Affinity-Mediated Homogeneous Electrochemical Aptasensor on a Graphene Platform for Ultrasensitive Biomolecule Detection via Exonuclease-Assisted Target-Analog Recycling Amplification

Metallic nanostructure-based aptasensors for robust detection of proteins

There is a significant need for fast, cost-effective, and highly sensitive protein target detection, particularly in the fields of food, environmental monitoring, and healthcare. The integration of high-affinity aptamers with metal-based nanomaterials has played a crucial role in advancing the development of innovative aptasensors tailored for the precise detection of specific proteins. Aptamers offer several advantages over commonly used molecular recognition methods, such as antibodies. Recently, a variety of metal-based aptasensors have been established. These metallic nanomaterials encompass noble metal nanoparticles, metal oxides, metal-carbon nanotubes, carbon quantum dots, graphene-conjugated metallic nanostructures, as well as their nanocomposites, metal-organic frameworks (MOFs), and MXenes. In general, these materials provide enhanced sensitivity through signal amplification and transduction mechanisms. This review primarily focuses on the advancement of aptasensors based on metallic materials for the highly sensitive detection of protein targets, including enzymes and growth factors. Additionally, it sheds light on the challenges encountered in this field and outlines future prospects. We firmly believe that this review will offer a comprehensive overview and fresh insights into metallic nanomaterials-based aptasensors and their capabilities, paving the way for the development of innovative point-of-care (POC) diagnostic devices.

Surface-tethered electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions

The general electrochemical biosensors for telomerase detection require the immobilization of primers on the electrode surface for telomeric extension and hybridization reactions. However, immobilization of primers may suffer from the challenges of hindrance effect and configuration freedom, thus reducing the extension and hybridization efficiency. Herein, we developed a sensitive electrochemical biosensor for telomerase detection by integration of homogeneous extension and hybridization reactions and surface-tethered detection. In the presence of telomerase, the biotinylated primer (bio-primer) was efficiently elongated with telomeric repeats of (TTAGGG)_n at the 3' end in solution. Then, the extension product (bio-DNA) was hybridized with the signal probe DNA modified on the surface of ferrocene (Fc)-capped gold nanoparticle (AuNP). The bio-DNA/DNA/Fc-AuNP hybrids were then tethered by streptavidin-modified electrodes through the specific avidin-biotin interactions, thus producing strong electrochemical signals from the oxidation of Fc tags. The biosensor was successfully used to determine telomerase in HeLa cells and monitor the inhibition efficiency of inhibitor. A wide linear range for the detection of telomerase extracted from HeLa cells was attained. This method has great potential in clinical diagnosis and anti-cancer drug development, and should be beneficial for the fabrication of novel biosensors by integration of homogeneous catalysis and hybridization reactions.

Fluorescent Aptasensor for Highly Specific Detection of ATP Using a Newly Screened Aptamer

Owing to the significant roles of adenosine triphosphate (ATP) in diverse biological processes, ATP level is used to research and evaluate the physiological processes of organisms. Aptamer-based biosensors have been widely reported to achieve this purpose, which are superior in their flexible biosensing mechanism, with a high sensitivity and good biocompatibility; however, the aptamers currently used for ATP detection have a poor ability to discriminate ATP from adenosine diphosphate (ADP) and adenosine monophosphate (AMP). Herein, an ATP-specific aptamer was screened and applied to construct a fluorescent aptasensor for ATP by using graphene oxide (GO) and strand displacement amplification (SDA). The fluorescence intensity of the sensor is linearly related to the concentration of ATP within 0.1 μM to 25 μM under optimal experimental conditions, and the detection limit is 33.85 nM. The biosensor exhibits a satisfactory specificity for ATP. Moreover, the experimental results indicate that the biosensor can be applied to determine the ATP in human serum. In conclusion, the screened aptamer and the biosensor have promising applications in the determination of the real energy charge level and ATP content in a complex biological system.

Flow-homogeneous electrochemical sensing system based on 2D metal-organic framework nanozyme for successive microRNA assay

Considering DNA-based homogeneous electrochemical assay allows identification of targets to be carried out in a homogeneous solution, it would be of significance to develop the successive homogeneous assay system in dynamic solution for rapid disease diagnosis and high-throughput bioanalysis. In homogeneous assay, the work electrodes generally have capability of DNA capture but lack signal amplification, restricting its sensitivity. Here, a flow-homogeneous sensing system was proposed to realize the successive assay of microRNA, a model biomarker. Ultrathin 2D metal-organic framework (MOF) nanozymes with thickness of about 1 nm were facilely prepared by ultrasonic approach. Due to the excellent enzyme-like activity and adsorption capacity towards single-strand DNA (ssDNA), MOF nanozymes adsorbed on electrode simultaneously played two roles of ssDNA collector and signal-amplifier. To adapt the recoverable electrode to on-line monitoring, duplex-specific nuclease-assisted circle reaction was conducted to produce the turn-on amplified signal. Flow injection device was employed to realize the recycling of electrodes and the successive microRNA assay. The assay strategy showed low limit of detection (0.12 pM, S/N = 3) for microRNA, excellent renewability and acceptable reliability for real sample assay. The established system exerts the advantages of DNA-based homogeneous electrochemical sensing strategy. This work would not only expand homogeneous electrochemical assay to successive bioassay, but also provide the possibility for practical application of homogeneous sensing strategy.

