Target-triggered catalytic hairpin assembly and TdT-catalyzed DNA polymerization for amplified electronic detection of thrombin in human serums

Advances in novel biosensors in biomedical applications

Biosensors, devices capable of detecting biomolecules or bioactive substances, have recently become one of the important tools in the fields of bioanalysis and medical diagnostics. A biosensor is an analytical system composed of biosensitive elements and signal-processing elements used to detect various biological and chemical substances. Biomimetic elements are key to biosensor technology and are the components in a sensor that are responsible for identifying the target analyte. The construction methods and working principles of biosensors based on synthetic biomimetic elements, such as DNAzyme, molecular imprinted polymers and aptamers, and their updated applications in biomedical analysis are summarised. Finally, the technical bottlenecks and future development prospects for biomedical analysis are summarised and discussed.

Single gold nanowire-nanoparticles conjugated system: Fabrication and sensing application

Single-entity-based sensing platform has many advantages for real-time assays, such as single-molecule analysis, or targets detection in confined environment. In this contribution, a new single Au nanowire (NW) - Au@Pt/Au nanoparticles (Au@Pt/Au NPs) conjugated system was established and used for the detection of thrombin by using surface-enhanced Raman spectroscopy (SERS) technique. This method was mainly based on electrostatic attraction between the capture (thrombin aptamer) and probe molecules (crystal violet, CV) on the surface of Au NW - Au@Pt/Au NPs conjugation, reducing the adsorption of CV molecules on conjugation surface, and resulting the decrease of SERS signals. The addition of thrombin could bind with thrombin aptamer due to specific interaction, leading to the decrease of electrostatic effect from thrombin aptamer for CV diffusion to conjugation surface, and the SERS signals could be recovered. This thrombin sensing method showed high sensitivity and selectivity, and the linear range for thrombin assay was 0.01 nM-100 nM with a detection limit of 1.35 pM. This single Au NW - Au@Pt/Au NPs conjugation has more SERS hotspots and small overall size, which offers unparalleled advantages over other sensing system and can be applicable for real time analysis, especially at single molecule/cell level.

Bifunctional TiO2 Nanoflower-Induced H4TCBPE Aggregation Enhanced Electrochemiluminescence for an Ultrasensitive Assay of Organophosphorus

In this work, the aggregation-induced emission ligand 1,1,2,2-tetra(4-carboxylbiphenyl)ethylene (H4TCBPE) was rigidified in the Ti-O network to form novel electrochemiluminescence (ECL) emitter H4TCBPE-TiO2 nanospheres, which acted as an effective ECL emitter to construct an "on-off" ECL biosensor for ultrasensitive detection of malathion (Mal). H4TCBPE-TiO2 exhibited excellent ECL responses due to the Ti-O network that can restrict the intramolecular free motions within H4TCBPE and then reduce the nonradiative relaxation. Moreover, TiO2 can act as an ECL co-reaction accelerator to promote the generation of sulfate radical anion (SO4•-), which interacts with H4TCBPE in the Ti-O network to produce enhanced ECL response. In the presence of Mal, numerous ligated probes (probe 1 to probe 2, P1-P2) were formed and released by copper-free click nucleic acid ligation reaction, which then hybridized with hairpin probe 1 (H1)-modified H4TCBPE-TiO2-based electrode surface. The P1-P2 probes can initiate the target-assisted terminal deoxynucleoside transferase (TdTase) extended reaction to produce long tails of deoxyadenine with abundant biotin, which can load numerous streptavidin-functionalized ferrocenedicarboxylic acid polymer (SA-PFc), causing quenching of the ECL signal. Thus, the ultrasensitive ECL biosensor based on H4TCBPE-TiO2 ECL emitter and click chemistry-actuated TdTase amplification strategy presents a desirable range from 0.001 to 100 ng/mL and a detection limit low to 9.9 fg/mL. Overall, this work has paved an avenue for the development of novel ECL emitters, which has opened up new prospects for ECL biosensing.

