Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives

Aptamer-based sensors for fluid biopsies of protein disease markers

Fluid biopsy technology, characterized by its minimally invasive nature, speed, and continuity, has become a rapidly advancing and widely applied real-time diagnostic technique. Among various biomarkers, proteins represent the most abundant class of disease indicators. The sensitive and accurate detection of protein markers in bodily fluids is significantly influenced by the control exerted by recognition ligands. Aptamers, which are structurally dynamic functional oligonucleotides, exhibit high affinity, specific recognition of targets, and notable characteristics of high editability and modularity. These features make aptamer universal "recognition-capture" components, contribute to a significant leap in their applications within the biosensor domain. In this context, we provide a comprehensive review of the extensive application of aptamer-based biosensors in fluid biopsy. We systematically compile the characteristics and construction strategies of aptamer-based biosensors tailored for fluid biopsy, including aptamer sequences, affinity (KD), fluid background, sensing technologies, sensor construction strategies, incubation time, detection performance, and influencing factors. Furthermore, a comparative analysis of their advantages and disadvantages was conducted. In conclusion, we delineate and deliberate on prospective research trajectories and challenges that lie ahead in the realm of aptamer-based biosensors for fluid biopsy.

EXPAR for biosensing: recent developments and applications

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

A stable colorimetric biosensor for highly selective detection of malathion residue in food based on aptamer-regulated laccase-mimic activity

Malathion causes a serious threat to human health due to its widespread use in the environment. Herein, a novel and stable smartphone-integrated colorimetric biosensor for malathion detection is firstly established based on aptamer-enhanced laccase-mimicking activity. The results indicate that the M17-F aptamer can increase the affinity of Ag2O nanoparticles to the substrate 2,4-dichlorophenol and enhance their laccase-mimicking activity. Thus, abundant semiquinone radicals are produced in the catalytic system, which are combined with chromogenic agent to generate dark red products. The corresponding RGB values for the colour change of the solution can be easily obtained using smartphones, which is used for the rapid detection of malathion. The established biosensor for malathion has a limit of detection as low as 5.85 nmol·L-1, and displays good selectivity for other competitive pesticides. Moreover, further studies have verified the applicability of the biosensor in actual samples, indicating that it may have the potential for application in malathion detection in food.

Sensitive fluorescence assay of chloramphenicol coupled with two-level isothermal amplification using a self-powered catalyzed hairpin assembly and entropy-driven circuit

Two levels of nucleic acids-based isothermal amplification normally require a long reaction time due to the low concentration of catalyst, which limits its practical application. A sensitive fluorescence assay of chloramphenicol (CAP) was developed coupled with two-level isothermal amplification using a self-powered catalyzed hairpin assembly (CHA) and entropy-driven circuit (EDC). CAP can bind with its aptamer to open its closed structure. The opened hairpin can initiate self-powered CHA and EDC. The product of CHA can circularly catalyze the CHA with increasing concentration. In principle, the product of CHA plays the role of catalyst and increases with the progression of the reaction. Compared with the normal two levels of amplification, the amplification efficiency of our strategy is much higher due to the self-powered reaction by the CHA product. Thus, the reaction time is shortened to 110 min in this strategy. Moreover, the detection limit for CAP can achieve 0.1 pM and shows promising prospects for practical application.

Dual-mode colorimetric and photothermal aptasensor for detection of kanamycin using flocculent platinum nanoparticles

