An All-in-One Aptasensor Integrating Enzyme Powered Three-Dimensional DNA Machine for Antibiotic Detection

Bisphenol a monitoring by commercial pregnancy test strips transformed by DNA walking machine

Frequently occurred food contamination issues bring about a tremendous global demand for point-of-care testing (POCT) devices. Pregnancy test strip (PTS) retains the highest POCT market share and a low cost of $0.10 per test, but challenged by limited analytical sensitivity and non-autonomous signal transduction for drink contaminant monitoring. Herein, we developed a DNA walking machine-assisted commercial PTS method for on-site bisphenol A (BPA) analysis. DNAzyme was operated as the efficient autonomous catalytic walker chain to drive the DNA machine for the amplified signal output of BPA in drink samples. A detection limit of 16.8 pg/mL was obtained. The POCT strategy constructed in this work has the characteristics of low cost, convenient operation and high analytical sensitivity, represents an attractive option for biosensing and on-site drink safety monitoring.

An all-in-one enzyme-free fluorescent aptasensor integrating localized catalyzed hairpin assembly for sensing antibiotics in food with improved detection efficiency

Enzyme-free signal amplification fluorescent aptasensors depending on multi-component freely diffusing probes have become indispensable tools for antibiotic detection in food, but they suffer from low detection efficiency and tedious operation steps. Herein, an all-in-one enzyme-free fluorescent aptasensor integrating localized catalyzed hairpin assembly (L-CHA) was designed for antibiotic detection with improved detection efficiency. In the designed aptasensor, a double-stranded DNA reactant containing an antibiotic aptamer and a primer as well as two paired hairpin DNA reactants were immobilized on one spatial-confinement DNA scaffold (that is a DNA tetrahedron). Upon addition of the target antibiotic kanamycin, the activated primer initiated L-CHA, generating an amplified fluorescence signal. Compared with previously reported enzyme-free signal amplification fluorescent aptasensors, the designed aptasensor integrated the functions of target recognition, signal transduction, and L-CHA signal amplification into a single probe. In this all-in-one design, the reactants in this aptasensor were confined to a compact space for a higher local concentration, which improved detection efficiency. In particular, this aptasensor achieved sensitive detection of kanamycin within 60 min with a low detection limit of 0.019 ng mL-1. Additionally, the designed aptasensor depended on a single probe rather than multi-component probes, leading to simplified operation steps. Furthermore, this aptasensor was employed for detecting kanamycin in spiked milk samples with recoveries of 96.00% to 108.60%, indicating an acceptable accuracy. Therefore, this L-CHA-based all-in-one enzyme-free fluorescent aptasensor offers a prospective tool for antibiotic detection in the field of food safety.

Enzyme-Assisted Solid-Phase Microextraction Coupled with a DNA Nanowalker for Dual-Amplified Detection of Chloramphenicol in Animal-Derived Food Products

Chloramphenicol (CAP), an aminoalcohol antibiotic, exerts its action on bacterial ribosomes, thereby obstructing protein synthesis. However, the use of CAP in husbandry may lead to its excessive accumulation in animal-derived food products. This presents potential risks to consumer health. This study developed a novel dual-amplification fluorescence detection method by integrating enzyme-assisted solid-phase microextraction (SPME) with a Fe3O4@Au NP-based DNA nanowalker for the detection of CAP in food. The combination of a quartz rod-based SPME biosensor and DNA nanowalker effectively eliminated matrix interference, enabling the conversion of CAP and enhancement of detection signals through two cyclic amplification processes. The strategy demonstrated high sensitivity with a limit of detection of 28.1 aM as well as a wide linear range from 0.1 fM to 1 nM (with R2 > 0.99). This method also demonstrates robust stability and accuracy in detecting trace amounts of CAP in both authentic and prepared positive samples.

An inverted tetrahedron-mediated DNA walker for sulfadimethoxine detection

An inverted DNA tetrahedron-mediated modular DNA walker was developed for the determination of sulfadimethoxine. The inverted DNA tetrahedron scaffold raises several advantages of recognition module including appropriate lateral space, multiple recognition domains, and cost-effectiveness. The proposed inverted DNA tetrahedron-based recognition module exhibited better binding affinity and kinetics toward target antibiotic than that of other DNA tetrahedron counterparts. Upon specific binding with target, the released bipedal DNA walking strand hops to the signal amplification module and moves stochastically with assistant of nicking enzyme. By coupling these two modules, a good linear relationship between the fluorescence intensity of supernatant and the concentration of sulfadimethoxine was achieved in the range 0.1-100 nM, and the limit of detection was 64.7 pM. Furthermore, this modular DNA walker had also successfully applied to spiked honey and milk samples with satisfactory recoveries from 91.5 to 108.8%, demonstrating its practical sensing capability.

