Simple electrochemical sensing of attomolar proteins using fabricated complexes with enhanced surface binding avidity

A dual-core 3D DNA nanomachine based on DNAzyme positive feedback loop for highly sensitive MicroRNA imaging in living cells

A double 3D DNA walker nanomachine by DNAzyme self-driven positive feedback loop amplification for the detection of miRNA was constructed. This method uses two gold nanoparticles as the reaction core, and because of the spatial confinement effect the local concentration of the reactants increase the collision efficiency was greatly improved. Meanwhile, the introduction of positive feedback loop promotes the conversion efficiency. In presence of miRNA-21, a large amount of DNAzyme was released and hydrolyze the reporter probe, resulting the recovery of fluorescence signal. The linear range for miRNA-21 is 0.5-60 pmol/L, and the detection limit is 0.41 pmol/L (S/N = 3). This nanomachine has been successfully used for accurate detection of miRNA-21 expression levels in cell lysates. At the same time, it can enter cells for intracellular miRNA-21 fluorescence imaging, distinguishing tumor cells from normal cells. This combination of in vitro detection and imaging analysis of living cells can achieve the goal of jointly detecting cancer markers through multiple pathways, providing new ideas for early diagnosis and screening of diseases.

Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4

Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL-1 and a detection limit of 0.46 pg mL-1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.

DNAzyme-driven bipedal DNA walker triggered to hybridize silver nanoparticle probes for electrochemical detection of amyloid-β oligomer

Amyloid-β oligomer has been considered as a promising molecular biomarker for the diagnosis of Alzheimer's disease due to their significant neural synapse toxicity. Therefore, it is essential to create an easy approach for the selective detection of Amyloid-β oligomer that has high sensitivity and cheap cost. In this work, we developed an innovative enzyme-free electrochemical aptasensor based on the DNAzyme-driven DNA bipedal walker tactics for sensing Amyloid-β oligomer. Bipedal DNA walkers demonstrate a wider walking region, better walking kinetics, and higher amplification effectiveness than typical DNA walkers. The Mg²⁺-dependent DNAzyme drove the DNA walker, and the binding-induced DNA walker can sequentially shear MBs and form MB fragment structure. Finally, the detection probes modified AgNPs hybridized with the MB fragment structure, resulting in the multiplication of AgNPs on the electrode surface. Electrochemical stripping of AgNPs was used to test the performance of the obtained electrochemical sensor. In particular, a low detection limit of 5.94 fM and a wide linear range of 0.01 pM-0.1 nM were attained. The detection of Amyloid-β oligomer in human serum was then carried out using this bipedal DNA walker biosensor, which shown good selectivity and outstanding reproducibility, indicating its usefulness in bioanalysis.

Recent advances in electrochemical proximity ligation assay

Proximity ligation assay (PLA) is a vigorously developed homogeneous immunoassay assisted by DNA combining dual recognition of target protein by pairs of proximity probes, in which the detection of protein is tactfully converted to the detection of DNA. The booming developments in PLA have enabled a variety of ultrasensitive assays for the detection of protein and this concept of PLA is also extended to the detection of nucleic acids and some small molecule. The association between PLA and electrochemical method, defined as electrochemical proximity ligation assay (ECPLA), has gained much interests in disease diagnosis, food safety and environmental assays with the advantages, such as broad range of targets, simplicity, low cost and rapid response. In this review, we took a different perspective to present the history of PLA, the classical ECPLA biosensing methodology as well as the developments of ECPLA based on several key parameters, such as sensitivity, selectivity, reusability and generalization. In addition, the developments of PLA with electrochemiluminescence as readout are also presented. Finally, perspective and some unresolved challenges in ECPLA that can potentially be addressed have also been discussed.

