Label-free cascade amplification strategy for sensitive visual detection of thrombin based on target-triggered hybridization chain reaction-mediated in situ generation of DNAzymes and Pt nanochains

Aptasensors Based on Non-Enzymatic Peroxidase Mimics: Current Progress and Challenges

Immunoassays based on antibodies as recognizing elements and enzymes as signal-generating modules are extensively used now in clinical lab diagnostics, food, and environmental analyses. However, the application of natural enzymes and antibodies has some drawbacks, such as relatively high manufacturing costs, thermal instability, and lot-to-lot variations that lower the reproducibility of results. Oligonucleotide aptamers are able to specifically bind their targets with high affinity and selectivity, so they represent a prospective alternative to protein antibodies for analyte recognition. Their main advantages include thermal stability and long shelf life, cost-efficient chemical synthesis, and negligible batch-to-batch variations. At the same time, a wide variety of non-protein peroxidase mimics are now available that show strong potential to replace protein enzymes. Here, we review and analyze non-protein biosensors that represent a nexus of these two concepts: aptamer-based sensors (aptasensors) with optical detection (colorimetric, luminescent, or fluorescent) based on different peroxidase mimics, such as DNAzymes, nanoparticles, or metal-organic frameworks.

Sensitive ratiometric sensor for Al(III) detection in water samples using luminescence or eye-vision

A facile, quick, and sensitive ratiometric luminescence sensor is designed for detection aluminum ions in water samples using luminescence or eye-vision. This approach relies on the emission change of the europium(III) complex with 3-(2-naphthoyl)-1,1,1,-trifluoro acetone (3-NTA) after interaction with various concentration of aluminum ions. The addition of aluminum ions suppressed the Eu(III) emission at 615 nm under 333 nm excitation, while simultaneously enhancing the ligand emission at 480 nm. Optimum detection was obtained in methanol. The quantification of aluminum ions using ratiometric method was determined by plotting the luminescence ratio (F_480nm/F_615nm) versus aluminum ions concentration. The calibration plot was obtained within the range 0.1-100 µM with LOD = 0.27 µM. Additionally, the concentration of aluminum ions can be estimated semi-quantitatively by visually observing the luminescence colour change of the probe from red to light green and then to dark green after being excited by a UV lamp with 365 nm. As far as we are aware, this is the first luminescent lanthanide complex-based ratiometric probe for the detection of aluminum ions. The probe showed remarkable aluminum ions selectivity relative to that of other metal ions. The suggested sensor was used effectively to identify aluminum ions in water samples with good results.

Recent Progresses in Development of Biosensors for Thrombin Detection

Thrombin is a serine protease with an essential role in homeostasis and blood coagulation. During vascular injuries, thrombin is generated from prothrombin, a plasma protein, to polymerize fibrinogen molecules into fibrin filaments. Moreover, thrombin is a potent stimulant for platelet activation, which causes blood clots to prevent bleeding. The rapid and sensitive detection of thrombin is important in biological analysis and clinical diagnosis. Hence, various biosensors for thrombin measurement have been developed. Biosensors are devices that produce a quantifiable signal from biological interactions in proportion to the concentration of a target analyte. An aptasensor is a biosensor in which a DNA or RNA aptamer has been used as a biological recognition element and can identify target molecules with a high degree of sensitivity and affinity. Designed biosensors could provide effective methods for the highly selective and specific detection of thrombin. This review has attempted to provide an update of the various biosensors proposed in the literature, which have been designed for thrombin detection. According to their various transducers, the constructions and compositions, the performance, benefits, and restrictions of each are summarized and compared.

Catalytic antimicrobial therapy using nanozymes

Nanozymes are nanomaterials with enzyme-like characteristics, which catalyze the conversion of enzyme substrates and follow enzymatic kinetics under physiological conditions. As a new generation of artificial enzymes, nanozymes provide alternative approaches for those upon enzymatic catalysis. Compared with natural enzymes, nanozymes have the advantages of simple preparation, good stability and low cost, which makes nanozymes promising for application in many fields, such as antimicrobial infection treatment. Many studies have reported that nanozymes are capable of killing a number of pathogenic bacteria with resistance, fungi as well as viruses, and have shown great curative effects for diseases caused by these pathogens. Herein, we summarize the application of nanozymes for antibacterial, antiviral, and antifungal therapies and outline the issues needing resolution in the future. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.

