed template probe. Upon the addition of phi29 DNA polymerase, a rolling circle amplification (RCA) reaction is initiated to produce large numbers of Mg2+-dependent DNAzyme repeats. Subsequently, the DNAzymes cyclically digest the signal probes, liberating numerous Cy5 molecules that can be precisely counted by single-molecule imaging. Taking advantage of the sequence specificity of the polymerase/ligase-mediated gap-filling and ligation as well as the high amplification efficiency of RCA, this biosensor shows excellent specificity and high sensitivity with a detection limit of 5.96 × 10-16 M. It can be applied to screen FTO inhibitors and quantify FTO activity at the single-cell level. Moreover, the proposed strategy can accurately distinguish the FTO expression level in tissues of healthy individuals and breast cancer patients, providing a new platform for drug discovery, m6A modification-related research, and clinical diagnostics.

Development of a chiral electrochemical sensor based on copper-amino acid mercaptide nanorods for enantioselective discrimination of tryptophan enantiomers.

Chirality is an important property of nature and it regulates fundamental phenomena in nature and organisms. Here, we develop a chiral electrochemical sensor based on copper-amino acid mercaptide nanorods (L-CuCys NRs) to discriminate tryptophan (Trp) isomers. The chiral L-CuCys NRs are prepared in alkaline solution based on the facile coordination reaction between the sulfhydryl groups of L-Cys and copper ions. Since the stability constant (K) of L-CuCys NRs with L-Trp (752) are much higher than that of L-CuCys NRs with D-Trp (242), the cross-linking bonds between L-CuCys NRs and L-Trp are more stable than those between L-CuCys NRs and D-Trp. Consequently, this electrochemical sensor can selectively recognize the Trp isomers with an enantiomeric electrochemical difference ratio (IL-Trp/ID-Trp) of 3.22, and it exhibits a detection limit of 0.26 µM for L-Trp. Moreover, this electrochemical sensor can quantitatively measure Trp isomers in complex samples. Importantly, this electrochemical sensor has the characteristics of high stability, good repeatability, easy fabrication, low cost, and efficient discrimination of tryptophan (Trp) isomers.

Target-activated T7 transcription circuit-mediated multiple cycling signal amplification for monitoring of flap endonuclease 1 activity in cancer cells.

The structure-specific endonuclease flap endonuclease 1 (FEN1) is an essential functional protein in DNA replication and genome stability, and it has been identified as a promising biomarker and drug target for multiple cancers. Herein, we develop a target-activated T7 transcription circuit-mediated multiple cycling signal amplification platform for monitoring FEN1 activity in cancer cells. In the presence of FEN1, the flapped dumbbell probe is cleaved to generate a free 5' flap single-stranded DNA (ssDNA) with the 3'-OH terminus. The ssDNA can hybridize with the T7 promoter-bearing template probe to trigger the extension with the aid of Klenow fragment (KF) DNA polymerase. Upon the addition of T7 RNA polymerase, an efficient T7 transcription amplification reaction is initiated to produce abundant single-stranded RNAs (ssRNAs). The ssRNA can hybridize with a molecular beacon to form an RNA/DNA heteroduplex that can be selectively digested by DSN to generate an enhanced fluorescence signal. This method exhibits good specificity and high sensitivity with a limit of detection (LOD) of 1.75 × 10-6 U µL-1. Moreover, it can be applied for the screening of FEN1 inhibitors and the monitoring of FEN1 activity in human cells, holding great potential in drug discovery and clinical diagnosis.

Construction of Genetically Encoded Light-Up RNA Aptamers for Label-free and Ultrasensitive Detection of CircRNAs in Cancer Cells and Tissues.