DNAzyme-driven bipedal DNA walker for label-free and signal-on electrochemical detection of amyloid-β oligomer

As a common technique for detecting AβO, the enzyme-linked immunosorbent assay (ELISA) method is time-consuming, high in cost, and poor in stability. Therefore, it is necessary to develop a highly sensitive, method-simple and low-cost method for the selective detection of AβO. Here, we created a novel signal-on and label-free electrochemical aptamer sensor for the detection of AβO based on a DNAzyme-driven DNA bipedal walking strategy. Compared with common DNA walkers, bipedal DNA walkers exhibit larger walking areas and faster walking kinetics, and provide higher amplification efficiency. The DNAwalker is powered by an Mg²⁺-dependent DNAzyme, and the binding-induced DNAwalker continuously clamps the MB, unlocking several active G-quadruplex-forming sequences. These G-quadruplexes can be further combined by hemin to generate a G-quadruplex/heme complex, resulting in an amperometric signal, resulting in a broad proportional band from 0.1 pM to 1 nM and an excellent detection range of 46 fM. A bipedal DNA walker aptamer sensor can detect human serum AβO with remarkable specificity, high reproducibility and practical application value.

Stimuli-Responsive Three-Dimensional DNA Nanomachines Engineered by Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces

Stimuli-responsive nanomachines are attractive tools for biosensing, imaging, and drug delivery. Herein, we demonstrate that the orientation of macromolecules and subsequent dynamic interactions at the biomolecule-nanoparticle (bio-nano) interfaces can be rationally controlled to engineer stimuli-responsive DNA nanomachines. The success of this design principle was demonstrated by engineering a series of antibody-responsive DNA walkers capable of moving persistently on a three-dimensional track made of DNA functionalized gold nanoparticles. We show that drastically different responses to antibodies could be achieved using DNA walkers of identical sequences but with varying number or sites of modifications. We also show that multiple interfacial factors could be combined to engineer stimuli-responsive DNA nanomachines with high sensitivity and modularity. The potential of our strategy for practical uses was finally demonstrated for the amplified detection of antibodies and small molecules in both buffer and human serum samples. Unlike many DNA-based nanomachines, the performance of which could be significantly hindered by the matrix of serum, our system shows a matrix-enhanced sensitivity as a result of the engineering approach at the bio-nano interface.

DNAzyme Walker for Homogeneous Detection of Enterovirus EV71 and CVB3

When dealing with infectious pathogens, the risk of contamination or infection in the process of detecting them is nonnegligible. Separation-free detection will be beneficial in operation and safety. In this work, we proposed a DNAzyme walker for homogeneous and isothermal detection of enterovirus. The DNAzyme is divided into two inactivate subunits. When the subunit-conjugated antibody binds to the target virus, the activity of the DNAzyme recovers as a result of spatial proximity. The walker propels, and the fluorescence recovers. The final fluorescence intensity of the reaction mixture is related to the concentration of the target virus. The detection limit of this proposed method is 6.6 × 10⁴ copies/mL for EV71 and 4.3 × 10⁴ copies/mL for CVB3, respectively. Besides, this method was applied in detection of EV71 in clinical samples with a satisfactory result. The entire experiment is easy to operate, and the proposed method has great potential for practical use.

Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices

Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.

An interparticle relatively motional DNA walker and its sensing application

DNA molecular machines are DNA self-assemblies that perform quasi-mechanical movement at the micro-nano scale, and have attracted increasing attention in the fields of biosensing, drug delivery and biocomputing. Herein, we report the concept and operation of an interparticle relatively motional DNA walker. The walker is composed of walking particles (WPs) and track particles (TPs). The WPs and TPs are obtained by respective functionalization of locked walking strands containing DNAzyme sequences and fluorophore-labelled track strands containing substrate sequences onto gold nanoparticles (AuNPs). Triggered by the target that specifically unlocks the walking strand, the liberated walking strands cooperatively hybridize with the track strands. The track strand gets cleaved by the DNAzyme, accompanied by the fluorophore release. The adjacent walking strand on the WP subsequently hybridizes to the next track strand, inducing the relative motion of the WP around the TP. After walking along the surface of one TP, the WP can continue to interact with another TP. As a result of the improved moving freedom and area, the interparticle motional mode induces high continuity and achieves large signal accumulation. Taking Zika virus RNA fragments (ZIKV-RNA) as a model target, the DNA walker shows a high sensitivity with a detection limit of 118 pM, and can reliably detect the target in biological fluids due to the stability of its components. The constructed DNA walker provides a new type of free and robust motion mode between particles and holds potential in clinical diagnosis.