Application of DNA-fueled molecular machines in food safety testing

Food is consumed by humans, which is indispensable to human life. Therefore, considerable attention of the whole society has been paid to food safety. Over the last few years, dramatic social development has brought new challenges to food safety, making developing new and quick methods for on-site food safety testing an important necessity. As a result, DNA-fueled molecular machines, characterized by high efficiency, accuracy, and sensitivity in testing, have come into the spotlight, based on which sensors can be constructed to detect toxic and harmful substances in food products. This study reviewed recent research on several DNA-fueled molecular machines, including DNA tweezers, DNA walkers, and DNA origami, for rapidly detecting toxic and harmful substances. Based on the above studies, the sensitivity and timeliness of several DNA molecular machines were summarized and compared, and the development prospect of DNA fuel molecular machines in the field of food safety detection was prospected.

Localization of multiple DNAzymes as a branchedzyme-powered nanodevice for the immunoassay of tumor biomarkers

Traditional immunoassay methods often face challenges due to the labeling procedure of protein enzymes, the use of multiple antibodies, and severe conditions. To address these limitations, we propose the concept of incorporating branchedzyme-powered nanodevices into immunoassays. In this strategy, multiple DNAzymes are localized onto gold nanoparticles (AuNPs) along with substrates. The localization format facilitates intramolecular reactions between DNAzymes and substrates, leading to accelerated kinetics of the nanodevice. Upon the formation of an immunocomplex with an antibody on a 96-well plate, the branchedzyme-powered nanodevice catalytically releases multiple fluorescent signals under ambient temperature, eliminating the need for secondary antibodies. The branched DNAzymes exhibit catalytic properties similar to those of protein enzymes, thus simplifying the assay procedure and achieving isothermal detection. Furthermore, the detection process can be controlled by the addition or deletion of cofactors. Additionally, the affinity ligand can be easily modified to construct nanodevices specific to different targets without requiring extensive redesign. This strategy has demonstrated successful quantification of tumor biomarkers such as alpha-fetoprotein (AFP) and prostate-specific antigen (PSA) at subpicomolar concentrations, showcasing its suitability for clinical applications. Consequently, the branchedzyme-powered nanodevice represents a valuable addition to the immunoassay toolbox, opening new possibilities for clinical diagnostics.

Metal-organic frameworks/metal nanoparticles as smart nanosensing interfaces for electrochemical sensors applications: a mini-review

Metal-organic frameworks (MOFs) are porous materials with huge specific surface area and abundant active sites, which are composed of metal ions or clusters and organic ligands in the form of coordination bonds. In recent years, MOFs have been successfully applied in many fields due to their excellent physical, chemical, and biological properties. Electrochemical sensors have advantages such as economy, portability, and sensitivity, making them increasingly valued in the field of sensors. Many studies have shown that the electrode materials will affect the performance of electrochemical sensors. Therefore, the research on electrode materials is still one of the hotspots. MOFs are also commonly used to construct electrochemical sensors. However, electrochemical sensors prepared from single MOFs have shortcomings such as insufficient conductivity, low sensitivity, and poor electrochemical catalytic ability. In order to compensate for these defects, a new type of nanocomposite material with very ideal conductivity was formed by adding metal nanoparticles (MNPs) to MOFs. The combination of the two is expected to be widely applied in the field of sensors. This review summarizes the applications of various MNPs/MOFs composites in the field of electrochemical sensors and provides some references for the development of MNPs/MOFs composites-based electrochemical sensors in the future.