Circular RNAs (circRNAs) as endogenous non-coding RNAs are characterized by covalently closed circular structures, and they widely exist in mammalian cells. The aberrant expression of circRNAs may result in various diseases. Herein, we demonstrate the construction of genetically encoded light-up RNA aptamers for ultrasensitive and label-free detection of circRNA mitochondrial tRNA translation optimization 1 (circMTO1) in cancer cells and tissues. The light-up RNA aptamers are generated by proximity ligation-activated recombinase polymerase amplification (RPA)-assisted transcription amplification. When circMTO1 is present, it initiates the proximity ligation reaction, activating RPA to produce numerous long double-stranded DNAs containing T7 promoters. Subsequently, the RPA products are identified by T7 RNA polymerase, initiating the transcription amplification reaction to generate abundant Spinach RNA aptamers. Spinach RNA aptamers can bind with DFHBI (3,5-difluoro-4-hydroxybenzylidene imidazolidinone) dye to produce a distinct fluorescence signal with near-zero background. This biosensor exhibits excellent selectivity and high sensitivity with a limit of detection of 2.54 aM. It can accurately monitor cellular circMTO1 at the single-cell level and discriminate the expression of circMTO1 between breast cancer patient tissues and healthy tissues. Notably, this biosensor can be employed to measure other nucleic acids by altering the corresponding target recognition sequences, providing a valuable platform for cancer diagnosis and biomedical study.

CRISPR/Cas12a-enhanced single-molecule counting for sensitive detection of flap endonuclease 1 activity at the single-cell level.

We develop a new fluorescent biosensor for flap endonuclease 1 (FEN1) assay based on CRISPR/Cas12-enhanced single-molecule counting. This biosensor is simple, selective, and sensitive with a detection limit of 2.325 × 10-5 U and it is applicable for inhibitor screening, kinetic parameter analysis, and quantifying cellular FEN1 with single-cell sensitivity.

Controllable assembly of dendritic DNA nanostructures for ultrasensitive detection of METTL3-METTL14 m6A methyltransferase activity in cancer cells and human breast tissues.

N6-Methyladenosine (m6A) is a reversible chemical modification in eukaryotic messenger RNAs and long noncoding RNAs. The aberrant expression of RNA methyltransferase METTL3-METTL14 complex may change the m6A methylation level and cause multiple diseases including cancers. The conventional METTL3-METTL14 assays commonly suffer from time-consuming procedures and poor sensitivity. Herein, we develop a controllable amplification machinery based on MazF-activated terminal deoxynucleotidyl transferase (TdT)-assisted dendritic DNA structure assembly for ultrasensitive detection of METTL3-METTL14 complex activity in cancer cells and breast tissues. The presence of METTL3-METTL14 complex catalyzes the formation of m6A in detection probe, effectively preventing the cleavage of methylated detection probes by MazF. The methylated detection probes with 3'-OH termini can function as the primers for template-free polymerization catalyzed by TdT on magnetic beads (MBs), producing long chains of poly-thymidine (poly-T) sequences. Then poly-T sequences hybridize with signal probes that contain poly-adenine (poly-A) sequence, inducing TdT-mediated polymerization and the subsequent hybridization with more poly-A signal probes for generating dendritic DNA nanostructures assembled on MBs. After magnetic separation and elevated temperature treatment, the signal probes are disassembled from MBs to generate a high fluorescence signal. This method possesses excellent specificity and high sensitivity with a limit of detection (LOD) of 2.61 × 10-15 M, and it can accurately quantify cellular METTL3-METTL14 complex at single-cell level. Furthermore, it can screen inhibitors, evaluate kinetic parameters, and discriminate breast cancer tissues from normal tissues.

Mix-and-Detection Assay with Multiple Cyclic Enzymatic Repairing Amplification for Rapid and Ultrasensitive Detection of Long Noncoding RNAs in Breast Tissues.