Applications of hybridization chain reaction optical detection incorporating nanomaterials: A review

The development of powerful, simple and cost-effective signal amplifiers has significant implications for biological research and analysis. Hybridization chain reaction (HCR) has attracted increasing attention because of its enzyme-free, simple, and efficient amplification. In the HCR process, an initiator probe triggered a pair of metastable hairpins through a cross-opening process to propagate a chain reaction of hybridization events, yielding a long-nicked double-stranded nucleic acid structure. To achieve more noticeable signal amplification, nanomaterials, including graphene oxide, quantum dots, gold, silver, magnetic, and other nanoparticles, were integrated with HCR. Various types of colorimetric, fluorescence, plasmonic analyses or chemiluminescence optical sensing strategies incorporating nanomaterials have been developed to analyze various targets, such as nucleic acids, small biomolecules, proteins, and metal ions. This review summarized the recent advances of HCR technology pairing diverse nanomaterials in optical detection and discussed their challenges.

Applications of DNA-nanozyme-based sensors

Since the discovery of the enzyme-like activities of nanomaterials, the study of nanozymes has become one of the most popular research frontiers of diverse areas including biosensors. DNA also plays a very important role in the construction of biosensors. Thus, the idea of combined applications of nanozymes with DNA (DNA-nanozyme) is very attractive for the development of nanozyme-based biosensors, which has attracted considerable interest of researchers. To date, many sensors based on DNA-functionalized or templated nanozymes have been reported for the detection of various targets and highly accelerated the development of nanozyme-based sensors. In this review, we summarize the main applications and advances of DNA-nanozyme-based sensors. Additionally, perspectives and challenges are also discussed at the end of the review.

Proximity hybridization triggered hybridization chain reaction for label-free electrochemical homogeneous aptasensors

A label-free homogeneous electrochemical aptasensor was developed for detection of thrombin based on proximity hybridization triggered hybridization chain reaction induced G-quadruplex formation. Thrombin promoted the formation of a complex via the proximity hybridization of the aptamer DNA strands, which unfolded the molecular beacon, the stem part of molecular beacon as a primer to initiate the hybridization chain reaction process. Thus, with the electrochemical indicator hemin selectively intercalated into the multiple G-quadruplexes, a significant electrochemical signal drop is observed, which is dependent on the concentration of the target thrombin. Thus, using this"signal-off" mode, label-free homogeneous electrochemical strategy for sensitive thrombin assay with a detection limit of 44 fM is realized. Furthermore, this method also exhibits additional advantages of simplicity and low cost, since both expensive labeling and sophisticated probe immobilization processes are avoided. Its high sensitivity, acceptable accuracy, and satisfactory versatility of analytes led to various applications in bioanalysis.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.

Immuno-HCR based on contact quenching and fluorescence resonance energy transfer for sensitive and low background detection of Escherichia coli O157:H7

Escherichia coli O157:H7 makes a major threat to human health. Aiming to detect Escherichia coli O157:H7 sensitively, hybridization chain reaction signal amplified immunoassay (immuno-HCR) based on contact quenching (CQ) and fluorescence resonance energy transfer (FRET) was developed. The background of the new designed HCR hairpins (CQ-FRET hairpins) was reduced by contact-quenching fluorescein (FAM) and breaking FRET from donor (FAM) to acceptor (Cy5). The F/F₀ ratio of CQ-FRET hairpins (37.02) was obviously higher than that of two other common HCR fluorescent hairpins (CQ hairpins, 21.45; FRET hairpins, 4.61). The limit of detection of the assay was 3.5 × 10¹ CFU/mL and obviously lower than that of CQ hairpins based immuno-HCR (3.28 × 10³ CFU/mL) and FRET hairpins based immuno-HCR (6.49 × 10⁴ CFU/mL). The proposed low fluorescent background immuno-HCR with high sensitivity which was verified in contaminated milk samples could be potentially used in the detection of various pathogens.

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

Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.

An enzyme-free and label-free visual sensing strategy for the detection of thrombin using a plasmonic nanoplatform

An enzyme-free and label-free visual sensing strategy was developed for sensitively detecting thrombin using a plasmonic nanoplatform. Both the thrombin-triggered catalytic hairpin assembly (CHA) amplification reaction and G-quadruplex/hemin DNAzyme-controlled plasmonic signal readout were engineered on an electrospun nanofibrous membrane. Owing to its large specific surface area and porous structure, the nanofibrous membrane enhanced the loading capacity of B-H2 and the interface interaction efficiency. This plasmonic nanoplatform was used to perform the sensitive and naked-eye detection of thrombin as low as 1.0 pM in human serum samples. This visual strategy can discriminate thrombin from other co-existing proteins very well. Moreover, the visual sensing platform exhibited excellent reusability and long-term stability. The proposed enzyme-free and label-free plasmonic nanoplatform is low-cost, easy to operate and highly sensitive, and has potential applications in the point-of-care detection of protein biomarkers.