Butanol accelerated entropy-driven DNA walking machine for rapid and ultrasensitive determination of alkaline phosphatase activity

Alkaline phosphatase (ALP) as an important biomarker as well as an index for the pasteurization degree of dairy food. However, there is a dilemma between the sensitivity and time-cost of ALP determination based on nucleic acid amplification approach. Herein, an ultrasensitive and rapid detection method for the ALP assay was developed based on entropy-driven DNA machine. In our design, the ALP catalyzed dephosphorylation of detection probe, which inhibited the digestion effect of lambda exonuclease. The remaining probe as a linker to tether the walking strand proximity to the surface of track strand modified gold nanoparticle, activating entropy-driven DNA machine. Accompany with walking strand moving, a large amount of assembled dye-labelled strand dissociated from gold nanoparticle with fluorescence recovery. More importantly, to further improve the walking efficiency, butanol was introduced to accelerated the signal amplification at interface, which short the incubation time from several hours to 5 min. Under the optimum condition, the change of fluorescence intensity was proportion to the concentration of ALP in the range from 0.05 U L^-1 to 5 U L^-1 with an ultralow limit of detection of 2.07 × 10^-3 U L^-1 was achieved, which is superior to other reported methods. Furthermore, the proposed method also successfully applied for the spiked milk sample assay with satisfactory recovery in the range of 98.83%-103.00%. This work proposed a new strategy for the application of entropy-driven DNA machine in the field of rapid and ultrasensitive detection.

Portable biosensor for on-site detection of kanamycin in water samples based on CRISPR-Cas12a and an off-the-shelf glucometer

On-site and cost-effective monitoring of antibiotic residue in water samples using a ubiquitous device that is readily available to the general public is a big challenge. Herein, we developed a portable biosensor for kanamycin (KAN) detection based on a glucometer and CRISPR-Cas12a. The aptamer-KAN interactions liberate the trigger C strand, which can initiate the hairpin assembly to produce numerous double-stranded DNA. After recognition by CRISPR-Cas12a, Cas12a can cleave the magnetic bead and invertase-modified single-stranded DNA. After magnetic separation, the invertase can convert sucrose into glucose, which can be quantified by a glucometer. The linear range of the glucometer biosensor is from 1 pM to 100 nM and the detection limit is 1 pM. The biosensor also exhibited high selectivity and the nontarget antibiotics had no significant interference with KAN detection. The sensing system is robust and can work in complex samples with excellent accuracy and reliability. The recovery values were in the range of 89-107.2 % for water samples and 86-106.5 % for milk samples. The relative standard deviation (RSD) was below 5 %. With the advantages of simple operation, low cost, and easy accessibility to the public, this portable pocket-sized sensor can realize the on-site detection of antibiotic residue in resource-limited settings.

Split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive detection of 17β-estradiol

DNA walker machines, as one of the dynamic DNA nanodevices, have attracted extensive interest in the field of analysis due to their inherent superiority. Herein, we reported a split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive, specific, and high-signal-background ratio determination of 17β-estradiol (E2) in food samples. Two split probes (STWS-a and STWS-b) were rationally designed that can undergo structural reassembled to serve as walking strands (STWS) under the induction of the target. Meanwhile, an intact E6-DNAzyme region was formed and activated at the tail of STWS. The activated E6-DNAzyme then continuously drives the 3D-DNA walker for signal amplification and specific detection of E2. Under optimal conditions, the proposed DNA walker-based biosensor exhibited excellent linearity in the range of 1 pM to 50 nM with a low limit of detection (LOD) of 0.28 pM, and good precision (2.7%) for 11 replicate determinations of 1 nM of E2. Furthermore, the developed DNA walker-based biosensor achieved excellent sensitive analysis of E2 in the complex food matrix with recoveries of 95.6-106.5%. This newly proposed split aptamer-based strategy has the advantages of ultrasensitive, high signal-to-background ratio, and high stability. Noteworthy, the successful operation of the DNA walker initiated by the split aptamer expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.

Spherical Nucleic Acids with Tailored DNA Conformation via Bromide Backfilling for the Detection of Kanamycin

Improper conformation of oligonucleotides on gold nanoparticles surface caused by unintended base adsorption, which hinders DNA hybridization and lowers colloidal stability. In this work, we treated spherical nucleic acids with Br^- , which serves as an efficient backfilling agent, to adjust the DNA conformation by displacing bases from gold surface. To investigate the effect of DNA conformation on interfacial recognition, a kanamycin fluorescent aptasensor was constructed with bromide backfilling treated spherical nucleic acids. In the presence of kanamycin, the anchored aptamer binding with target and the partially complementary reporter strand is dissociated from the surface of gold nanoparticles, resulting the fluorescence recovery of labelled fluorophore on the reporter strand. Under the optimum condition, the apparent binding affinity of the aptasensor with bromide backfilling was 2.2-fold than that of without backfilled one. The proposed aptasensor exhibited a good liner relationship between the concentration of kanamycin and fluorescence intensity change in the range of 200 nM to 10 μM and the limit of detection was calculated to be 71.53 nM. Moreover, this aptasensor was also successfully applied in spiked milk sample assay and the satisfactory recoveries was obtained in the range of 96.94-101.57%, which demonstrate its potential in practical application.