Chitosan (CS)-stabilized platinum nanoparticles (CS/PtNPs) were employed to develop a novel aptamer-based dual-mode colorimetric and photothermal biosensor for selective detection of kanamycin (KAN). As a peroxidase-like catalyst, the CS/PtNPs showed outstanding catalytic activity for the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2). As a stabilizing agent, CS excelled at fixing the KAN binding aptamer on the surface of the CS/PtNPs, amplifying their catalytic activity and enhancing colloidal dispersion and stability. The oxidized TMB (TMBox) functioned as a signal for the colorimetric, photothermal aptasensor because of its observable absorbance of light in the visible and near-infrared (NIR) regions. When light from a NIR laser was absorbed by the TMBox in the reaction solution, heat was generated in inverse proportion to the KAN concentration. The developed colorimetric and photothermal modes of the aptasensor showed a linear detection range of 0.1-50 and 0.5-50 μM, with a limit of detection (LOD) of 0.04 and 0.41 μM, respectively. Moreover, the aptasensor successfully determined KAN concentrations in spiked milk samples, verifying the reliability and reproducibility in practical applications. The dual-mode aptasensor based on CS/PtNPs for KAN detection, utilizing both color change and heat generation signals through a single probe (TMBox), demonstrates rapid response, simplicity in operation, cost-effectiveness, and high sensitivity. In addition, unlike typical immunoassays, this aptamer-based peroxidase-like nanozyme activation and inhibition strategy required no washing process, which was very effective in terms of reducing the time required for an assay and sustaining a high sensitivity.

DNA Nanospheres Assisted Spatial Confinement Signal Amplification for MicroRNA Imaging in Live Cancer Cells

DNA assemblies are commonly used in biosensing, particularly for the detection and imaging of microRNAs (miRNAs), which are biomarkers associated with tumor progression. However, the difficulty lies in the exploration of high-sensitivity analytical techniques for miRNA due to its limited presence in living cells. In this study, we introduced a DNA nanosphere (DS) enhanced catalytic hairpin assembly (CHA) system for the detection and imaging of intracellular miR-21. The single-stranded DNA with four palindromic portions and extending sequences at the terminal was annealed for assembling DS, which avoided the complex sequence design and high cost of long DNA strands. Benefiting from the multiple modification sites of DS, functional hairpins H1 (modified with Cy3 and BHQ2) and H2 were grafted onto the surface of DS for assembling DS-H1-H2 using a hybridization reaction. The DS-H1-H2 system utilized spatial confinement and the CHA reaction to amplify fluorescence signals of Cy3. This enabled highly sensitive and rapid detection of miR-21 in the range from 0.05 to 3.5 nM. The system achieved a limit of determination (LOD) of 2.0 pM, which was 56 times lower than that of the control CHA circuit with freedom hairpins. Additionally, the sensitivity was improved by 8 times. Moreover, DS-H1-H2 also showed an excellent imaging capability for endogenous miR-21 in tumor cells. This was due to enhanced cell internalization efficiency, accelerated reaction kinetics, and improved biostability. The imaging strategy was shown to effectively monitor the dynamic content of miR-21 in live cancer cells and differentiate various cells. In general, the simple nanostructure DS not only enhanced the detection and imaging capability of the conventional probe but also could be easily integrated with the reported DNA-free probe, indicating a wide range of potential applications.

Exonuclease-catalyzed recycling and annular four-footed DNA walking amplification-assisted "on-off-super on" signal transitions for photoelectrochemical biosensing of kanamycin

Photoelectrochemical (PEC) biosensors have exhibited a promising potential for assays of a large variety of analytes; however, how to realize their low background-based "super on" signal output is still a great challenge. Herein, we report a novel multiple nucleic acid amplification-assisted "on-off-super on" signal transition mechanism for the PEC biosensing of kanamycin antibiotics. The biosensing platform was constructed on a perylene-3,4,9,10-tetracarboxylic dianhydride-based photoelectrode, and its strong photocurrent could be well inhibited by an anchored ferrocene (Fc)-labeled hairpin DNA to produce a low background signal. Two target biorecognition-triggered exonuclease III-catalytic reactions were adopted to produce an annular four-footed DNA walker (AFW) and a methylene blue (MB)-labeled DNA strand. By using their synergistic effect to release Fc quenchers and simultaneously capture MB sensitizers, a "super on" signal output was realized. As a result, a very wide linear range from 10 fg mL-1 to 10 ng mL-1 and an ultra-low detection limit of 7.8 fg mL-1 were obtained. Meanwhile, the aptamer recognition-based homogeneous reaction and AFW-based multiple nucleic acid amplification effectively simplified the assay manipulation and well ensured the repeatability of the method. The satisfactory sample experiment results indicated its good reliability and accuracy for the antibiotic residue analysis application.