Multi-signal aptasensor for thrombin detection based on catalytically active gold nanoparticles and fluorescent silicon quantum dots

A multi-signal aptasensor for thrombin determination is proposed based on catalytically active gold nanoparticles (AuNPs) and fluorescent silicon quantum dots (SiQDs). Yellow 4-Nitrophenol (4-NP) could be converted to colorless 4-Aminophenol (4-AP) by catalytically active aptamer-modified AuNPs (S1-AuNPs). The SiQDs emitted strong blue fluorescence at 455 nm at the excitation wavelength of 367 nm. When thrombin was absent, S1-AuNPs could catalytically reduce yellow 4-NP to colorless 4-AP. When thrombin was added, the aptamer could be transformed into a G-quadruplex structure, which masked the surface-active catalytic sites of AuNPs and restrained the reduction of 4-NP. Thus, the fluorescence of SiQDs was greatly quenched by 4-NP through the inner filter effect (IFE), and the solution color remained yellow. As the concentration of thrombin increased, the catalytic activity of S1-AuNPs decreased. The concentration of 4-NP that was converted to 4-AP declined and the unconverted 4-NP increased. In this process, the absorption peak of 4-NP at 400 nm increased while the fluorescence emission of SiQDs at 455 nm decreased. The linear ranges of the fluorometric and colorimetric aptasensor were 0.5-30 nM and 0.3-30 nM, respectively. The limits of detection (LOD) for the two modes were 0.15 nM and 0.13 nM. Furthermore, a portable sensing platform was constructed by combining the smartphone-based device with the software ImageJ for the determination of thrombin. With the advantages of cost-effectiveness, simplicity of operation and broad applicability, this aptasensor provided a new perspective for on-site determination of thrombin in the clinical field.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Thrombin Determination Using Graphene Oxide Sensors with Co-Assisted Amplification

Graphene oxide (GO) is widely used in sensors. The detection of proteins based on bare GO has been developed; however, the detection sensitivity needs to be improved. In this paper, a novel GO-DNA sensor for thrombin detection was developed using an aptamer linked to the surface of GO. Polyethylene glycol (PEG) was further used to prevent thrombin from nonspecific adsorption and to improve the sensitivity of the sensor for detection of thrombin. In order to improve the limit of detection for thrombin, we developed a GO and RecJf exonuclease co-assisted signal amplification strategy, and a detection limit of 24.35 fM for thrombin was achieved using this strategy. The results show that it is a promising method in analytical applications.

Self-Customized Multichannel Exponential Amplifications Regulate Powered Monitoring of Terminal Deoxynucleotidyl Transferase Activity

The discovery and function analysis of terminal deoxynucleotidyl transferase (TdT) add a new dimension to the understanding of leukemia mechanisms and stimulate the development of new analytical tools for leukemia diagnosis. Herein, taking advantage of the inherent property of TdT for performing DNA synthesis using only single-stranded DNA as the nucleic acid substrate, we developed a self-customized multichannel exponential amplification (SMEA) system for the fluorescent sensing of TdT activity. The SMEA design employs an intermolecular DNA interaction made of a nicking site-incorporated elongation primer (EP) and a nicking site-incorporated poly-thymine tailed molecular beacon (Poly-T-MB). The absence of TdT is unable to bridge the relationship between EP and Poly-T-MB, ensuring the SMEA has an ultralow background. The presence of TdT, however, leads to the elongation of EP to poly-adenine tailed EP (Poly-A-EP) under a dATP pool responsible for further hybridization with numerous Poly-T-MB. With the aid of polymerase and nickase to react with the hybridization product of Poly-A-EP/(Poly-T-MB)_n, it can cause bidirectional strand nicking, polymerization, and displacement in many cycles and channels. In this case, the SMEA is found to be associated with the configuration transformation and splitting of all Poly-T-MBs for a significant fluorescence enhancement. Depending on this high target signal amplification and strong background inhibition abilities, the SMEA sensing system is powerful for the qualitative and quantitative determination of TdT activity, showing that it has great promise for biomedical study and disease diagnosis.

Framework nucleic acid-wrapped protein-inorganic hybrid nanoflowers with three-stage amplified fluorescence polarization for terminal deoxynucleotidyl transferase activity biosensing

Herein, we proposed a terminal deoxynucleotidyl transferase (TdT), a potential biomarker of lymphoid tumors, responsive fluorescence polarization (FP)- sensing protocol based on framework nucleic acid (FNA)-wrapped protein-inorganic hybrid nanoflowers. To achieve this goal, a pair of poly-A-composed extension primers (EPa and EPb) was designed, and protein-inorganic hybrid nanoflowers were synthesized by a biomineralization reaction. EPa was labeled with carboxyfluorescein (FAM) fluorophore to create the preliminary FP signal. EPb was labeled with biotin to conjugate with hybrid nanoflowers. Upon introduction of TdT into the dTTP pool, both EPa and EPb can be catalyzed by TdT to incorporate numerous T bases, thereby facilitating intermolecular hybridization between 'A' and 'T' bases. The final assembled FNA-wrapped hybrid nanoflowers with greatly enhanced molecular volume and weight restrict the free rotation of attached FAMs, causing a great FP enhancement from a designated three-stage FP amplification. Under optimized conditions, the TdT can be detected with a detection limit of 0.023 U/mL and a linear detection from 0.1 U/mL to 100 U/mL within 20 min. As a proof-of-concept study, the first exploitation of FNA and protein-inorganic nanoflowers to improve the FP signal and the merit of FP without sample separation and washing opens a new avenue for biochemical study and disease diagnosis.