Heterogeneous sensing of post-translational modification enzymes by integrating the advantage of homogeneous analysis

Heterogeneous analysis has great application prospects in the detection of post-translational modification (PTM) enzymes with the advantages of signal enhancement, less sample demand, and high sensitivity and selectivity. Nevertheless, once the substrate was fixed on a solid interface, the steric hindrance might limit the approaching of catalytic center to the substrate, thus reducing the efficiency of PTM. Herein, we suggested that the avidin-modified interface could be used to develop heterogeneous sensing platforms with biotin-labeled substrates as the probes, in which the enzymatic PTM was performed in solution and the heterogeneous assay was conducted on a solid surface. The sensing strategy integrates the advantages but overcomes the defects of both homogeneous and heterogeneous assays. Protein kinase A (PKA) and histone acetyltransferase (HAT) were determined as the examples by using sequence-specific peptide substrates. The signal changes were monitored by HRP-based colorimetric assay and antibody-amplified surface plasmon resonance (SPR). The methods were used for analysis of cell lysates and evaluation of inhibition efficiency with satisfactory results. The strategy can be used for the detection of a variety of biological enzymes and provide a new idea for the design of various heterogeneous biosensors. Thus, this work should be of great significance to the popularization and practical application of biosensors.

Three-dimensional self-powered DNA walking machine based on catalyzed hairpin assembly energy transfer strategy

Herein, catalyzed hairpin assembly is implemented as an automated strategy, which can respond in living cells to detect specific target DNA. Using the principle of catalyzed hairpin assembly (CHA), the auxiliary chain connects the fuel and starting chain to form a triple-stranded DNA to complete such a single system. Hundreds of single systems are modified on gold nanoparticles as DNA orbitals. Through the specific recognition of base complementation, the target DNA can realize the automatic walking of the three-dimensional fluorescence machine. This is a novel walking nanomachine that has a simple structure and can independently exist in cells to achieve automatic operation.

Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: Advances, challenges, and opportunities

Clinical diagnostic tests should be quick, reliable, simple to perform, and affordable for diagnosis and treatment of diseases. In this regard, owing to their novel properties, biosensors have attracted the attention of scientists as well as end-users. They are efficient, stable, and relatively cheap. Biosensors have broad applications in medical diagnosis, including point-of-care (POC) monitoring, forensics, and biomedical research. The electrochemical nucleic acid (NA) biosensor, the latest invention in this field, combines the sensitivity of electroanalytical methods with the inherent bioselectivity of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The NA biosensor exploits the affinity of single-stranded DNA/RNA for its complementary strand and is used to detect complementary sequences of NA based on hybridization. After the NA component in the sensor detects the analyte, a catalytic reaction or binding event that generates an electrical signal in the transducer ensues. Since 2000, much progress has been made in this field, but there are still numerous challenges. This critical review describes the advances, challenges, and prospects of NA-based electrochemical biosensors for clinical diagnosis. It includes the basic principles, classification, sensing enhancement strategies, and applications of biosensors as well as their advantages, limitations, and future prospects, and thus it should be useful to academics as well as industry in the improvement and application of EC NA biosensors.

Versatile photoelectrochemical and electrochemiluminescence biosensor based on 3D CdSe QDs-DNA nanonetwork-SnO2 nanoflower coupled with DNA walker amplification for HIV detection

A novel 3D CdSe quantum dots (QDs)-DNA nanonetwork was assembled to sensitize the mesoporous SnO₂ photoelectrochemical (PEC) substrate, which was coupled with a biped-DNA walker multiple amplification technique to design a versatile electrochemiluminescence (ECL) and PEC biosensor for dual detection of HIV. Firstly, the photosensitive CdSe QDs and SnO₂ nanoflowers have well-matched band-edge energy level, thus their complex can promote effective transfer of the photogenerated carriers, and show better PEC and ECL property. Then, a novel 3D CdSe QDs-DNA nanonetwork was assembled and loaded with a large amount of QDs, which was used as multifunctional PEC and ECL probes. Moreover, the target-triggered biped DNA walker-cascade amplification method was introduced to generate a large amount of output DNA, which was used to link numerous 3D CdSe QDs-DNA nanonetwork probes to the electrode, generating greatly amplified signals for sensitive assay of HIV. The highly photosensitive 3D CdSe QDs-DNA reticulated nanomaterials have high stability and controllability, and display significantly improved PEC and ECL signals of the biosensor. This method opened a new photoelectric nanocomposite of QDs-sensitized SnO₂ nanoflower, and developed a versatile biosensing strategy using the 3D CdSe QD_S DNA sensitization probes for ultra-sensitive detection of biomolecules, which is important for the early diagnosis of diseases.