Dual-Functional Tetrahedron Multivalent Aptamer Assisted Amplification-Free CRISPR/Cas12a Assay for Sensitive Detection of Salmonella

Salmonellosis continues to impose a significant economic burden globally. Rapid and sensitive detection of Salmonella is crucial to preventing the outbreaks of foodborne illnesses, yet it remains a formidable challenge. Herein, a dual-functional tetrahedron multivalent aptamer assisted amplification-free CRISPR/Cas12a assay was developed for Salmonella detection. In the system, the aptamer was programmatically assembled on the tetrahedral DNA nanostructure to fabricate a multivalent aptamer (TDN-multiApt), which displayed a 3.5-fold enhanced avidity over the monovalent aptamer and possessed four CRISPR/Cas12a targeting fragments to amplify signal. Therefore, TDN-multiApt could directly activate Cas12a to achieve the second signal amplification without any nucleic acid amplification. By virtue of the synergism of high avidity and cascaded signal amplifications, the proposed method allowed the ultrasensitive detection of Salmonella as low as 7 cfu mL-1. Meanwhile, this novel platform also exhibited excellent specificity against target bacteria and performed well in the detection of various samples, indicating its potential application in real samples.

Combining hybrid nanoflowers with hybridization chain reaction for highly sensitive detection of SARS-CoV-2 nucleocapsid protein

BACKGROUND

COVID-19 (coronavirus disease 2019) pandemic has had enormous social and economic impacts so far. The nucleocapsid protein (N protein) is highly conserved and is a key antigenic marker for the diagnosis of early SARS-CoV-2 infection.

RESULTS

In this study, the N protein was first captured by an aptamer (Aptamer 58) coupled to magnetic beads (MBs), which in turn were bound to another DNA sequence containing the aptamer (Aptamer 48-Initiator). After adding 5'-biotinylated hairpin DNA Amplifier 1 and Amplifier 2 with cohesive ends for complementary hybridization, the Initiator in the Aptamer 48-Initiator began to trigger the hybridization chain reaction (HCR), generating multiple biotin-labeled DNA concatamers. When incubated with synthetic streptavidin-invertase-Ca3(PO4)2 hybrid nanoflower (SICa), DNA concatamers could specifically bind to SICa through biotin-streptavidin interaction with high affinity. After adding sucrose, invertase in SICa hydrolyzed sucrose to glucose, whose concentration could be directly read with a portable glucometer, and its concentration was positively correlated with the amount of captured N protein. The method is highly sensitive with a detection limit as low as 1 pg/mL.

SIGNIFICANCE

We believe this study provided a practical solution for the early detection of SARS-CoV-2 infection, and offered a new method for detecting other viruses through different target proteins.

Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.

Aptamers: Features, Synthesis and Applications

Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.

Flexible and Stretchable Organic Electrochemical Transistors for Physiological Sensing Devices

Flexible and stretchable bioelectronics provides a biocompatible interface between electronics and biological systems and has received tremendous attention for in situ monitoring of various biological systems. Considerable progress in organic electronics has made organic semiconductors, as well as other organic electronic materials, ideal candidates for developing wearable, implantable, and biocompatible electronic circuits due to their potential mechanical compliance and biocompatibility. Organic electrochemical transistors (OECTs), as an emerging class of organic electronic building blocks, exhibit significant advantages in biological sensing due to the ionic nature at the basis of the switching behavior, low driving voltage (<1 V), and high transconductance (in millisiemens range). During the past few years, significant progress in constructing flexible/stretchable OECTs (FSOECTs) for both biochemical and bioelectrical sensors has been reported. In this regard, to summarize major research accomplishments in this emerging field, this review first discusses structure and critical features of FSOECTs, including working principles, materials, and architectural engineering. Next, a wide spectrum of relevant physiological sensing applications, where FSOECTs are the key components, are summarized. Last, major challenges and opportunities for further advancing FSOECT physiological sensors are discussed.