A SERS-LFA biosensor combined with aptamer recognition for simultaneous detection of thrombin and PDGF-BB in prostate cancer plasma

An innovative surface-enhanced Raman spectroscopy and lateral flow assay (SERS-LFA) biosensor combined with aptamer recognition had been developed for the convenient, rapid, sensitive and accurate detection of thrombin and platelet-derived growth factor-BB (PDGF-BB) associated with prostate cancer simultaneously. During the biosensor operation, thrombin and PDGF-BB in the sample were recognized and combined by thiol-modified aptamers immobilized on Au-Ag hollow nanoparticles (Au-Ag HNPs) surface and biotinylated aptamers immobilized on the test lines of the biosensor. Thus, thrombin and PDGF-BB were simultaneously captured between detection aptamers and capture aptamers in a sandwich structure. Finite difference time domain simulation confirmed that 'hot spots' appeared at the gaps of Au-Ag HNPs dimer in the enhanced electromagnetic field compared to that of a single Au-Ag HNP, indicating that the aggregated Au-Ag HNPs owned a good SERS signal amplification effect. The detection limits of thrombin and PDGF-BB in human plasma were as low as 4.837 pg ml^-1and 3.802 pg ml^-1, respectively. Moreover, the accuracy of the biosensor which was applied to detect thrombin and PDGF-BB in prostate cancer plasma had been verified. This designed biosensor had broad application prospects in the clinical diagnosis of prostate cancer.

Amplified and label-free electrochemical detection of a protease biomarker by integrating proteolysis-triggered transcription

Cell-free synthetic biology provides a promising strategy for developing high-performance biosensors by integrating with advanced testing technologies. However, the combination of synthetic biology with electrochemical testing techniques is still underdeveloped. Here, we proposed an electrochemical biosensor for the label-free and ultrasensitive detection of target protease biomarker by coupling a protease-responsive RNA polymerase (PR) for signal amplification. Taking tumor biomarker matrix metalloprotease-2 (MMP-2) as a model protease, we employed PR to transduce each proteolysis reaction mediated by MMP-2 into multiple programmable RNA outputs that can be captured by the DNA probes immobilized on a gold electrode. Moreover, the captured RNAs are designed to contain a guanine-rich sequence that can form G-quadruplex and bind to hemin in the presence of potassium ions. In this scenario, the activity of MMP-2 is converted and amplified into the electrochemical signals of hemin. Under the optimal conditions, this PR-based electrochemical biosensor enabled the sensitive detection of MMP-2 in a wide linear dynamic range from 10 fM to 1.0 nM, with a limit of detection of 7.1 fM. Moreover, the proposed biosensor was further applied in evaluating MMP-2 activities in different cell cultures and human tissue samples, demonstrating its potential in the analysis of protease biomarkers in complex clinical samples.

Activation of catalytic DNAzyme by binding-induced DNA displacement for homogeneous assay

The sensitive assays for protein, especially for the DNA-based assay, are often dependent on the amplification procedure with assistance of enzyme. Compared with a protein enzyme, deoxyribozyme (DNAzyme) exhibits similar catalytic activity and specificity and better flexibility. In this work, we streamlined the binding induced DNA displacement (BINDD) strategy for the activation of DNAzyme cleavage. Since the intrinsic element of DNAzyme is the nucleic acids, it is easy to join the BINDD by hybridization with an affinity probe. The activity of DNAzyme was initiated by the BINDD reaction mediated by the recognition affinity probe with target proteins. Upon DNAzyme release, it was able to catalyze and cleave the predesigned substrates, generating the enhanced fluorescence signal indicating the protein concentration. Such a constructed homogeneous assay is available and effective in human serum when it was used for detection of platelet derived growth factor-BB (PDGF-BB) and prostate specific antigen (PSA), with detection limits of 100 pM and 200 pM, respectively.

An electrochemical Hg2+ sensor based on signal amplification strategy of target recycling

In this work, an unmodified homogeneous electrochemical sensor based on electrochemical bonding and catalytic hairpin assembly (CHA) was first constructed for the high sensitivity detection of Hg²⁺. Herein, tetraferrocene, a synthesized compound, was used as a signal marker that modified both ends of the hairpin probe to amplify the electrochemical signal. The interaction of T-Hg²⁺-T could induce the catalytic self-assembly of hairpins by means of auxiliary DNA. The rigid DNA triangle that was formed easily reaches the electrode and induced Au-S self-assembly assisted by potential, allowing tetraferrocene to reach the electrode surface and generate a sensitive electrochemical signal. CHA and tetraferrocene signal markers accomplished dual signal amplification, and the limit of detection was 0.12 pM. Differential pulse voltammetry experiments in the presence of tetraferrocene redox indicator show that the linear response range of electrochemical biosensors to mercury ions is 0.2-2000 pM, This technology offers good selectivity and high recognition efficiency for the detection of mercury ions and has broad application prospects in actual sample detection.