Recent Advances in Nanozyme Research

As a new generation of artificial enzymes, nanozymes have the advantages of high catalytic activity, good stability, low cost, and other unique properties of nanomaterials. Due to their wide range of potential applications, they have become an emerging field bridging nanotechnology and biology, attracting researchers in various fields to design and synthesize highly catalytically active nanozymes. However, the thorough understanding of experimental phenomena and the mechanisms beneath practical applications of nanozymes limits their rapid development. Herein, the progress of experimental and computational research of nanozymes on two issues over the past decade is briefly reviewed: (1) experimental development of new nanozymes mimicking different types of enzymes. This covers their structures and applications ranging from biosensing and bioimaging to therapeutics and environmental protection. (2) The catalytic mechanism proposed by experimental and theoretical study. The challenges and future directions of computational research in this field are also discussed.

Electrochemiluminescence Immunosensor Based on Au Nanocluster and Hybridization Chain Reaction Signal Amplification for Ultrasensitive Detection of Cardiac Troponin I

Measurement of cardiac troponin I in the blood is crucial for the early diagnosis of acute myocardial infarction. Herein, a novel and ultrasensitive electrochemiluminescence (ECL) immunosensor has been developed for determination of cardiac troponin I (cTnI) by using Au nanoclusters and hybridization chain reaction (HCR) signal amplification. In this ECL immunosensor, Au nanoclusters were dual-labeled at each end of hairpin DNA (H₁ and H₂) and acted as the luminophore. DNA initiator strands (T₁) and secondary antibody (Ab₂) were conjugated on Au nanoparticles (AuNPs) to obtain a smart probe (Ab₂-AuNP-T₁). In the presence of target cTnI, the sandwiched immunocomplex composed of cTnI, Ab₁, and Ab₂-AuNP-T₁ was formed. Then the initiator strands T₁ of Ab₂-AuNP-T₁ opened the hairpin DNA structures and triggered a cascade of hybridization events. Consequently, a large number of Au NCs were indirectly modified on the surface of the electrode, which could react with the coreactant (K₂S₂O₈) and emit a strong ECL signal. Under the optimal conditions, the immunosensor exhibited a wide detection range for cTnI from 5 fg/mL to 50 ng/mL and a low detection limit of 1.01 fg/mL (S/N = 3). Because of the excellent specificity, stability, and reproducibility of the proposed ECL-HCR sensor, it has a great application prospect for cTnI detection in clinical diagnosis.

Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes (II)

An updated comprehensive review to help researchers understand nanozymes better and in turn to advance the field.

A dual-channel homogeneous aptasensor combining colorimetric with electrochemical strategy for thrombin

In this protocol, a dual-channel homogeneous aptasenor was proposed for protein molecule determination, employing thrombin as target analyte. The colorimetric and electrochemical transducers were combined in a single analytical system for signal readout. In this dual-channel sensing strategy, the G-quadruplex sequence was released and incorporated with hemin to form DNAzyme for naked-eye colorimetric detection. Meanwhile, the hydroxyapatite nanoparticle as signal probe was combined with magnetic nanoparticles to construct sandwich-type structure for generating the electrochemical current when thrombin was present in solution. By introducing two kinds of reporter probes and transducers, this dual-channel sensor produced two different kinds of signal to improve the analytical accuracy and diversity. The results revealed that the dual-channel sensor achieved the quantatitive determination of thrombin with low limit of detection (0.40 fM) and wide range (0.1 fM to 1 nM), which offer a promise for rapid and accurate detection of biomolecule.

Chemical and Biological Sensing Using Hybridization Chain Reaction

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

One-step colorimetric detection of an antibody based on protein-induced unfolding of a G-quadruplex switch

A simple colorimetric assay is developed for the sensitive and selective detection of an antibody, which combines a protein binding-induced signaling approach with a novel DNAzyme-based conformational switching strategy.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

Detection of Thrombin Based on Fluorescence Energy Transfer between Semiconducting Polymer Dots and BHQ-Labelled Aptamers

Carboxyl-functionalized semiconducting polymer dots (Pdots) were synthesized as an energy donor by the nanoprecipitation method. A black hole quenching dye (BHQ-labelled thrombin aptamers) was used as the energy acceptor, and fluorescence resonance energy transfer between the aptamers and Pdots was used for fluorescence quenching of the Pdots. The addition of thrombin restored the fluorescence intensity. Under the optimized experimental conditions, the fluorescence of the system was restored to the maximum when the concentration of thrombin reached 130 nM, with a linear range of 0-50 nM (R² = 0.990) and a detection limit of 0.33 nM. This sensor was less disturbed by impurities, showing good specificity and signal response to thrombin, with good application in actual samples. The detection of human serum showed good linearity in the range of 0-30 nM (R² = 0.997), with a detection limit of 0.56 nM and a recovery rate of 96.2-104.1%, indicating that this fluorescence sensor can be used for the detection of thrombin content in human serum.