Structural and photoactive properties of self-assembled peptide-based nanostructures and their optical bioapplication in food analysis

BACKGROUND

Food processing plays an important role in the modern industry because food quality and security directly affect human health, life safety, and social and economic development. Accurate, efficient, and sensitive detection technology is the basis for ensuring food quality and security. Optosensor-based technology with the advantage of fast and visual real-time detection can be used to detect pesticides, metal ions, antibiotics, and nutrients in food. As excellent optical centres, self-assembled peptide-based nanostructures possess attractive advantages, such as simple preparation methods, controllable morphology, tunable functionality, and inherent biocompatibility.

AIM OF REVIEW

Self-assembled peptide nanostructures with good fabrication yield, stability, dispersity in a complex sample matrix, biocompatibility, and environmental friendliness are ideal development goals in the future. Owing to its flexible and unique optical properties, some short peptide self-assemblies can possibly be used to achieve the purpose of rapid and sensitive detection of composition in food, agriculture, and the environment, expanding the understanding and application of peptide-based optics in analytical chemistry.

KEY SCIENTIFIC CONCEPT OF REVIEW

The self-assembly process of peptides is driven by noncovalent interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and π-π stacking, which are the key factors for obtaining stable self-assembled peptide nanostructures with peptides serving as assembly units. Controllable morphology of self-assembled peptide nanostructures can be achieved through adjustment in the type, concentration, and pH of organic solvents and peptides. The highly ordered nanostructures formed by the self-assembly of peptides have been proven to be novel biological structures and can be used for the construction of optosensing platforms in biological or other systems. Optosensing platforms make use of signal changes, including optical signals and electrical signals caused by specific reactions between analytes and active substances, to determine the content or concentration of an analyte.

Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing

In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg²⁺ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg²⁺, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.

Synthetic Biology-Empowered Hydrogels for Medical Diagnostics

Synthetic biology is strongly inspired by concepts of engineering science and aims at the design and generation of artificial biological systems in different fields of research such as diagnostics, analytics, biomedicine, or chemistry. To this aim, synthetic biology uses an engineering approach relying on a toolbox of molecular sensors and switches that endows cellular hosts with non-natural computing functions and circuits. Importantly, this concept is not only limited to cellular approaches. Synthetic biological building blocks have also conferred sensing and switching capability to otherwise inactive materials. This principle has attracted high interest for the development of biohybrid materials capable of sensing and responding to specific molecular stimuli, such as disease biomarkers, antibiotics, or heavy metals. Moreover, the interconnection of individual sense-and-respond materials to complex materials systems has enabled the processing of, for example, multiple inputs or the amplification of signals using feedback topologies. Such systems holding high potential for applications in the analytical and diagnostic sectors will be described in this chapter.

Fe3O4@polydopamine and Exo III-assisted homogeneous biorecognition reaction for convenient and ultrasensitive detection of kanamycin antibiotic

Herein, we report a Fe3O4@polydopamine (PDA) nanocomposite and exonuclease III (Exo III)-assisted homogeneous fluorescence biosensing method for ultrasensitive detection of kanamycin (Kana) antibiotic. A hairpin DNA containing the Kana-aptamer sequence (HP) was first designed for the highly specific biorecognition of the target analyte. Because of the aptamer biorecognition-induced structural change of HP and the highly effective catalyzed reaction of Exo III, a large amount of fluorophore labels were released from the designed fluorescence DNA probe. During the homogeneous reaction process, the Exo III-assisted dual recycling significantly amplified the fluorescence signal output. Moreover, the excessive probes were easily adsorbed and separated by the Fe3O4@PDA nanocomposite, which decreased the background signal and increased the signal-to-noise ratio. These strategies result in the excellent analytical performance of the method, including a very low detection limit of 0.023 pg mL-1 and a very wide linear range of six orders of magnitude. In addition, this method has convenient operation, excellent selectivity, repeatability and satisfactory reliability, and does not involve the design and utilization of complicated DNA sequences. Thus, it exhibits a promising prospect for practical applications.