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.

Colorimetric nanoplatform for visual determination of cancer cells via target-catalyzed hairpin assembly actuated aggregation of gold nanoparticles

According to aptamer-mediated hairpin DNA cascade amplifier and gold nanoparticles aggregation, an optical platform for cancer cells determination has been proposed. High-affinity chimeric aptamers were used for cancer cell detection and also as an initiator for beginning hairpin assembly to construct three-way junction (3WJ) nanostructures. These three hairpins were modified at 3' ends with biotin. In the presence of target cell, chimeric aptamer binds to its ligand on cell surface and initiates 3WJ nanostructures formation. These 3WJ nanostructures interact with streptavidin-modified gold nanoparticles (AuNPs) via non-covalent biotin-streptavidin interactions and create a crossover lattice of nanoparticles. This event leads to AuNPs aggregation and red-shifting. The results were confirmed by gel electrophoresis and UV-visible spectrophotometry. The dynamic range of this assay is 25 to 10⁷ cells with a detection limit of 10 cells which is respectively 9 and 4 times more significant than the sensitivity of AuNP-based approaches without amplification and enzyme-mediated signal amplification. Graphical abstract.

Highly sensitive host-guest mode homogenous electrochemical thrombin signal amplification aptasensor based on tetraferrocene label

The development of sensitive and convenient detection methods to monitor thrombin without the use of enzymes or complex nanomaterials is highly desirable for the diagnosis of cardiovascular diseases. In this article, tetraferrocene was first synthesized and then a sensitive and homogeneous electrochemical aptasensor was developed for thrombin detection based on host-guest recognition between tetraferrocene and β-cyclodextrin (β-CD). In the absence of thrombin, the double stem-loop of thrombin aptamer (TBA) prevented tetraferrocenes labeled at both ends from entering the cavity of β-CD deposited on gold electrode surface. After binding with thrombin, the stem-loop structure of TBA opened and transformed into special G-quarter structure, forcing tetraferrocene into the cavity of β-CD. As a result, thrombin allowed eight ferrocene molecules to reach the gold electrode surface, greatly amplifying the response signal. The obtained aptasensors showed dynamic detection range from 4 pM to 12.5 nM with detection limit around 1.2 pM. Overall, the results indicate that the proposed aptasensors are promising for future rapid clinical detection of thrombin and development of signal amplification strategies for detection of various proteins.

Novel Chemiluminescence Sensor for Thrombin Detection Based on Dual-Aptamer Biorecognition and Mesoporous Silica Encapsulated with Iron Porphyrin

Thrombin is a marker of blood-related diseases, and its detection is of great significance in the fields of medical and biological research. Herein, a novel chemiluminescence (CL) sensor for thrombin detection was prepared based on dual-aptamer biorecognition and mesoporous silica encapsulated with iron porphyrin. Mesoporous silica encapsulated with hematin by aptamer1 (Apt1/hematin/M-SiO₂) and magnetic microspheres modified with aptamer2 (Apt2/NH₂-MS) were successfully prepared, and the two materials were used to construct a CL sensor to detect thrombin. Primarily, Apt2/NH₂-MS is used for pretreatment separation of thrombin samples by the biorecognition effect between the aptamer (Apt2) and target (thrombin). Then, thrombin/Apt2/NH₂-MS is again recognized with Apt1 on the surface of Apt1/hematin/M-SiO₂ and Apt1/thrombin/Apt2/NH₂-MS is formed, so dual-aptamer biorecognition is realized. Meanwhile, the generated Apt1/thrombin/Apt2/NH₂-MS makes Apt1 shed off the surface of M-SiO₂ and release hematin. The released hematin can catalyze the luminol-H₂O₂ CL reaction. Therefore, a sandwich-type CL sensor was constructed based on dual-aptamer biorecognition and hematin catalysis for the detection of thrombin. The sensor has a linear range of 7.5 × 10^-15 to 2.5 × 10^-10 mol·L^-1 and a detection limit of 2.2 × 10^-15 mol·L^-1 and also exhibits excellent selectivity, reproducibility, and stability. The sensor was successfully used for the detection of thrombin in serum samples, which makes it possible to apply the sensor in the detection of thrombin in actual samples.