A new electrochemical immunoassay for prion protein based on hybridization chain reaction with hemin/G-quadruplex DNAzyme

In this work, a new electrochemical immunosensor was developed for prion protein assay based on hybridization chain reaction (HCR) with hemin/G-quadruplex DNAzyme for signal amplification. In this amplification system, the hemin/G-quadruplex DNAzyme simultaneously mimicked the biocatalytic functions for H₂O₂ reduction and L-cysteine oxidation. In the presence of L-cysteine, the hemin/G-quadruplex catalyzed the oxidation of L-cysteine to L-cystine. At the same time, H₂O₂ was produced under the oxygen condition. Then, the hemin/G-quadruplex could quickly catalyze the reduction of H₂O₂, mimicking the catalytic performance of horseradish peroxidase (HRP). Under the optimal conditions, the immunosensor showed a wide linear response range from 0.5 pg/mL to 100 ng/mL with the low detection limit of 0.38 pg/mL (3σ). By changing the specific antibody, this strategy could be easily extended to detect the infectious isoform of prion (PrP^Sc) and other proteins. Based on its good analytical performance, the developed method shows great potential applications in diagnosis of prion diseases at presymptomatic stage and bioanalysis.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

A dual-cycling biosensor for target DNA detection based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification

Based on the toehold-mediated strand displacement reaction and exonuclease III assisted amplification, a sensitive and simple target DNA biosensor was established.

Switching Peroxidase-Mimic Activity of Protein Stabilized Platinum Nanozymes by Sulfide Ions: Substrate Dependence, Mechanism, and Detection

In the present work, we use β-casein as a model protein to prepare a smart β-casein stabilized Pt nanoparticle (CM-PtNP) with peroxidase mimicking activity and systematically investigate sulfide-mediated switching effect and mechanism of CM-PtNP nanozyme's activity. Sulfide-mediated activity switching effect depends heavily on the physicochemical properties of nanozymes and the identity of substrate. On one hand, the binding of sulfide to a Pt nanozyme surface leads to the transform from Pt²⁺ to Pt⁰, resulting in more active sites and the activity "switching on"; on the other hand, the binding of sulfide ions via Pt-S interaction blocks the active sites, resulting in the activity "switching off". For substrates 3,3',5,5'-tetramethylbenzidine and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) diammonium salt, the two factors play different decisive roles since the interaction of substrate molecules with nanozyme allows their different distributions on nanozyme surfaces. By virtue of this specific response, excellent sulfide colorimetric sensors with different limits of detection were developed based on CM-PtNP with different substrates. This is the first report about a fundamental understanding of how substrates influence the anion-mediated activity switching effect by illuminating the nature of anion-nanozyme interaction and nanozyme-substrate interaction. This may be useful to rationally predict the environment factors on the activities of the nanozyme and to design an effective signal amplification based on target-induced nanozyme deactivation/activation.

A colorimetric aptamer biosensor based on cationic polythiophene derivative as peroxidase mimetics for the ultrasensitive detection of thrombin

A colorimetric assay for the ultrasensitive determination of thrombin was presented, in which the cationic polythiophene derivative was used as catalyst of the 3,3',5,5'-tetramethylbenzidine (TMB)-H₂O₂ reaction and the thrombin-binding aptamer (TBA) was used as inducing polymer's different conformation elements. It was found the cationic polythiophene derivative, poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-t-hiophene hydrochloride] (PMNT), can catalyze the oxidation reaction of TMB in the presence of H₂O₂ to produce a blue color solution. The catalytic activity of PMNT on the TMB-H₂O₂ reaction was closely relevant to the conformation of PMNT. The absorbance of TMB-H₂O₂ was distinctly increased in the presence of TBA. With the addition of thrombin, TBA interacted with thrombin to form a G-quadruplex structure. The conformational change weakened the catalytic activity of PMNT and resulted in a decrease in the absorbance. The colorimetric sensor could detect thrombin down to 4pM with high selectivity against other interfering proteins. This work is not only of importance for a better understanding of the unique properties of cationic polythiophenes derivative but also have great potential for medical diagnostics and therapy for human health.

Target-induced cyclic DNAzyme formation for colorimetric and chemiluminescence imaging assay of protein biomarkers

A target-induced cyclic strategy for DNAzyme formation was developed for simple and sensitive colorimetric and chemiluminescence detection of protein biomarkers.