Concatenated dynamic DNA network modulated SERS aptasensor based on gold-magnetic nanochains and Au@Ag nanoparticles for enzyme-free amplification analysis of tetracycline

Tetracycline (TC) poses a great threat to food and environmental safety due to its misuse in animal husbandry and aquaculture. Therefore, an efficient analytical method is needed for the detection of TC to prevent possible hazards. Herein, a cascade amplification SERS aptasensor for sensitive determination of TC was constructed based on aptamer, enzyme-free DNA circuits, and SERS technology. The capture probe and signal probe were obtained by binding DNA hairpins H1 and H2 to the prepared Fe₃O₄@hollow-TiO₂/Au nanochains (Fe₃O₄@h-TiO₂/Au NCs) and Au@4-MBA@Ag nanoparticles, respectively. The dual amplification of EDC-CHA circuits significantly facilitated the sensitivity of the aptasensor. Additionally, the introduction of Fe₃O₄ simplified the operation of the sensing platform due to its superb magnetic capability. Under optimal conditions, the developed aptasensor exhibited a distinct linear response to TC with a low limit of detection of 15.91 pg mL^-1. Furthermore, the proposed cascaded amplification sensing strategy exhibited excellent specificity and storage stability, and its practicability and reliability were verified by TC detection of real samples. This study provides a promising idea for the development of specific and sensitive signal amplification analysis platforms in the field of food safety.

Simultaneous screening of multiple diarrhetic shellfish poisons with group-specific split aptamers and silver nanocluster beacon

Poisoning events concerning diarrhetic shellfish poisons (DSPs) are increasing continually. It is extremely necessary to develop simple analysis methods for screening simultaneously different types of DSPs from food-related samples. Okadaic acid (OA) and its analogues, i.e., dinophysistoxin-1 (DTX-1) and dinophysistoxin-2 (DTX-2), are the prevalent DSPs. Herein, a facile and label-free fluorescent aptasensor targeting the three DSPs was constructed with a pair of group-specific split aptamers and silver nanocluster beacon. In presence of the targets, the DNA templates attached at the ends of the split aptamers would be dragged close to trigger enhanced fluorescence signals from silver nanoclusters. The aptasensor offered high sensitivity and good selectivity, with limit of detection of 2.282 nmolL^-1, 19.38 nmolL^-1, and 13.61 nmolL^-1 for OA, DTX-1, and DTX-2, respectively. Moreover, the applicability of aptasensor was well verified with shellfish and seawater samples. This study provides good reference for further exploration on analysis methods for food-related molecules.

Electrochemical aptasensor based on the engineered core-shell MOF nanostructures for the detection of tumor antigens

It is essential to develop ultrasensitive biosensors for cancer detection and treatment monitoring. In the development of sensing platforms, metal-organic frameworks (MOFs) have received considerable attention as potential porous crystalline nanostructures. Core-shell MOF nanoparticles (NPs) have shown different diversities, complexities, and biological functionalities, as well as significant electrochemical (EC) properties and potential bio-affinity to aptamers. As a result, the developed core-shell MOF-based aptasensors serve as highly sensitive platforms for sensing cancer biomarkers with an extremely low limit of detection (LOD). This paper aimed to provide an overview of different strategies for improving selectivity, sensitivity, and signal strength of MOF nanostructures. Then, aptamers and aptamers-modified core-shell MOFs were reviewed to address their functionalization and application in biosensing platforms. Additionally, the application of core-shell MOF-assisted EC aptasensors for detection of several tumor antigens such as prostate-specific antigen (PSA), carbohydrate antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), human epidermal growth factor receptor-2 (HER2), cancer antigen 125 (CA-125), cytokeratin 19 fragment (CYFRA21-1), and other tumor markers were discussed. In conclusion, the present article reviews the advancement of potential biosensing platforms toward the detection of specific cancer biomarkers through the development of core-shell MOFs-based EC aptasensors.