Electrochemical biosensors based on nucleic acid aptamers

During recent decades, nucleic acid aptamers have emerged as powerful biological recognition elements for electrochemical affinity biosensors. These bioreceptors emulate or improve on antibody-based biosensors because of their excellent characteristics as bioreceptors, including limitless selection capacity for a large variety of analytes, easy and cost-effective production, high stability and reproducibility, simple chemical modification, stable and oriented immobilization on electrode surfaces, enhanced target affinity and selectivity, and possibility to design them in target-sensitive 3D folded structures. This review provides an overview of the state of the art of electrochemical aptasensor technology, focusing on novel aptamer-based electroanalytical assay configurations and providing examples to illustrate the different possibilities. Future prospects for this technology are also discussed. Graphical abstract.

A "signal-on" electrochemical biosensor based on DNAzyme-driven bipedal DNA walkers and TdT-mediated cascade signal amplification strategy

In this work, a dual amplified signal enhancement approach based on coupling deoxyribozyme (DNAzyme)-driven bipedal DNA walkers (BDW) and terminal deoxynucleotidyl transferase (TdT)-mediated DNA elongation signal amplifications has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. In presence of thrombin, the BDW complex, which is comprised from the target thrombin and two DNAzyme-containing probes, can exhibit autonomous cleavage behavior on the surface of the substrate DNA (SD) modified electrode, and remove the cleaved DNA fragment from the electrode surface. Subsequently, the TdT can catalyze the elongation of the SD with free 3'-OH termini and formation of many G-quadruplex sequence replicates with the presence of 2'-deoxyaguanosine-5'-triphosphate (dGTP) and adenosine 5'-triphosphate (dATP) at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a "signal-on" and completely label-free fashion. Under optimized conditions, the response peak current was linear with the concentration of thrombin in the range from 0.5 pM to 100000 pM with detection limit of 0.31 pM. This research provides us a sustainable idea for the hyphenated multiple amplification strategies and a stable and effective method for the detection of protein biomarkers.

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

Nucleic acids are considered as perfect programmable materials for cascade signal amplification and not merely as genetic information carriers. Among them, catalytic hairpin assembly (CHA), an enzyme-free, high-efficiency, and isothermal amplification method, is a typical example. A typical CHA reaction is initiated by single-stranded analytes, and substrate hairpins are successively opened, resulting in thermodynamically stable duplexes. CHA circuits, which were first proposed in 2008, present dozens of systems today. Through in-depth research on mechanisms, the CHA circuits have been continuously enriched with diverse reaction systems and improved analytical performance. After a short time, the CHA reaction can realize exponential amplification under isothermal conditions. Under certain conditions, the CHA reaction can even achieve 600 000-fold signal amplification. Owing to its promising versatility, CHA is able to be applied for analysis of various markers in vitro and in living cells. Also, CHA is integrated with nanomaterials and other molecular biotechnologies to produce diverse readouts. Herein, the varied CHA mechanisms, hairpin designs, and reaction conditions are introduced in detail. Additionally, biosensors based on CHA are presented. Finally, challenges and the outlook of CHA development are considered.

Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase

The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

A signal amplification strategy and sensing application using single gold nanoelectrodes

In this work, a label-free electrochemical apta-nanosensor was fabricated on a single gold nanodisk electrode (AuNDE) for thrombin sensing with high sensitivity via a novel signal amplification strategy. This recognition platform was fabricated via self-assembly of helper DNA (HP-DNA), thrombin-binding aptamer (TBA) and gold nanoparticle (AuNP)-DNA complexes to form a sandwich structure on the AuNDE surface. A novel signal amplification strategy via designed AuNP-DNA complexes was introduced using Ru(NH3)63+ as the signal reporter based on the electrostatic interaction. In the presence of thrombin, the strong interaction between the TBA and target led to the dissociation of sandwich DNA complexes from the AuNDE, which resulted in the reduction current of Ru(NH3)63+. This proposed sensing platform showed a wide detection range of 0.1 pM-5 nM and a low detection limit of 0.02 pM. Considering the small overall dimensions and high sensitivity, this nanosensor can be potentially applied for bioanalysis in living biosystems.