Long noncoding RNAs (lncRNAs) are valuable biomarkers and therapeutic targets, and they play essential roles in various pathological and biological processes. So far, the reported lncRNA assays usually suffer from unsatisfactory sensitivity and time-consuming procedures. Herein, we develop a mix-and-read assay based on multiple cyclic enzymatic repairing amplification (ERA) for sensitive and rapid detection of mammalian metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1). In this assay, we design two three-way junction (3WJ) probes including a 3WJ template and a 3WJ primer to specifically recognize lncRNA MALAT1, and the formation of a stable 3WJ structure induces cyclic ERA to generate triggers. The resulting triggers subsequently hybridize with a free 3WJ template and act as primers to initiate new rounds of cyclic ERA, generating abundant triggers. The hybridization of triggers with signal probes forms stable double-stranded DNA duplexes that can be specifically cleaved by apurinic/apyrimidinic endonuclease 1 to produce a high fluorescence signal. This assay can be carried out in a mix-and-read manner within 10 min under an isothermal condition (50 °C), which is the rapidest and simplest method reported so far for the lncRNA MALAT1 assay. This method can sensitively detect lncRNA MALAT1 with a limit of detection of 0.87 aM, and it can accurately measure endogenous lncRNA MALAT1 at the single-cell level. Moreover, this method can distinguish lncRNA MALAT1 expression in breast cancer patient tissues and their corresponding healthy adjacent tissues. Importantly, the extension of this assay to different RNAs detection can be achieved by simply replacing the corresponding target recognition sequences.

Target-activated cascade transcription amplification lights up RNA aptamers for label-free detection of metalloproteinase-2 activity.

We demonstrate that target-activated cascade transcription amplification lights up RNA aptamers for label-free detection of metalloproteinase-2 (MMP-2) activity with zero background. This assay exhibits good specificity and high sensitivity with a limit of detection (LOD) of 0.6 fM. Moreover, it can analyze enzyme kinetic parameters, screen inhibitors, and accurately quantify MMP-2 in cancer cells and clinical serums.

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.

[Remediation Performance via the Passivation of a Porous Biomorph Genetic Composite of α-Fe2O3/Fe3O4/C Using a Bamboo Template on As(â ¤) Contaminated Soils].

Red soil from Guangxi, China was selected as the background soil, and a porous biomorphic genetic composite of α-Fe2O3/Fe3O4/C comprising a bamboo template (PBGC-Fe/C) was used as a passivator to remediate As(Ⅴ) contaminated soils. The performance of PBGC-Fe/C was characterized by Scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FT-IR). The results showed that PBGC-Fe/C could improve the passivation effect of As(Ⅴ) from the contaminated soils compared with a single passivation material. Under the conditions of a 5% dose addition, 25% water content, and particle size of 100 mesh, the stability rates of PBGC-Fe/C on As(Ⅴ) contaminated soils with different concentrations of 500 mg·kg-1 and 1000 mg·kg-1 could reach 80.95% and 73.49%, respectively. The porous biomorphic genetic composite of bamboo charcoal provided a large number of adsorption sites for As(Ⅴ), and the acidity of the soil was favorable for the remediation of As(Ⅴ) via passivation. Moreover, PBGC-Fe/C could not only adsorb and fix As(Ⅴ), but also promoted the stabilization of As species. Chemical complexation and ion exchange played major roles in this passivation process.

[Passivation and Remediation Effects and Mechanisms of Plant Residual Modified Materials on Lead-Contaminated Soils].

The specific characteristics and mechanism of passivation of Pb in soil were studied using HAP/C composite (PBGC-HAP/C) as passivation, and using proportion of PBGC-HAP/C, particle size and type of passivator, soil moisture content, soil pH value of Pb, and particle size of the material as influencing factors. The results showed that with an increase in dosage of the passivator and passivation time, the passivation effect increases gradually. Reducing the particle size of the passivator is beneficial to improving the passivation effect. pH has a greater impact on passivation, with the passivation effect obviously rising with increased pH, and the passivation rate in an alkaline environment can reach above 99%. An increase in water content is beneficial to the improvement of the passivation effect, but the contribution is not significant. Through comparative analysis of the XPS, XRD, and FT-IR of materials before and after passivation, the results indicated that the passivation of PBGC-HAP/C to Pb is mainly through direct and indirect effects. Direct effects include physical adsorption, chemical complexation, electrostatic interaction, ion exchange, and precipitation; the indirect effect is mainly enhanced by increasing the pH value of the organic matter.