A Colorimetric Aptasensor for Ochratoxin A Detection Based on Tetramethylrhodamine Charge Effect-Assisted Silver Enhancement

A novel colorimetric aptasensor based on charge effect-assisted silver enhancement was developed to detect ochratoxin A (OTA). To achieve this objective, gold nanoparticles (AuNPs), which can catalyze silver reduction and deposition, were used as the carrier of the aptamers tagged with a positively charged tetramethylrhodamine (TAMRA). Due to the mutual attraction of positive and negative charges, the TAMRA attracted and retained the silver lactate around the AuNPs. Thus, the chance of AuNP-catalyzed silver reduction was increased. The charge effect-assisted silver enhancement was verified by tagging different base pair length aptamers with TAMRA. Under optimized conditions, the as-prepared OTA aptasensor had a working range of 1 × 10²-1 × 10⁶ pg mL^-1. The detection limit was as low as 28.18 pg mL^-1. Moreover, the proposed aptasensor has been successfully applied to determine OTA in actual samples with satisfactory results.

Controllable DNA nanodevices regulated by logic gates for multi-stimulus recognition

DNA biosensors have attracted considerable attention due to their great potential in environmental monitoring and medical diagnosis. Despite the great achievements, the single function and uncontrollability of the sensors restrict their further application. Therefore, it is necessary to construct controllable nanodevices with both sensing and responding capabilities to external stimuli. Herein, we develop a strategy to engineer structure-switching biosensors which can respond to external stimuli while preserving the sensing capability. The engineered nanodevice consists of an actuation module and a sensing module. Initially, the sensing module is disabled by a blocker strand which acts as an allosteric switch. Once the stimuli-responsive actuation module displaces the blocker DNA, the sensing module is activated. Based on the strategy, the engineered nanodevice could recognize both the target and external stimuli. As a demonstration of this strategy, a controllable Hg²⁺ sensor was designed, in which a 'YES', 'AND', and 'OR' logic gate is employed as the actuation module respectively to facilitate recognition of oligonucleotide inputs. The modular nature of the proposed strategy makes it easily generalizable to other structure-switching sensors. As a demonstration of this, we successfully apply it to the ATP sensor. The proposed strategy has potential in the fields of programmable biosensing, disease diagnosis, DNA computing, and intelligent nanodevices.

Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection

In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.

Preliminary evaluation of a 64Cu-labeled DNA aptamer for PET imaging of glioblastoma

To develop a DNA aptamer-based PET tracer for imaging of glioblastoma. 5 mM of NOTA-AS1411, 60-min, and 37 °C were selected as the optimal condition for 64Cu radiolabeling of AS1411. 64Cu-NOTA-AS1411 remained stable in PBS and 100% mouse serum for at least six hours. From the PET images, 64Cu-NOTA-AS1411 tended to be excreted out through the kidneys and there was high tracer accumulation in the bladder. There was a higher tumor uptake in the AS1411 group than that in the control group. 64Cu-NOTA-AS1411 is a suitable potential PET tracer for imaging murine glioblastoma.

DNA-based customized functional modules for signal transformation

Information on the temporal and spatial scale of cellular molecules in biological systems is crucial for estimating life processes and may be conducive to an improved understanding of disease progression. This intracellular and extracellular information is often difficult to obtain at the same time due to the limitations of accessibility and sensing throughput. DNA is an excellent material for in vivo and in vitro applications, and can be used to build functional modules that can transform bio-information (input) into ATCG sequence information (output). Due to their small volume and highly amenable programming, DNA-based functional modules provide an opportunity to monitor a range of information, from transient molecular events to dynamic biological processes. Over the past two decades, with the advent of customized strategies, a series of functional modules based on DNA networks have been designed to gather different information about molecules, including the identity, concentration, order, duration, location, and potential interactions; the action of these modules are based on the principle of kinetics or thermodynamics. This paper summarizes the available DNA-based functional modules that can be used for biomolecular signal sensing and transformation, reviews the available designs and applications of these modules, and assesses current challenges and prospects.