Application of tetrahedral -deoxyribonucleic acid electrochemistry platform coupling aptazymes and hybridized hairpin reactions for the measurement of extracellular adenosine triphosphate in plants

Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme. In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity, releasing cleaved ssDNA, which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When G-quadruplex@AuNPs (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H₂O₂, enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.

Recent Developments in Aptasensors for Diagnostic Applications

Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

Magnetic-Assisted Methylene Blue-Intercalated Amplified dsDNA for Polarity-Switching-Mode Photoelectrochemical Aptasensing

Organic dyes are typically applied as photosensitizers in photoelectrochemical (PEC) cells but have not been reported in polarity-reversal-mode PEC sensors with excellent sensitivity and accuracy. Herein, an elegant and robust PEC biosensor for carcinoembryonic antigen (CEA) has been designed by photocurrent polarity switching of CdTe quantum dots (QDs), which is obtained by embedding methylene blue (MB) into amplified double-stranded DNA (dsDNA) anchored to the superparamagnetic Fe₃O₄@SiO₂. The target-triggered Exo III-assisted cyclic amplification strategy and in situ magnetic enrichment enable the remarkable sensitivity. The extraction of target-analogue single-stranded DNA (output DNA) contributes to high selectivity resulting from the elimination of possible interferences in real samples or matrixes. Particularly, this exclusive polarity-reversal-mode PEC aptasensing can efficiently eliminate the false-positive or false-negative signals, leading to accurate measurements. Moreover, different from the probes and layer-by-layer assembled photoelectric beacons on electrodes in advance, this rational split-type approach is doomed to help the PEC biosensor with additional merits of convenient fabrication, short time consumption, wider linearity, as well as outstanding reproducibility and stability in practical applications. In light of the ability of MB acting as a kind of signal probe in typical electrochemical sensors, certainly, this ingenious design can not only be extended to a wide variety of target monitoring but also provide new ideas for the construction of high-performance electrochemical and PEC biosensors.

Advances in Electrochemical Aptasensors Based on Carbon Nanomaterials

Carbon nanomaterials offer unique opportunities for the assembling of electrochemical aptasensors due to their high electroconductivity, redox activity, compatibility with biochemical receptors and broad possibilities of functionalization and combination with other auxiliary reagents. In this review, the progress in the development of electrochemical aptasensors based on carbon nanomaterials in 2016–2020 is considered with particular emphasis on the role of carbon materials in aptamer immobilization and signal generation. The synthesis and properties of carbon nanotubes, graphene materials, carbon nitride, carbon black particles and fullerene are described and their implementation in the electrochemical biosensors are summarized. Examples of electrochemical aptasensors are classified in accordance with the content of the surface layer and signal measurement mode. In conclusion, the drawbacks and future prospects of carbon nanomaterials’ application in electrochemical aptasensors are briefly discussed.

Graphene-family materials in electrochemical aptasensors

The study of graphene-based carbon nanocomposites has remarkably increased in recent years. Functionalized graphene-based nanostructures, including graphene oxide and reduced graphene oxide, have great potential as new innovative electrode materials in the fabrication of novel electrochemical sensors. Electrochemical sensors based on aptamers attracted great attention because of their high sensitivity and selectivity, and simple instrumentation, as well as low production cost. Aptamers as a potent alternative to antibodies are functional nucleic acids with a high tendency to specific analytes. Electrochemical aptasensors show specific recognition ability for a wide range of analytes. Although aptamers are selected in vitro in contrast to antibodies, they are interesting due to advantages like high stability, easy chemical modifications, and the potential to be employed in nanostructured device fabrication or electrochemical sensing devices. Recently, new nanomaterials have shown a significant impact on the production of electrochemical sensors with high efficiency and performance. This review aims to give an outline of electrochemical aptasensors based on the graphene family materials and discuss the detection mechanism in this type of aptasensors. The present review summarizes some of the recent achievements in graphene-based aptasensors and includes their recent electroanalytical applications. Graphical Abstract Graphical Abstract.