Colorimetric and electrochemical (dual) thrombin assay based on the use of a platinum nanoparticle modified metal-organic framework (type Fe-MIL-88) acting as a peroxidase mimic

An electrochemical and colorimetric dual-readout method is described for the determination of thrombin. A platinum nanoparticle (Pt NP) modified metal organic framework (MOF) acts as a peroxidase (POx) mimic that causes the formation of a blue product from 3,3',5,5'-tetramethylbenzidine (TMB) and hydrogen peroxide, with an absorption maximum at 650 nm. In addition, gold nanoparticles enrich initiators that trigger the hybridization chain reaction for dual signal amplification to generate an electrochemical current typically measured at 0.31 V (from -0.5 to -0.1 V) and allow quantitation of thrombin with high sensitivity and over a wide detection range. The colorimetric and electrochemical (dual) thrombin assay produces two kinds of signals which warrants accuracy, diversity, and an option for visual inspection. The dual-channel sensor allows for the quantitative determination of thrombin with a low detection limit (0.33 fM) for the electrochemical method and 0.17 pM for the colorimetric method) and over a wide detection range (1 fM to 10 nM for electrochemical method and 0.5 pM to 1 nM for colorimetric method). The electrochemical detection limit is lower than that of colorimetry, and the linear range is wider, which is more suitable for further quantitative analysis of the target. Graphical abstract Schematic representation of a colorimetric and electrochemical (dual) thrombin assay based on the use of a platinum nanoparticle modified metal-organic framework for color development and hybridization chain reaction for electrochemical signal. C-TBA: complementary sequences of thrombin aptamer, TBA: thrombin aptamer, I-Au NPs: initiators enriched by gold nanoparticles, S-AuE: sensing gold electrode, RS-AuE: reacted sensing gold electrode, TB: thrombin, MB: Methylene Blue, HCR: hybridization chain reaction.

Simple label-free and sensitive fluorescence determination of human 8-oxoG DNA glycosylase 1 activity and inhibitionviaTdT-assisted sequence extension amplification

Label-free and sensitive detection of hOGG1 activity and inhibitionviaTdT-assisted sequence extension signal amplification.

An electric potential modulated cascade of catalyzed hairpin assembly and rolling chain amplification for microRNA detection

MicroRNAs serve as a new type of biomarker for multifarious diseases due to its critical roles in post transcriptional gene regulation. Herein, we firstly integrate the catalyzed hairpin assembly (CHA) and rolling circle amplification (RCA) into an electrochemical biosensor for sensitive and specific detection of miR-21. Meanwhile, an electric potential was employed to modulate the efficiency of CHA occurred on the electrode, which offer a simple but effective method to surmount the accessibility problem of probes. The biosensor achieved an ultrasensitive determination of miR-21 with a low limit of detection of 13.5 fM and a linear range from 15 fM to 250 pM. This research encourages us to challenge the hyphenated multiple amplification strategies and provides a stable and effective method for the detection of diseases-related miRNAs in peripheral biofluids, as well as paves a road for the future clinical diagnostics and treatment of disease.

Development of a Luminescent Dinuclear Ir(III) Complex for Ultrasensitive Determination of Pesticides

To improve the G-quadruplex specificity of Ir(III) complexes, a novel dinuclear Ir(III) complex (Din Ir(III)-1) was designed and synthesized through connecting two mononuclear Ir(III) complexes via a diphenyl bridge. Din Ir(III)-1 presents 3.4-4.1-fold enhancements for G-quadruplex relative to ssDNA and 4.3-5.3-fold enhancements relative to dsDNA in luminescence intensity, respectively, demonstrating an excellent G-quadruplex selectivity. Ascribed to its superior specificity to G-quadruplex, Din Ir(III)-1 was employed to construct a highly sensitive luminescent pesticides' detection platform. The detection is based on acetylcholinesterase (AChE)-catalyzed hydrolysis product-induced DNA conformational transformation and subsequent terminal deoxynucleotidyl transferase (TdT) directed G-quadruplex formation. The assay exhibited a linear response between the emission intensity of Din Ir(III)-1 and the pesticide concentration in the range of 0.5-25 μg/L ( R² = 0.994), and the limit of detection for the pesticide was as low as 0.37 μg/L when using aldicarb as the model pesticide. Moreover, this strategy demonstrates good applicability for the pesticide detection in real samples. It is also versatile for the detection of other organophosphate or carbamate pesticides, which have the inhibition ability toward AChE. Therefore, the proposed approach is scalable for practical application in food safety and environmental monitoring fields and will provide promising solutions for the assay of pesticide residues.