Mismatch-fueled catalytic hairpin assembly mediated ultrasensitive biosensor for rapid detection of MicroRNA

Herein, a mismatch-fueled catalytic hairpin assembly (MCHA) was rationally engineered, which possessed higher amplification efficiency and faster rate than catalytic hairpin assembly (CHA). Once input target microRNA-21(miRNA-21) triggers the MCHA, the hairpin DNA H1 will be opened to form the duplex H1-miRNA-21, then the mismatched hairpin DNA H2 could easily hybridize with H1-miRNA-21 to generate duplex H1-H2 and the miRNA-21 could be released to enter next cycle, thus generating amounts of output products. Impressively, the MCHA realizes a pretty shorter complete reaction time of 40 min and quite higher amplification efficiency of 9.56 × 10⁶, which dramatically transcended the barrier: low amplification times and long reaction time in traditional CHA. As a proof of the concept, the elaborated MCHA as a hyper-efficiency and high-speed DNA signal-magnifier was successfully applied in ultrasensitive and rapid detection of miRNA-21 with the detection limit of 0.17 fM, which exploited an ingenious nucleic acid signal amplification technique for sensitive and fast detection of biomarkers in biosensing assay and clinic diagnose.

DNA Nanowire Guided-Catalyzed Hairpin Assembly Nanoprobe for In Situ Profiling of Circulating Extracellular Vesicle-Associated MicroRNAs

Extracellular vesicle-associated miRNAs (EV-miRNAs) are emerging as a new type of noninvasive biomarker for disease diagnosis. Their relatively low abundance, however, makes accurate detection challenging. Here, we designed a DNA nanowire guided-catalyzed hairpin assembly (NgCHA) nanoprobe for profiling EV-miRNAs. NgCHA showed high penetrability to EVs, which allowed rapid delivery of the probes into EVs. In the presence of targeted miRNAs within EVs, a fluorescent signal could be generated and amplified by confining the catalytic hairpin assembly system within the nanowires, thus greatly enhancing the analytical sensitivity. We showed that EV-miRNAs from various cell lines could be accurately quantified by NgCHA in situ. By using a four-EV-miRNA panel, this platform can identify patients with breast cancer at an early stage with 95.2% sensitivity and 86.7% specificity. Its applications for risk assessment as well as cancer type prediction were also successfully demonstrated. This platform is sensitive, low-cost, and simple compared with current methods. It may thus serve as a promising tool for the noninvasive diagnosis and monitoring of cancers and other diseases through EV-miRNA profiling.

A novel aptamer RRS assay platform for ultratrace melamine based on COF-loaded Pd nanocluster catalytic amplification

Two COFs of BzBD and BzBD loaded Pd nanoclusters (BzBD_Pd) were prepared using 1,3,5-benzenetricarboxaldehyde (Bz), benzidine (BD) and CO reducing agent, and were characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), infrared spectroscopy (IR) and other techniques. BzBD_Pd can strongly catalyze the new and stable Au@NiP nanoreaction that exhibit a strong resonance Rayleigh scattering (RRS) peak at 538 nm and a surface plasmon resonance (SPR) absorption peak at 395 nm, and the sensitive and facile RRS technique was used to study the indicator reaction. Combining the nanocatalytic amplification reaction with specific aptamer (Apt) of some target molecules such as melamine (ML), urea (UR) and bisphenol A (BPA), a simple, sensitive and selective Apt RRS assay platform was established. The linear range of the RRS detection platform for melamine is 0.0025-0.04 nmol/L, and the detection limit (DL) is 1.96 × 10^-4 nmol/L. In addition, ML in real sample was analyzed, the stability of BzBD, BzBD_Pd, PdNPs and the catalytic mechanism of COF_Pd were also considered.

An aptamer-based SERS–LFA biosensor with multiple channels for the ultrasensitive simultaneous detection of serum VEGF and osteopontin in cervical cancer patients

In this work, a novel surface-enhanced Raman scattering and lateral flow assay (SERS–LFA) biosensor with multiple channels based on an aptamer has been proposed.