Electrochemical aptasensors for cancer diagnosis in biological fluids - A review

The tunability of SELEX procedure is an essential feature to supply bioaffinity receptors (aptamers) almost on demand for analytical and therapeutic purposes. This longstanding ambition is, however, not straightforward. Non-invasive cancer diagnosis, so called liquid biopsy, requires collection of body fluids with minimal or no sample pretreatment. In those raw matrices, aptamers must recognize minute amounts of biomarkers that are not unique entities but large sets of variants evolving with the disease stage. The susceptibility of aptasensors to assay conditions has driven the selection of aptamers to natural environments to ensure their optimum performance in clinical samples. We present herein a compilation of the SELEX procedures in natural milieus. By revising the electrochemical aptasensors applied to clinical samples for cancer diagnosis and tracing back to the original SELEX we analyze whether aptamers raised using these SELEX strategies are being incorporated to the diagnostic devices and how aptasensors are finding their way to a market dominated by antibody-based assays.

DNA branched junctions induced the enhanced fluorescence recovery of FAM-labeled probes on rGO for detecting Pb2

The reduced graphene oxide (rGO) could strongly adsorb and quench the fluorescence of dye-labeled single-stranded DNA (ssDNA); thus, it is widely applied in fluorescent sensors. However, these sensors may suffer from a limited sensitivity due to the low fluorescence recovery when adding the complementary DNA (cDNA) sequence. In this work, the powerful DNA branched junctions were constructed to improve the fluorescence recovery of FAM-labeled probe on rGO. In the presence of target Pb²⁺, the ribonucleotide (rA) in the substrate was cleaved specifically and the catalytic hairpin assembly of three metastable hairpins was further initiated, accompanied by the formation of DNA branched junctions. Then, the liberated Pb²⁺ could be recyclable. Impressively, the DNA branched junctions not only hybridize with the FAM-labeled probes with a high efficiency, but also are significantly undesirable for the rGO. Thus, a high fluorescence recovery of FAM-labeled probe on rGO was expected. The integration of the high fluorescence recovery and dual-cycle signal amplification endows the sensing strategy with a good performance for Pb²⁺ detection, including low detection limit (0.17 nM), good selectivity, and satisfactory practical applicability. The proposed DNA branched junctions offer a novel avenue to improve the fluorescence recovery of the dye-labeled probes on rGO for biological analysis.

Graphene/aptamer probes for small molecule detection: from in vitro test to in situ imaging

Small molecules are key targets in molecular biology, environmental issues, medicine and food industry. However, small molecules are challenging to be detected due to the difficulty of their recognition, especially in complex samples, such as in situ in cells or animals. The emergence of graphene/aptamer probes offers an excellent opportunity for small molecule quantification owing to their appealing attributes such as high selectivity, sensitivity, and low cost, as well as the potential for probing small molecules in living cells or animals. This paper (with 130 refs.) will review the application of graphene/aptamer probes for small molecule detection. We present the recent progress in the design and development of graphene/aptamer probes enabling highly specific, sensitive and rapid detection of small molecules. Emphasis is placed on the success in their development and application for monitoring small molecules in living cells and in vivo systems. By discussing the key advances in this field, we wish to inspire more research work of the development of graphene/aptamer probes for both on-site or in situ detection of small molecules and its applications for investigating the functions of small molecules in cells in a dynamic way. Graphical abstract Graphene/aptamer probes can be used to construct different platforms for detecting small molecules with high specificity and sensitivity, both in vitro and in situ in living cells and animals.

Fluorescence amplified sensing platforms enabling miRNA detection by self-circulation of a molecular beacon circuit

We have proposed a novel strategy for miRNA detection through enzyme-free signal amplification by self-circulation of the hybridization between the miRNAs and molecular beacon (MB) circuits. Unlike general MB-based miRNA detection based on the one-to-one (1 : 1) hybridization between MBs and miRNA, our system consists of four species of MBs (MBs A, B, C and D) (MB circuits) and is activated by a hybridization chain reaction. MBs stably coexist as hairpin structures that hardly show fluorescence signals in the absence of target miRNA. After miRNA detection, this MB circuit is able to generate fluorescence signals and amplify the fluorescence signal, contributing to improvement in detection sensitivity under iso-thermal conditions without an enzyme. Furthermore, in vitro and in vivo studies have proven that MB circuits can detect low levels of miRNA with high sensitivity, compared to when only one MB alone is used. Therefore, the MB circuits can provide a useful platform for target miRNA detection.

Electrical Property of Graphene and Its Application to Electrochemical Biosensing

Graphene, a single atom thick layer of two-dimensional closely packed honeycomb carbon lattice, and its derivatives have attracted much attention in the field of biomedical, due to its unique physicochemical properties. The valuable physicochemical properties, such as high surface area, excellent electrical conductivity, remarkable biocompatibility and ease of surface functionalization have shown great potentials in the applications of graphene-based bioelectronics devices, including electrochemical biosensors for biomarker analysis. In this review, we will provide a selective overview of recent advances on synthesis methods of graphene and its derivatives, as well as its application to electrochemical biosensor development. We believe the topics discussed here are useful, and able to provide a guideline in the development of novel graphene and on graphene-like 2-dimensional (2D) materials based biosensors in the future.