A facile DNA strand displacement reaction sensing strategy of electrochemical biosensor based on N-carboxymethyl chitosan/molybdenum carbide nanocomposite for microRNA-21 detection

Herein, we report a facile enzyme-free microRNA (miRNA) target-triggered strand displacement reaction (SDR) amplification strategy with ferrocene (Fc) as a signal molecule to fabricate a two-dimensional electroactive molybdenum carbide (Mo₂C)-based biosensor. In the presence of miRNA-21, SDR was initiated and many hairpin DNA1 (HDNA1) and hairpin DNA2 (HDNA2) duplexes, which could be captured by probe DNA leading the Fc-modified HDNA2 close to the electrode surface, were produced continuously. MiRNA-21 could be detected by monitoring the redox signal of Fc. The prepared N-carboxymethyl chitosan/Mo₂C nanocomposite featured excellent conductivity, great dispersion, and multiple functional groups (amine groups). When the nanocomposite was introduced to a miRNA biosensor electrode interface to ensure its strong connection to the DNA probe, the developed miRNA-21 biosensor demonstrated a reliable linear range of 1.0 fM to 1.0 nM with a detection limit of 0.34 fM and showed good selectivity, reproducibility, and stability. The biosensor was employed to detect miRNA-21 in human serum samples, and it showed great potential in the early clinical diagnosis of various genetic diseases.

A chemiluminescence aptasensor for thrombin detection based on aptamer-conjugated and hemin/G-quadruplex DNAzyme signal-amplified carbon fiber composite

In this work, a highly sensitive and selective chemiluminescence (CL) aptasensor was prepared for thrombin (THR) detection based on aptamer-conjugated and hemin/G-quadruplex DNAzyme signal-amplified carbon fiber composite (HG-DNAzyme/T-Apt/SiO₂@GO@CF). Initially, SiO₂@GO@CF was successfully prepared and characterized by Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FT-IR). Thrombin aptamer (T-Apt) as an identification element and simulated enzyme - hemin/G-quadruplex DNAzyme (HG-DNAzyme) as a signal-amplified material, were applied in the CL aptasensor. Then, the immobilization properties of SiO₂@GO@CF and adsorption properties of T-Apt/SiO₂@GO@CF were studied. Lastly, HG-DNAzyme/T-Apt/SiO₂@GO@CF was applied in construction of the CL aptasensor. When THR existed, HG-DNAzyme was desorbed from the surface of T-Apt/SiO₂@GO@CF and catalyzed the CL system of luminol-H₂O₂. Under optimized CL conditions, THR was measured with the linear concentration range of 1.5 × 10^-14 to 2.5 × 10^-11 moL/L and the detection limit of 6.3 × 10^-15 moL/L (3δ). The proposed CL aptasensor was used to the determination of THR in human serum samples and recoveries ranged from 99.0% to 102.4%. Those satisfactory results illustrated the CL aptasensor could achieve highly sensitive and selective detection of THR and revealed potential application in practical samples.

Highly sensitive fluorometric determination of thrombin by on-chip signal amplification initiated by terminal deoxynucleotidyl transferase

The article describes an on-chip amplification scheme initiated by a terminal deoxynucleotidyl transferase (TdT) for highly sensitive fluorometric determination of protein. Two thrombin-binding aptamers were designed to capture thrombin as they can form a sandwich structure for improved specificity. An amino-modified aptamer (TBA29) was first immobilized on a silicon chip. After capture of thrombin, a second aptamer (TBA15) was conjugated to the second binding site of thrombin. The 3'-terminal of aptamer TBA15 is exposed on the chip surface, and then fluorescein-labeled 12-dATP associates to the 3'-terminal with the help of TdT. This results in signal amplification, and eventually leads to highly sensitive detection. Under optimal conditions, fluorescence intensity is linearly related to the logarithm of thrombin concentration in the range of 100 fM - 0.1 μM, and the detection limit is as low as 2.0 fM. The assay is sensitive and selective even over potentially interfering proteins and in the presence of human serum. Graphical abstract Schematic strategy for thrombin detection. Two thrombin-binding aptamers were designed to capture thrombin to form a sandwich structure for improved specificity. The protein detection is based on TdT initiated on-chip fluorescent amplification.

Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses

We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.

Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.

Bifunctional aptamer-mediated catalytic hairpin assembly for the sensitive and homogenous detection of rare cancer cells

The presence of cancer cells in body fluids confirms the occurrence of metastasis and guides treatment. A simple, fast, and homogeneous fluorescent method was developed to detect cancer cells based on catalytic hairpin assembly (CHA) and bifunctional aptamers. The bifunctional aptamer had a recognition domain for binding to target cancer cells and an initiator domain for triggering the CHA reaction. In the presence of target cells, the bifunctional aptamer was released from the inhibitor and initiated a cascade reaction of assembly and disassembly of the hairpins. Separation of the fluorophores from the quenchers produced fluorescence signals. The proposed strategy showed high specificity for discriminating normal cells and leukocytes, and the detection limit was 10 cells/mL, which was lower than that of previous aptasensors. This assay was further tested using four kinds of clinical samples spiked with target cells to confirm its applicability. We developed a simple, rapid, and cost-effective method for the detection of cancer cells that did not require purification, and the approach holds great potential for bioanalysis and early diagnosis.