Integrated individually electrochemical array for simultaneously detecting multiple Alzheimer's biomarkers

Simultaneous detection of multiple biomarkers is benefit for reducing the detection cycles, avoiding the false-positive signals, and providing the cross validation, which provide the opportunity to understand the pathogenic mechanisms and achieve precise early diagnosis. Here, we demonstrate the mini-pillar-based individual electrochemical array for simultaneous detection of multiple biomarkers. On such platform, the mini-pillar could confine the microdroplet as individual and open-channel microreactor, which is extremely helpful for reducing reagent consumption and extracting internal information, and the electrodes array embedded in mini-pillar are integrated on one side to achieve multiple and simultaneous electrochemical sensing. The introduction of gold nanodendrites by electrodeposition has greatly enhanced sensitivity via improving probe-binding capacity and response signals. Sensitive and selective detection of multiple Alzheimer's biomarkers including Tau, ApoE4, Amyloid-β and miRNA-101 on such mini-pillar-based biosensor is also achieved. Such biosensor platform with the advantages of high-yield, high sensitivity, low-waste and multiple signals output shows great promise in sensing multiple biomolecules for disease diagnosis and health monitoring.

An anchored monopodial DNA walker triggered by proximity hybridization for amplified amperometric biosensing of nucleic acid and protein

This work designed an anchored monopodial DNA walker to amplify amperometric biosensing signal for sensitive detection of nucleic acid and protein. The biosensing surface was constructed by self-assembling hairpin DNA1 (H1) and small amount of P1-W (probe DNA1 hybridized with walking DNA) on a gold electrode. In the presence of target molecule, the walker could be triggered by the surface proximity hybridization product of P1, target and P2 to induce the cyclic hybridization of H1 with ferrocene modified hairpin DNA2 (H2-Fc), which took electroactive Fc to the electrode surface for amplified amperometric detection of the target. By linking P1 and P2 with dual specific DNA strands, aptamers or antibodies to recognize the target for proximity hybridization of P1 and P2, the walker amplified amperometric strategy could be used for highly sensitive biosensing of different targets. Using DNA and thrombin as the target models, the proposed biosensing methods achieved the linear range from 0.2 pM to 2 nM with a detection limit of 0.11 pM and 1.0 pM to 10 nM with a detection limit of 0.61 pM, respectively. The specific recognition process endowed the strategy with high selectivity and potential applications.

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.

Binding-Induced 3D-Bipedal DNA Walker for Cascade Signal Amplification Detection of Thrombin Combined with Catalytic Hairpin Assembly Strategy

As an important biomarker, thrombin (TB) is a major player in thrombosis and hemostasis and has attracted increasing attention involving its determination. Herein a universal and ultrasensitive fluorescence biosensor based on a binding-induced 3D-bipedal DNA walker and catalytic hairpin assembly (CHA) strategy has been proposed for cascade signal amplification detection of thrombin. In this study, we designed two proximity probes (foot 1 and foot 2) which include a specific affinity ligand for TB binding and a Pb²⁺-dependent DNAzyme tail sequence. In the presence of TB, the simultaneous binding of TB to foot 1 (F1) and foot 2 (F2) via TB aptamer (TBA) brings the tail sequences into close proximity and the melting temperature for tail sequences and track DNA is increased, allowing the Pb²⁺-dependent DNAzyme to cleave the track DNA into two short fragments which have lower affinities for the DNAzyme and, finally, leading to the release of trigger DNA (T-DNA) for subsequent CHA reaction. In the meantime, the dissociated DNA walkers (F1 and F2) explore adjacent unwound track DNA, and the walking procedure is conducted. Unlike the conventional unipedal DNA walkers that anchor foot DNA and track DNA on the same sensing surface, the proposed 3D-bipedal DNA walking machine can not only increase the local concentration of track DNA but can also improve the walking efficiency and expand the range of the walkers to some extent due to the two free feet. Moreover, with the advantages of superior sensitivity and excellent specificity, this biosensing platform exhibits a huge potential in practical application in biomedical research and clinical diagnosis.