Chronocoulometric aptamer based assay for staphylococcal enterotoxin B by target-triggered assembly of nanostructured dendritic nucleic acids on a gold electrode

A rapid and ultrasensitive method is described for the detection of staphylococcal enterotoxin B (SEB). It is based on the formation of a dendritic DNA superstructure by integrating (a) target-induced triggering of DNA release with (b) signal amplification by a hybridization chain reaction. Partially complementary pairing of aptamer and trigger DNA forms a duplex structure. The capture DNA is then placed on the surface of a gold electrode through gold-thiol chemistry. In the presence of SEB, the aptamer-target conjugate is compelled to form. This causes the release of trigger DNA owing to a strong competition with SEB. The trigger DNA is subsequently hybridized with the partial complementary sequences of the capture DNA to trigger HCR with three auxiliary DNA sequances (referred to as H1, H2, H3). Finally, the dendritic DNA superstructure is bound to hexaammineruthenium(III) cation by electrostatic adsorption and assembled onto the modified gold electrode. This produces an amplified electrochemical signal that is measured by chronocoulometry. Under optimal conditions, the charge difference increases linearly with the logarithm of the SEB concentrations in the range from 5 pg·mL^-1 to 100 ng·mL^-1 with a detection limit as low as 3 pg·mL^-1 (at S/N = 3). Graphical abstract An electrochemical switching strategy is presented for the sensitive detection of Staphylococcus enterotoxin B based on target-triggered assembly of dendritic nucleic acid nanostructures.

Graphene-based aptasensors: from molecule-interface interactions to sensor design and biomedical diagnostics

Graphene-based nanomaterials have been widely utilized to fabricate various biosensors for environmental monitoring, food safety, and biomedical diagnostics. The combination of aptamers with graphene for creating biofunctional nanocomposites improved the sensitivity and selectivity of fabricated biosensors due to the unique molecular recognition and biocompatibility of aptamers. In this review, we highlight recent advances in the design, fabrication, and biomedical sensing application of graphene-based aptasensors within the last five years (2013-current). The typical studies on the biomedical fluorescence, colorimetric, electrochemical, electrochemiluminescence, photoelectrochemical, electronic, and force-based sensing of DNA, proteins, enzymes, small molecules, ions, and others are demonstrated and discussed in detail. More attention is paid to a few key points such as the conjugation of aptamers with graphene materials, the fabrication strategies of sensor architectures, and the importance of aptamers on improving the sensing performances. It is expected that this work will provide preliminary and useful guidance for readers to understand the fabrication of graphene-based biosensors and the corresponding sensing mechanisms in one way, and in another way will be helpful to develop novel high performance aptasensors for biological analysis and detection.

Ultrasensitive and simple fluorescence biosensor for detection of the mecA gene of Staphylococcus aureus by using an exonuclease III-assisted cascade signal amplification strategy

In this work, a label-free fluorescence biosensor for ultrasensitive and simple detection of the mecA gene of Staphylococcus aureus was proposed by using an exonuclease III (Exo III)-assisted cascade signal amplification strategy. The 3' end-extruding hairpin probe (HP) acted as the target recognition element and the caged G-quadruplex was used as the signal reporter. Without the mecA gene, the HP probe cannot be digested by Exo III, as the G-rich sequences are blocked in the stem of the HP probe. In the presence of the mecA gene, the hybridization of the mecA gene with the 3' end-extruding HP probe triggers the digestion reaction of Exo III, liberating the mecA gene and the mecA gene analogue. Both the released mecA gene and the mecA gene analogue can hybridize with other HP probes and activate another round of the cleavage reaction. Consequently, the released free G-quadruplex is "lit up" by N-methylmesoporphyrin IX (NMM), displaying a dramatically enhanced fluorescence intensity. This sensing platform showed a high sensitivity towards the mecA gene with a detection limit as low as 2.4 fM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits excellent selectivity for the mecA gene in the presence of other interfering DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the mecA gene in a real food sample with satisfactory results. Owing to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a promising platform for the detection of other genes by substituting the target-recognition element.