3-D DNA nanodevices for on-site sensitive detection of antibiotic residues in food

Developing convenient and sensitive detection methods for antibiotic residues in food is beneficial for ensuring food quality and human health. The tough challenges that limit the development of sensitive, quantitative, portable, on-the-spot antibiotic detectors are the lack of simple and effective target recognition and signal amplification strategies, and direct digital quantification. Herein, we developed a visual digital quantitative aptasensor, based on a binding-induced 3-D DNA nanomachine signal probe, for the simple and sensitive, on-the-spot detection of antibiotics.

Enzyme-powered cascade three-dimensional DNA machine for the ultrasensitive determination of kanamycin

DNA walking machines have been widely used in rapid and sensitive detection. In this work, we develop a single enzyme-powered DNA cascade machine for the ultrasensitive determination of kanamycin. To construct the cascade manner, two types of single-legged three-dimensional DNA walking machine are employed to implement integrated target recognition, signal transduction and signal amplification. Upon adding kanamycin to trigger the upstream machine, the sequential enzymatic cleavage drives the autonomous movement of the walking strand and produces plenty of dye-labeled fragments with fluorescence recovery. Meanwhile, these fragments also serve as walking strands to activate the downstream machine for cascade signal amplification. Taking advantage of this cascade DNA machine, ultrasensitive determination can be accomplished in 60 min. Under the optimum conditions, this method was highly selective toward kanamycin with a detection limit of 28 fM. This cascade signal amplification shows great potential for the rapid screening of antibiotics in food.

Integrating Target-Triggered Aptamer-Capped HRP@Metal-Organic Frameworks with a Colorimeter Readout for On-Site Sensitive Detection of Antibiotics

Colorimetric analytical strategies exhibit great promise in developing on-site detection methods for antibiotics, while substantial recent research efforts remain problematic due to dissatisfactory sensitivity. Taking this into account, we develop a novel colorimetric sensor for in-field detection of antibiotics by using aptamer (Apt)-capped and horseradish peroxidise (HRP)-embedded zeolitic metal azolate framework-7 (MAF-7) (Apt/HRP@MAF-7) as target recognition and signal transduction, respectively. With the substrate 3,3',5,5'-tetramethylbenzidine (TMB)-impregnated chip attached on the lid, the assay can be conveniently operated in a tube and reliably quantified by a handheld colorimeter. Hydrophilic MAF-7 can not only prevent HRP aggregation but also enhance HRP activity, which would benefit its detection sensitivity. Besides, the catalytic activity of HRP@MAF-7 can be sealed through assembling with Apt and controllably released based on the bioresponsivity via forming target-Apt complexes. Consequently, a significant color signal can be observed owing to the oxidation of colorless TMB to its blue-green oxidized form oxTMB. As a proof-of-concept, portable detection of streptomycin was favorably achieved with excellent sensitivity, which is superior to most reported methods and commercial kits. The developed strategy affords a new design pattern for developing on-site antibiotics assays and immensely extends the application of enzyme embedded metal-organic framework composites.

Paper-based electrochemiluminescence determination of streptavidin using reticular DNA-functionalized PtCu nanoframes and analyte-triggered DNA walker

A paper-based electrochemiluminescence (ECL) biosensor characterized by the signal amplification of reticular DNA-functionalized PtCu nanoframes (DNA-PtCuTNFs) and analyte-triggered DNA walker was developed for sensitive streptavidin assay. Silver microflower functionalized paper-based sensing platform was prepared to fix the hairpin strand (S1). With addition of the streptavidin, plenty of DNA walkers consisting of the walking strands (S2) labeled with biotin and streptavidin were established, which protected S2 from digestion via the terminal protection mechanism. The sequential introduction of the DNA walker and capture probe initiated the hairpin structure opening of S1 and strand displacement reaction (SDR) happening, causing the S2 release. Subsequently, S1 hybridized with S3. The free S2 further hybridized with adjacent S1 to trigger the next cycle. After multiple cycles, the DNA-PtCuTNFs, the fire-new signal enhancer, with remarkable peroxidase activity, were successfully attached onto the paper electrode via metal-catalyst-free click chemistry. Based on the SDR of the DNA walker and the catalysis of DNA-PtCuTNFs, a significantly boosted ECL signal of luminol was obtained. Under the optimal conditions, the developed sensor for streptavidin assay exhibited a low detection limit of 33.4 fM with a linear range from 0.1 pM to 0.1 μM. Graphical abstract.