An enzyme-free and label-free signal-on aptasensor based on DNAzyme-driven DNA walker strategy

Herein, a signal-on electrochemical aptasensor for highly sensitive detection of thrombin (TB) was constructed based on the DNAzyme-driven DNA walker strategy. We developed a new dual functional hairpin DNA (HP) containing a substrate sequence of the Mg²⁺-dependent DNAzyme (in the loop region) and the G-quadruplex forming segment (in the stem region). The DNA walker (TBA₂-DWs), containing a TB aptamer and an enzymatic sequence, was introduced onto gold electrode (GE) by aptamers-target specific recognition, and thus initiated the enzymatic sequences to hybridize with the substrate sequence. Then, the DNA walker could repeatedly bind and cleave HP in the assistance of Mg²⁺, unlocking many active G-quadruplex forming sequences. Finally, hemin can further bind the G-quadruplex to form G-quadruplex/hemin complexes and generate enhanced current output. The aptasensor for TB assay showed a linear detection range from 1 pM to 60000 pM with a lower detection limit of 0.58 pM. And more, the proposed detection strategy was enzyme-free and label-free.

A simple and sensitive electrochemiluminescence aptasensor for determination of ochratoxin A based on a nicking endonuclease-powered DNA walking machine

Ochratoxin A (OTA) poses a serious threat to the health of human beings and animals. In this paper, a simple and sensitive electrochemiluminescence (ECL) aptasensor was constructed to detect OTA based on electrochemiluminescence resonance energy transfer (ECL-RET) and a nicking endonuclease-powered DNA walking machine. Originally, the signal of cadmium sulfide semiconductor quantum dots (CdS QDs) was quenched efficiently by Cy5. After the addition of OTA, the walker autonomously hybridized with Cy5-labeled DNA and released plenty of Cy5-DNA from the electrode surface with the help of a nicking endonuclease. As a result, the signal of CdS QDs recovered efficiently. As an artificial and popular signal amplification technique, the DNA walking machine greatly improved the sensitivity. Under optimal conditions, the aptasensor not only detected OTA in a linear range from 0.05 nM to 5 nM with a detection limit of 0.012 nM (S/N = 3), but also showed an excellent selectivity for OTA over other mycotoxins.

Silver-ion-mediated Mg2+-dependent DNAzyme activity for amplified fluorescence detection of cysteine

Schematic illustration of a DNAzyme-based fluorescent biosensor for amplified Cys detection.

A rolling circle amplification-assisted DNA walker triggered by multiple DNAzyme cores for highly sensitive electrochemical biosensing

A DNA walker triggered by multiple DNAzyme cores was constructed with the assistance of rolling circle amplification for electrochemical biosensing.

A reusable electrochemical sensor for one-step biosensing in complex media using triplex-forming oligonucleotide coupled DNA nanostructure

Here we report an electrochemical DNA (E-DNA) sensor to detect a variety of analytes by using a novel interfacial probe that rationally integrates triplex-forming oligonucleotide (TFO) into a tetrahedral DNA nanostructure (TDN). In the presence of analyte, the blocked TFO is released and subsequently binds the edge of TDN to form a triplex DNA structure, which confines the redox reporter to be in close proximity to the underlying electrode and enhances the electrochemical signal. Thanks to the unique design and property of the probe, the proposed sensor could efficiently suppress the background signal (from 0.69 μA to 0.092 μA) and thus enhance the signal-to-noise ratio, resulting in improved sensing performance. Furthermore, the sensor displays new merits such as rapid response (∼35 min), one-step operation, easy regeneration (buffer change) and good generality (changing recognition element) compared with traditional TDN-based E-DNA sensor using enzyme displays signal transducer. In addition, to demonstrate real-world applicability of this new sensor, we have successfully detected different analytes (e.g., DNA, protein, and metal ion) in the complex media (e.g., serum, blood, and lake water), implying its considerable potential for precise bioanalysis in the future.