A label-free and signal-amplifiable assay method for colorimetric detection of carcinoembryonic antigen

In this work, an innovative colorimetric assay method for the determination of carcinoembryonic antigen is developed with aptamer probes utilized as recognition element. DNA hybridization chain reaction is used as signal amplification technique, and peroxidase-mimicking hemin/G-quadruplex-assisted catalytic oxidation of 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) is deployed as signal reporting mechanism. The detection principle was firstly verified by using gel electrophoresis analysis and absorbance measurements. After condition optimization, a detection limit was theoretically determined as 24.8 ng/ml. Furthermore, the method exhibited good selectivity and satisfactory recovery rates (92.2%-108.6%) in serum samples. Moreover, the sensing scheme is easily extended for the detection of other analytes via similar target-aptamer recognition principle. To sum up, this is an enzyme- and label-free, cost-effective yet signal-amplifiable assay scheme for the determination of tumor markers with promising simplicity and selectivity, practical utility, and potential universality.

A novel liquid crystal-based aptasensor for ultra-low detection of ochratoxin a using a π-shaped DNA structure: Promising for future on-site detection test strips

Ochratoxin A (OTA) as the most dangerous mycotoxin is produced by Aspergillus Ochraceus and Penicillium verrucosum. OTA can be found in beverages and foodstuffs that induces the teratogenic, nephrotoxic, carcinogenic, and immunosuppressive effects on humans. Hence, developing highly sensitive methods for its detection is of great importance. Herein, a novel aptasensor was designed for the label-free monitoring of the ultra-low OTA levels by a combination of the superiority of aptamers and long-range orientational order of liquid crystals (LCs). The aptasensing strategy was based on the conformational switch of the immobilized π-shaped DNA structure on the glass substrate in presence of the target. A shift in the orientation of LCs from random to homeotropic state led to the apparent alteration of the optical appearance of the aptasensor platform from bright to dark. The LC-based aptasensor especially detects OTA at the ultra-trace level as low as 0.63 aM with comparable selectivity. The aptasensor could detect OTA successfully in the grape juice, coffee, and human serum samples. The LC-based aptasensor paves a way for developing portable and real-time sensing probes with high performance for food safety control and clinical application.

Aptamer-decorated porous microneedles arrays for extraction and detection of skin interstitial fluid biomarkers

The detection of biomarkers in body fluids plays a great role in the diagnosis, treatment, and prognosis of diseases. Here, we present novel aptamer-decorated porous microneedles (MNs) arrays to realize the extraction and detection of biomarkers in skin interstitial fluid (ISF) in situ. The porous MNs arrays are fabricated by replicating the negative molds comprising glass microspheres with a UV-curable ethoxylated trimethylolpropane triacrylate (ETPTA). As the MNs arrays combine the superiorities of porous structure and aptamers, their specific surface area increased significantly to 6.694 m²/g, thus vast of stable aptamer probes with a concentration of 0.9459 μM could be immobilized. In addition, the MNs arrays could extract skin ISF into their porous structure on the basis of the capillarity principle, and subsequently capture and detect skin ISF biomarkers without sample post-process. Taking advantage of these features, we further demonstrated a highly sensitive and rapid detection of ISF endotoxin in the concentration ranges of 0.0342 EU/mL to 8.2082 EU/mL from rats model injected with endotoxin via tail vein by using such aptamer-decorated porous MNs arrays, with the limit of detection (LOD) of 0.0064 EU/mL. These results indicated that the aptamer-decorated porous MNs arrays possess great potential for non-invasive extraction and detection of biomarkers in clinical applications.

A multimer-based SERS aptasensor for highly sensitive and homogeneous assay of carcinoembryonic antigens

Carcinoembryonic antigens (CEAs) are known as one of the most common tumor markers. Their facile and affordable detection is critical for early diagnosis of malignant tumors, especially in resource-constrained settings. Here, we report a novel multimer-based surface-enhanced Raman scattering (SERS) aptasensor for a specific CEA assay. The aptasensor is fabricated through aptamer-assisted self-assembly of silver-coated gold nanoparticles (Au@Ag NPs), and the self-assembled multimeric structure possesses abundant hot-spots to provide high SERS response. When CEA is introduced, the specific recognition of CEA by aptamers will lead to the disassembly of Au@Ag multimers due to the lack of a bridging aptamer between Au@Ag NPs. As a result, the number of hot-spots in the multimeric system is decreased, and the intensity at 1585 cm-1 of the SERS reporter (4-mercaptobenzoic acid, 4-MBA) on the surface of NPs will also be decreased. The Raman intensity is proportional to the logarithm of the concentration of CEA. The detection sensitivity can be down to the pg mL-1 level. The analytical method only needs a droplet of 2 μL of sample, and the detection time is less than 20 min. The multimer-based SERS aptasensor can be applied in sensitive and inexpensive detection of CEA in serum samples.