Chimeric DNA-Functionalized Titanium Carbide MXenes for Simultaneous Mapping of Dual Cancer Biomarkers in Living Cells

Acquiring multilayer information on diverse biomarkers with different spatial distributions at the cellular level is crucial for monitoring the progression of cancers. Herein, a dual-signal-tagged chimeric DNA-functionalized titanium carbide MXenes nanoprobe (dcDNA-Ti₃C₂) that responds to biomarkers with different cellular locations from plasma membrane to cytoplasm was designed toward this end. In the presence of cancer biomarkers, including transmembrane glycoprotein mucin 1 (MUC1) and cytoplasmic microRNA-21 (miR-21), the recognition between MUC1 and its aptamer in the dcDNA-Ti₃C₂ probe induces the separation of TAMRA-MUC1 aptamer from Ti₃C₂ MXenes, thereby resulting in an increase in red fluorescence; and the hybridization of miR-21 with the hairpin probe triggers the increase of green fluorescence. As a result, dual analysis of MUC1 and miR-21 at low-nanomolar concentrations in vitro, as well as in situ simultaneous imaging of the biomarkers within MCF-7 breast cancer cells, was achieved. The feasibility of the nanoprobe was further demonstrated by monitoring the expression changes of both the biomarkers in cancer cells under different inhibitor combinations. Therefore, this strategy allows us to acquire the expression levels and spatial distributions of different biomarkers in living cells, providing a helpful tool for reliable diagnosis of cancers and basic understanding their progression.

MoS2/nitrogen doped graphene hydrogels p-n heterojunction: Efficient charge transfer property for highly sensitive and selective photoelectrochemical analysis of chloramphenicol

Constructing junctions between semiconductors is an effective way to promote charge separation and thus to improve the photoelectrochemical (PEC) performances, and specifically, p-n heterojunction is considered as a very promising structure. Herein, we designed and fabricated MoS₂/nitrogen doped graphene hydrogels (MoS₂/NGH) p-n heterojunction by a facile one-pot hydrothermal route. The as-fabricaterd MoS₂/NGH heterostructures demonstrated the excellent PEC activity, exhibiting enhanced photocurrent intensity by the fast transfer and separation rate of photogenerated electron-hole owing to the construction of p-n heterojunction. Based on the high PEC performances of the MoS₂/NGH heterostructure, a novel sensitive PEC sensor was developed for the determination of chloramphenicol (CAP) with the assistance of aptamer. In the presence of target molecules, the as-fabricated PEC sensor could recognize the CAP quickly and then consume the holes in the interface of heterostructures, inhibiting the recombination of photogenerated electron-hole pairs, resulting the enhanced photocurrent. Specially, with the concentration of CAP increased, the photocurrent enhanced gradually. Excellent linearity was obtained in the concentration range from 32.3 ng/L to 96.9 μg/L, and the limit of detection was 3.23 ng/L. Moreover, the as-fabricated PEC sensor exhibited rapid response, high stability, low-cost and high selectivity, which could be successfully applied to the analysis of CAP in honeycomb samples.

Highly stable Ni-MOF comprising triphenylamine moieties as a high-performance redox indicator for sensitive aptasensor construction

Electroactive metal-organic frameworks (MOFs) with large surface area and manipulatable structural properties show promise as a new type of signal probe for electrochemical biosensing application. In this work, an electroactive Ni-MOF, assembled by the redox-active ligands 4,4',4″-Tricarboxytriphenylamine (H₃TCA), a triphenylamine derivatives, as the electroactive source and magnetic ordered Ni₄O₄ clusters as electronic transport nodes, is first designed and applied for electrochemical aptasensing of thrombin (Tb). The designed Ni-MOF probe realizes a stable and sensitive electrochemical signal output based on simple sandwich-type aptasensing because the high-content TCA active sites and good magnetic ordered intermediate of Ni₄O₄ clusters are periodically arranged in well-defined porous structure of the MOF. The Ni-MOF probe assembled by redox-active ligand presents the high stability and can be directly applied in electrochemical aptasensor, avoiding any post-modification and the addition of redox mediators. As a result, the constructed electrochemical aptasensor shows a wide linear relationship for Tb from 0.05 pM to 50 nM and a detection limit of 0.016 pM (S/N = 3). Furthermore, the proposed aptasensor is successfully applied to analysis of target Tb in real serum sample with satisfactory results. The present work indicates that fabricating a redox-active organic molecule in functionalized MOFs offer a feasible strategy to design high-stable electroactive MOFs for construction of electrochemical biosensors with simplicity, high selectivity and sensitivity.

Electrochemical detection of tobramycin based on enzymes-assisted dual signal amplification by using a novel truncated aptamer with high affinity

An aptamer with the length of only 15 nucleotides specific for tobramycin was obtained through rationally designed truncation from a previously reported long sequence. The structural and binding properties of the aptamer were characterized. The dissociation constant (K_d) was determined to be 42.12 nM, indicating high affinity of the aptamer for tobramycin. Then an electrochemical sensor based on this aptamer was developed, which employed an enzymes-assisted dual signal amplification cycle through target recycling and strand-displacement DNA polymerization. A hairpin probe containing the aptamer sequence was designed and used to start the production cycle of a short ssDNA fragment in the presence of tobramycin, with the help of phi29 DNA polymerase and nicking endonuclease Nt.AlwI. The ssDNA fragment was captured by a signal transduction probe modified on gold electrode to form a triple-helix structure. With the help of [Ru(NH₃)₆]³⁺, a significant electrochemical signal was observed in differential pulse voltammetry (DPV). Under the optimal conditions, the current in DPV is linearly related with the concentration of tobramycin in the range of 10-200 nM, and the detection limit is 5.13 nM. The electrochemical sensor showed high specificity for tobramycin when it was challenged by other antibiotics. In addition, the constructed sensor was used to detect tobramycin in milk and water samples, and showed satisfactory performance. Therefore, the screened aptamer as well as the developed sensor has great application prospects in the fields of food safety control, medical test and environment monitoring.