Design of a stretchable DNAzyme for sensitive and multiplexed detection of antibodies

Advanced methods for developing and applying responsive DNA nanodevices are of great interest. Herein, we report a stretchable DNAzyme that allows simple, multiplexed and sensitive fluorescent detection of antibodies. We find that rigid antibody can tightly stretch soft, antigen-labelled DNAzyme strand and disrupt the hybridization between DNAzyme and its substrate. Based on this finding, we develop a novel strategy to detect antibodies. Due to the robustness and high activity of DNAzyme, this assay can easily detect target as low as 1 ± 0.25 pM and achieve multiplexed detection by using a cocktail of DNAzymes. The proposed assay not only provides a new approach to readily measure antibody, but broadens the application of DNAzyme that is usually employed to detect metal ions or indirectly analyze biomolecules without the cumbersome design.

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

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

Molecular Machine Powered Surface Programmatic Chain Reaction for Highly Sensitive Electrochemical Detection of Protein

A bipedal molecular machine powered surface programmatic chain reaction was designed for electrochemical signal amplification and highly sensitive electrochemical detection of protein. The bipedal molecular machine was built through aptamer-target specific recognition for the binding of one target protein with two DNA probes, which hybridized with surface-tethered hairpin DNA 1 (H1) via proximity effect to expose the prelocked toehold domain of H1 for the hybridization of ferrocene-labeled hairpin DNA 2 (H2-Fc). The toehold-mediated strand displacement reaction brought the electrochemical signal molecule Fc close to the electrode and meanwhile released the bipedal molecular machine to traverse the sensing surface by the surface programmatic chain reaction. Eventually, a large number of duplex structures of H1-H2 with ferrocene groups facing to the electrode were formed on the sensor surface to generate an amplified electrochemical signal. Using thrombin as a model target, this method showed a linear detection range from 2 pM to 20 nM with a detection limit of 0.76 pM. The proposed detection strategy was enzyme-free and allowed highly sensitive and selective detection of a variety of protein targets by using corresponding DNA-based affinity probes, showing potential application in bioanalysis.

Design of DNA nanostructure-based interfacial probes for the electrochemical detection of nucleic acids directly in whole blood

Here we report a robust and sensitive DNA nanostructure-based electrochemical (E-nanoDNA) sensor that utilizes tetrahedral DNA nanostructures (TDNs) as an interfacial probe to detect biomolecules in a single-step procedure. In this study, we have firstly demonstrated that the use of TDNs can significantly suppress electrochemical background signals compared to traditional linear DNA probes upon introduction of base mismatches in the edges of TDNs. After further optimization of the two functional strands in the TDNs, quantitative, one-step detection of DNA can be achieved in the picomolar range in less than 10 min, and directly in complex media. Moreover, the baseline drift of this biosensor can be greatly decreased even after several hours in flowing whole blood in vitro, which suggests that the sensor holds potential to be employed in live animals. Furthermore, through replacing functional strands with aptamers or other DNA elements, this E-nanoDNA sensor can be easily used to probe various analytes, broadening the application range of the proposed sensor.

Allosteric kissing complex-based electrochemical biosensor for sensitive, regenerative and versatile detection of proteins