The aptamer-thrombin-aptamer sandwich complex-bridged gold nanoparticle oligomers for high-precision profiling of thrombin by dark field microscopy

We present a simple and efficient colorimetric assay strategy for ultrasensitive visual detection of human α-thrombin, which is essentially based on the formation of the DNA1-thrombin-DNA2 sandwich complex-bridged gold nanoparticle (Au NP) oligomers. Unlike the traditional colorimetric sensing strategies which induced the nanoparticle aggregates with uncontrolled aggregate size. In this work, the DNA1with rich G bases was firstly conjugated on the surfaces of Au NPs fixed on the hexadecyl trimethylammonium bromide (CTAB)-coated glass slide, and thrombin was captured by the DNA1. Then, the other DNA2 with rich G bases interacted with the former DNA1-thrombin complex and formed a DNA1-thrombin-DNA2 sandwich complex. The subsequently added Au NPs can be bound to the Au NP-DNA1-thrombin-DNA2 via Au-S bond to trigger the formation of Au NP oligomers, an apparent color change of the single Au NPs from green to yellow and red was observed under dark field microscopy. By measuring the intensity change of the yellow and red Au NPs, the concentration of target thrombin could be accurately quantified. As a proof of concept experiment, the formation of Au NP oligomers resulted in significantly improved sensitivity (10 fM of limit of detection and 20 fM of limit of quantity) and wider linear dynamic range of thrombin detection (20 fM-20 nM), the relative standard deviation (RSD) was less than 5.73% (n = 5). In addition, in order to validate the potential application in clinical diagnosis, the content of thrombin in a human serum samples was also quantified.

Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection

As important modulators of gene expression, microRNAs (miRNAs) have been identified as promising biomarkers with powerful predictive value in diagnosis and prognosis for several diseases, especially for cancers. Here we report a facile, multiple and sensitive miRNA detection method that uses conventional gel electrophoresis and catalytic hairpin assembly (CHA) system without any complex nanomaterials or enzymatic amplification. Methods: In this study, three pairs of hairpin probes are rationally designed with thermodynamically and kinetically preferable feasibility for the CHA process. In the present of target miRNA, the stem of the corresponding hairpin detection probe (HDP) will be unfolded and expose the concealed domain. The corresponding hairpin assistant probe (HAP) then replaces the hybridized target miRNA to form specific HDP/HAP complexes and releases miRNA based on thermodynamically driven entropy gain process, and the released miRNA triggers the next recycle to produce tremendous corresponding HDP/HAP complexes. Results: The results showed that the CHA gel assay can detect miRNA at fM levels and shows good capability of discriminating miRNA family members and base-mismatched miRNAs. It is able to analyze miRNAs extracted from cell lysates, which are consistent with the results of conventional polymerase chain reaction (PCR) method. Depending on the length of the designed hairpin probes, the CHA gel assay consisting of different hairpin probes effectively discriminated and simultaneously detected multiple miRNAs in homogenous solution and miRNAs extracted from cell lysates. Conclusion: The work highlights the practical use of a conventional gel electrophoresis for sensitive interesting nucleic acid sequences detection.

Novel electrochemical biosensor based on cationic peptide modified hemin/G-quadruples enhanced peroxidase-like activity

This work designed an artificial substrate peptide to synthesize peptide-hemin/G-quadruplex (peptide-DNAzyme) conjugates. In addition to enhancing catalytic activity of hemin/G-quadruplex, the peptide could also be induced and cleaved by prostate specific antigen (PSA). It was the first report on peptide-DNAzyme conjugates in application of the peptide biosensor. The polyethyleneimine-reduced graphene oxide@hollow platinum nanotubes (PEI-rGO@PtNTs) nanocomposites were cast on the glassy carbon electrode in order to form the interface of biocompatibility and huge surface area for bioprobes immobilization. In absence of PSA, the peptide-DNAzyme conjugates retained intact on the surface of the electrode to produce a strong response signal. But in presence of PSA, the peptide-DNAzyme conjugates were destroyed to release electron mediators, resulting in dramatical decrease of the electrochemicl signal. Therefore, the method had high sensitivity and super selectivity with the limit of detection calculated as 2.0 fg/mL. Furthermore, the strategy would be promising to apply for other proteases by transforming the synthetic peptide module of target.

Sensitive detection of intracellular microRNA based on a flowerlike vector with catalytic hairpin assembly

A flowerlike nanovector with horn-shaped tips is developed for in situ detection of intracellular microRNA with multiple signal outputs.