Colorimetric Detection of Kanamycin Residue in Foods Based on the Aptamer-Enhanced Peroxidase-Mimicking Activity of Layered WS2 Nanosheets

Although the colorimetric methods can easily meet the demands of point-of-care and ease-of-use for antibiotic detection, they still face many challenges in the accuracy and stability of assay. Herein, a facile and stable colorimetric aptasensor is first developed for kanamycin residue detection based on the aptamer-enhanced peroxidase-mimicking activity of layered WS₂ nanosheets. The investigation confirmed that aptamer sequences can improve the affinity of nanosheets to the chromogenic substrate 3,3'',5,5''-tetramethylbenzidine, resulting in a significant increase of the peroxidase-mimicking activity. Under the optimal conditions, the limit of detection of the proposed colorimetric aptasensor for kanamycin was determined to be as low as 0.6 μM, and such an aptasensor displays excellent selectivity against other competitive antibiotics. Moreover, further studies have verified the applicability of the established colorimetric aptasensor in several actual samples, indicating that the aptasensor may have bright application prospects for kanamycin detection in livestock husbandry and agriculture samples.

Cofactor-assisted three-way DNA junction-driven strand displacement

Toehold-mediated strand displacement is widely used to construct and operate DNA nanodevices. Cooperative regulation of strand displacement with diverse factors is pivotal in the design and construction of functional and dynamic devices. Herein, a cofactor-assisted three-way DNA junction-driven strand displacement strategy was reported, which could tune the reaction kinetics by the collaboration of DNA and other types of stimulus. This strategy is responsive to various inputs by incorporation of the specific sequence into the three-way junction structure. Specifically, the cooperation of multiple factors changes the conformation of the specific domain and promotes the reaction. To demonstrate the strategy, adenosine triphosphate (ATP), HG²⁺, and pH were used as cofactors to modulate the displacement reaction. The electrophoresis and fluorescence experiments showed that the cooperative regulation of the strand displacement reaction could be achieved by diverse factors using this strategy. The proposed strategy provides design flexibility for dynamic DNA devices and may have potential in biosensing and biocomputing.

Cooperative regulation of strand displacement with diverse factors was achieved by a cofactor-assisted three-way DNA junction-driven strategy. Using this strategy nanodevices reacted to various inputs by incorporating a specific sequence into the three-way junction structure.

Application of Multiplexed Aptasensors in Food Contaminants Detection

The existence of contaminants in food poses a serious threat to human health. In recent years, aptamer sensors (aptasensors) have been developed rapidly for the detection of food contaminants because of their high specificity, design flexibility, and high efficiency. However, the development of high-throughput, highly sensitive, on-site, and cost-effective methods for simultaneous detection of food contaminants is still restricted due to multiple signal overlap or mutual interference and cross-reaction between different analytes with similar molecular structures. To overcome these problems, this Review summarizes some effective strategies from the articles published in recent years about multiplexed aptasensors for the simultaneous detection of food contaminants. This work focuses on the application of multiplexed aptasensors to simultaneously detect antibiotics, pathogens, and mycotoxins in food. These aptasensors mainly contain fluorescent aptasensors, electrochemical aptasensors, surface-enhanced Raman scattering-based aptasensors, microfluidic chip aptasensors, and paper-based multiplexed aptasensors. In addition, this Review also covers the application of nucleic acid cycle amplification and nanomaterial amplification strategies to improve the detection sensitivity. Finally, the limitations and challenges in the design of multiplexed aptasensor are also taken into account.