Herein, an allosteric kissing complex-based electrochemical biosensor was ingeniously proposed for the simple, sensitive, regenerative and versatile detection of proteins. Two hairpins (Hp1 and Hp2) were designed and the Hp1 was immobilized on the electrode surface, which could form a kissing complex with Hp2 through the apical loop-loop or kissing interaction of the RNA-RNA base sequences. The Hp2 possesses the appended single-stranded tails on each end, which hybridize with the recognition element-conjugated DNA strands to construct a protein responsive switch of Hp2 scaffold. After kissing complex formation between the Hp2 scaffold and the immobilized Hp1, the streptavidin-labeled alkaline phosphatase (SA-ALP) can be introduced onto the electrode surface for the generation of electrochemical signal. In the presence of target protein, its binding to the recognition elements linked onto the Hp2 scaffold endows the steric strain to open the Hp2 stem, propagated by the disruption of the kissing complex structure, resulting into a decreased electrochemical signal related with the protein quantification. Also, the Hp1 immobilized electrode can be directly regenerated after protein-induced kissing complex dissociation. The current kissing complex-based electrochemical biosensing strategy can be easily extended for the detection toward different protein targets of interest by simply changing the recognition elements conjugated onto the Hp2 scaffold. The sensitive and selective detection toward proteins could be achieved with the detection limits toward Anti-Dig antibody and thrombin of about 1ng/mL and 10pM, respectively. The developed kissing complex-based protein biosensing strategy should be a beneficial supplement in current biosensor field, providing a promising means for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.

A gold nanoparticle-based four-color proximity immunoassay for one-step, multiplexed detection of protein biomarkers using ribonuclease H signal amplification

A gold nanoparticle-based four-color fluorescence proximity immunoassay was developed for multiplexed analysis of protein biomarkers using ribonuclease H signal amplification.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Binding-induced DNA walker for signal amplification in highly selective electrochemical detection of protein

A binding-induced DNA walker-assisted signal amplification was developed for highly selective electrochemical detection of protein. Firstly, the track of DNA walker was constructed by self-assembly of the high density ferrocene (Fc)-labeled anchor DNA and aptamer 1 on the gold electrode surface. Sequentially, a long swing-arm chain containing aptamer 2 and walking strand DNA was introduced onto gold electrode through aptamers-target specific recognition, and thus initiated walker strand sequences to hybridize with anchor DNA. Then, the DNA walker was activated by the stepwise cleavage of the hybridized anchor DNA by nicking endonuclease to release multiple Fc molecules for signal amplification. Taking thrombin as the model target, the Fc-generated electrochemical signal decreased linearly with logarithm value of thrombin concentration ranging from 10pM to 100nM with a detection limit of 2.5pM under the optimal conditions. By integrating the specific recognition of aptamers to target with the enzymatic cleavage of nicking endonuclease, the aptasensor showed the high selectivity. The binding-induced DNA walker provides a promising strategy for signal amplification in electrochemical biosensor, and has the extensive applications in sensitive and selective detection of the various targets.

Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin

The development of convenient and sensitive methods without involving any enzymes or complex nanomaterials for the monitoring of proteins is of great significance in disease diagnostics. In this work, we describe the validation of a new aptamer/protein proximity binding-triggered molecular machinery amplification strategy for sensitive electrochemical assay of thrombin in complex serum samples. The sensing interface is prepared by self-assembly of three-stranded DNA complexes on the gold electrode. The association of two distinct functional aptamers with different sites of thrombin triggers proximity binding-induced displacement of one of the short single-stranded DNAs (ssDNAs) from the surface-immobilized three-stranded DNA complexes, exposing a prelocked toehold domain to hybridize with a methylene blue (MB)-tagged fuel ssDNA strand (MB-DNA). Subsequent toehold-mediated strand displacement by the MB-DNA leads to the release and recycling of the aptamer/protein complexes and the function of the molecular machine. Eventually, a large number of MB-DNA strands are captured by the sensor surface, generating drastically amplified electrochemical responses from the MB tags for sensitive detection of thrombin. Our signal amplified sensor is completely enzyme-free and shows a dynamic range from 5 pM to 1 nM with a detection limit of 1.7 pM. Such sensor also has a high specificity for thrombin assay in serum samples. By changing the affinity probe pairs, the developed sensor can be readily expanded as a more general platform for sensitive detection of different types of proteins.

Dynamic sandwich-type electrochemical assay for protein quantification and protein–protein interaction

A versatile and sensitive electrochemical method for protein–protein interaction study based on DNAzyme has been proposed.

Proximity ligation-induced assembly of DNAzymes for simple and cost-effective colourimetric detection of proteins with high sensitivity

A novel colourimetric method for protein assays is proposed based on proximity ligation induced assembly of Mg(2+)-dependent DNAzymes, which may offer simple, cost-effective, sensitive and selective detection of the target protein.