Oligonucleotide-modulated photocurrent enhancement of a tetracationic porphyrin for label-free homogeneous photoelectrochemical biosensing

This work reports the first demonstration of an oligonucleotide-modulated label-free homogeneous photoelectrochemical (PEC) biosensing platform based on the adsorption of tetracationic porphyrin (denoted as TMPyP here) onto 1-naphthalenesulfonate anion (NS^-)-grafted indium tin oxide electrode (denoted as TMPyP-NS^--ITO), which generates a stable and rapid photocurrent response. We found that when NS^--ITO electrode was subjected to single-stranded oligonucleotide (ssON) before TMPyP adsorption, a remarkable enhancement of photocurrent intensity was observed from the resulted TMPyP-ssON-NS^--ITO electrode with high specificity towards oligonucleotide. A series of investigations were carried out to understand the mechanism of this oligonucleotide-modulated photocurrent enhancement phenomenon. Moreover, the studies of this robust photocurrent enhancement mechanism was successfully extended to develop a signal-on homogeneous PEC biosensing platform for, as a proof-of-concept, label-free M.SssI methyltransferase activity analysis through a judiciously and compatibly engineered signal transduction strategy consisted of hairpin-shaped oligonucleotide probe, restriction endonuclease HpaII, and Exonuclease I. The rationally designed homogeneous PEC biosensor exhibit sensitive PEC response toward M.SssI methyltransferase with a low detection limit of 3.5 mU/mL and a wide linear range from 0.01 to 120 U/mL. Additionally, we show that our homogeneous PEC biosensing platform can be also utilized to screen methyltransferase inhibitors. Therefore, this work will provide a distinctive paradigm for versatile homogeneous PEC biosensing platform that can be used as potential powerful tool toward innovative label-free bioanalytical purposes.

Homogeneous electrochemical aptasensor for mucin 1 detection based on exonuclease I-assisted target recycling amplification strategy

A sensitive and homogeneous electrochemical aptasensor was fabricated for the detection of mucin 1 (MUC1) by combining a well-designed DNA bulge-loop (L-DNA) structure with high-efficient exonuclease I (Exo I)-assisted target recycling amplification strategy. The L-DNA probe was constructed via the hybridization of the MUC1 aptamer and methylene blue (MB) labeled complementary DNA (cDNA) (cDNA-MB) and hence could not diffuse freely to the negatively charged ITO electrode surface due to the strong electrostatic repulsion, so small electrochemical signal was detected. The addition of MUC1 caused the dissociation of L-DNA structure due to the specificity between aptamer and MUC1. Then Exo I was implemented to digest the released cDNA-MB into mononucleotides and then produced short MB-labeled mononucleotides fragments (MB-MFs). As the MB-MFs contained few negative charges, it diffused easily to the negatively charged ITO electrode surface and resulted in the enhanced electrochemical signal. Meanwhile, the MUC1-aptamer complex was also specifically digested by Exo I, resulting in the liberation of MUC1 and hence realized the target recycling and then caused the amplification of the electrochemical signal. The enhanced electrochemical signal has a good linear relationship with logarithm of MUC1 concentration in the range of 1.0 pg mL^-1-50 ng mL^-1 with a limit of detection of 0.40 pg mL^-1 (S/N = 3). Additionally, the fabricated aptasensor has been successfully applied to detect MUC1 in serum samples with satisfactory results and thereby it exhibits great potential in the practical application of clinical diagnosis.

DNA-fueled target recycling-induced two-leg DNA walker for amplified electrochemical detection of nucleic acid

Taking advantage of the homogeneous and heterogeneous electrochemical biosensors, a simple, sensitive, and selective electrochemical biosensor is constructed by combining entropy-driven amplification (EDA) with DNA walker. This electrochemical biosensor realizes the biorecognition and EDA operation in homogeneous solution, which is beneficial to improve the recognition and amplification efficiency. A two-leg DNA walker generated by EDA can walk on the surface of gold electrode for cleaving the immobilized substrate DNA and releasing the electroactive labels, giving rise to a significant decrease of the electrochemical signal. The immobilization of the electroactive labels ensures the reproducibility and reliability of the biosensor. The present cascade amplification assay can be applied to detect target DNA with a detection limit of 0.29 fM, and base mutations can be easily distinguished. Moreover, the proposed electrochemical biosensor shows a satisfactory performance for the detection of target DNA in human serum. Thus, the novel electrochemical biosensor holds promising potential for a future application in disease diagnosis.