Colorimetric detection of proteins based on target-induced activation of aptazyme

The detection of protein is vital to fundamental research as well as practical applications. However, most detection methods depend on antibody-based assays which are faced with many shortcomings. Herein, we propose a colorimetric method for protein assays based on target-triggered activation of aptazyme, which may offer simple, rapid and cost-effective detection of the target protein. In this method, the conformation change of aptazyme induced by target protein is designed to be associated with aptazyme activation. Consequently, in the presence of the target protein, the designed DNA linkers will be cleaved into two fragments that fail to cross-link gold nanoparticles (GNPs), thus the color of GNP solution remains red, while the color will be changed in the absence of the target. Because of the advantages of aptazyme such as economic synthesis, stable, easy modification and its ability to accomplish signal recognition and signal amplification simultaneously, the method is thermostable, simple and cost-efficient. In this work, we have taken the detection of vascular endothelial growth factor (VEGF) as an example, which can present an analytical performance with as low as 0.1 nM detection limit, spanning a detection range of 3 orders of magnitude. What is more, the principle of this proposed new method can be extended as a universal assay method not only for the detection of analytes which have an aptamer but also for those analytes that have ligands.

Sensitive Bioanalysis Based on in-Situ Droplet Anodic Stripping Voltammetric Detection of CdS Quantum Dots Label after Enhanced Cathodic Preconcentration

We report a protocol of CdS-labeled sandwich-type amperometric bioanalysis with high sensitivity, on the basis of simultaneous chemical-dissolution/cathodic-enrichment of the CdS quantum dot biolabel and anodic stripping voltammetry (ASV) detection of Cd directly on the bioelectrode. We added a microliter droplet of 0.1 M aqueous HNO₃ to dissolve CdS on the bioelectrode and simultaneously achieved the potentiostatic cathodic preconcentration of Cd by starting the potentiostatic operation before HNO₃ addition, which can largely increase the ASV signal. Our protocol was used for immunoanalysis and aptamer-based bioanalysis of several proteins, giving limits of detection of 4.5 fg·mL⁻¹ for human immunoglobulin G, 3.0 fg·mL⁻¹ for human carcinoembryonic antigen (CEA), 4.9 fg·mL⁻¹ for human α-fetoprotein (AFP), and 0.9 fM for thrombin, which are better than many reported results. The simultaneous and sensitive analysis of CEA and AFP at two screen-printed carbon electrodes was also conducted by our protocol.

A signal amplification electrochemical aptasensor for the detection of breast cancer cell via free-running DNA walker

Herein, a signal magnification electrochemical aptasensor for the detection of breast cancer cell via free-running DNA walker is constructed. Theoretically, just one DNA walker, released by target cell-responsive reaction, can automatically cleave all D-RNA (a chimeric DNA/RNA oligonucleotide with a cleavage point rArU) anchored on electrode into shorter produces, giving rise to considerably detectable signal finally. Under the optimal conditions, the electrochemical signal decreased linearly with the concentration of MCF-7 cell. The linear range is from 0 to 500 cells mL(-1) with a detection limit of 47 cellsmL(-1). In a word, this approach may have advantages over traditional reported DNA machines for bioassay, particularly in terms of ease of operation, cost efficiency, free of labeling and of complex track design, which may hold great potential for wide application.

Emerging techniques for ultrasensitive protein analysis

Many important biomarkers for devastating diseases and biochemical processes are proteins present at ultralow levels. Traditional techniques, such as enzyme-linked immunosorbent assays (ELISA), mass spectrometry, and protein microarrays, are often not sensitive enough to detect proteins with concentrations below the picomolar level, thus requiring the development of analytical techniques with ultrahigh sensitivities. In this review, we highlight the recent advances in developing novel techniques, sensors, and assays for ultrasensitive protein analysis. Particular attention will be focused on three classes of signal generation and/or amplification mechanisms, including the uses of nanomaterials, nucleic acids, and digital platforms.