Enzyme-free Target Recycling and Double-Output Amplification System for Electrochemiluminescent Assay of Mucin 1 with MoS2 Nanoflowers as Co-reaction Accelerator

In this work, a sensitive electrochemiluminescent assay of mucin 1 (MUC1) was developed with the advantages of target recycling amplification strategy and effective MoS₂ nanoflower (MoS₂ NF)-based signal probe. Briefly, the target MUC1 triggered enzyme-free recycling and a double-output amplification process was executed to acquire masses of single-stranded DNA as a mimic target, which further participated in the catalytic hairpin assembly process for signal amplification. Meanwhile, MoS₂ NFs were prepared as an effective co-reaction accelerator, which not only possessed excellent catalytic performance for H₂O₂ decomposition to largely enhance the luminous intensity of N-(aminobutyl)- N-(ethylisoluminol) (ABEI)-H₂O₂ electrochemiluminescence system but also offered a desirable platform for ABEI-functionalized Ag nanoparticles (ABEI-Ag complexes) loading via Ag-S binding. The experimental results showed the proposed aptasensor had a good linear relationship in the range of 1 fg/mL to 10 ng/mL for MUC1 detection and the limit of detection was 0.58 fg/mL (S/N = 3). In addition, the aptasensor had nice stability and selectivity and huge potential to be applied in clinical research.

Electrochemical detection of NGF using a reduced graphene oxide- titanium nitride nanocomposite

There is a correlation between the severity of neurological impairment in patients that have suffered a cerebrovascular accident and the nerve growth factor (NGF) level. This study addressed the fabrication of a titanium nitride (TiN) and reduced graphene oxide (RGO)-based composite with remarkable electrocatalytic activity towards NGF oxidation in a phosphate buffer solution (PB, 0.1 M). The proposed electrochemical sensor was linearly related to the NGF concentration in the range of 10 nM-5 μM with a detection limit of 2.6 nM.

Triplex DNA formation-mediated strand displacement reaction for highly sensitive fluorescent detection of melamine

Since melamine is a strong hazard to human health, the development of new methods for highly sensitive detection of melamine is highly desirable. Herein, a novel fluorescent biosensing strategy was designed for sensitive and selective melamine assay based on the recognition ability of abasic (AP) site in triplex towards melamine and signal amplification by Mg²⁺-dependent DNAzyme. In this strategy, the melamine-induced formation of triplex DNA was employed to trigger the strand displacement reaction (SDR). The SDR process converted the specific target recognition into the release and activation of Mg²⁺-dependent DNAzyme, which could catalyze the cleavage of fluorophore/quencher labeled DNA substrate (FQ), resulting in a significantly increased fluorescent signal. Under the optimal conditions, the fluorescent signal has a linear relationship with the logarithm of the melamine concentration in a wide range of 0.005-50 μM. The detection limit was estimated to be 0.9 nM (0.1ppb), which is sufficiently sensitive for practical application. Furthermore, this strategy exhibits high selectivity against other potential interfering substances, and the practical application of this strategy for milk samples reveals that the proposed strategy works well for melamine assay in real samples. Therefore, this strategy presents a new method for the sensitive melamine assay and holds great promise for sensing applications in the environment and the food safety field.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

Dual-competitive lateral flow aptasensor for detection of aflatoxin B1 in food and feedstuffs

A novel dual-competitive lateral flow aptasensor (LFA) benefited from aptamer and lateral flow strips was first designed by using aflatoxin B₁ (AFB₁) as the model target. In this LFA assay, the target AFB₁ competed with AFB₁-hapten at T line for binding to Cy5-labeled AFB₁ aptamer and the complementary strand competed with the target AFB₁ for binding to Cy5-labeled AFB₁ aptamer at C line. The ratio of their fluorescent intensities at the T line and C line (ST/SC ratio) was employed in order to increase the sensitivity for target AFB₁ detection. This technique has the limit of detection (LOD) of 0.1ng/mL for AFB₁ within the linear range from 0.1ng/mL to 1000ng/mL. Subsequently, the LFA approach was validated using 11 kinds of food and feedstuff samples with a simple aqueous extraction protocol. The test results with different naturally contaminated feedstuffs indicated a good correlation between this LFA and a commercial ELISA kit. The assay can be completed within 20min and its sensitivity, specificity and reproducibility are highly satisfactory. This is the first LFA that has been rigorously validated, which will be greatly beneficial to development of commercial aptamer-based biosensors for food safety, environmental analysis, particularly in clinical diagnosis.