Assembly of multiple DNA components through target binding toward homogeneous, isothermally amplified, and specific detection of proteins

Proximity hybridization induced bipedal DNA walker for label-free electrochemical detection of apolipoprotein A4 based on DNA meditated Ag nanoparticles growth

Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. Here, we propose a neighboring hybridization induced catalyzed hairpin assembly (CHA) driven bipedal DNA walker that mediates hybridization of Ag nanoparticles (Ag NPs) with DNA probes for highly sensitive electrochemical quantitative detection of Apo-A4. Driven by CHA, this bipedal DNA walker can spread all over the surface of the sensor, induce the HP1-HP2 double chain structure, make the surface of the sensor negatively charged, and adsorb a large number of Ag ions. After chemical reduction with hydroquinone, the Ag NPs formed provide signal tracers for electrochemical dissolution analysis of the target. The Ag NPs formed by chemical reduction of hydroquinone can provide signal traces for electrochemical stripping analysis of target thrombin. The linear range of this method is from 10 pg mL-1 to 1000 ng mL-1, and the detection limit is 5.1 pg mL-1. This enzyme-free and labeling detection method provides a new strategy for rapid clinical detection of Apo-A4 and accurate identification of depression.

Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates

As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.

Label-free electrochemical homogeneous detection of the depression marker human apolipoprotein A4 based on proximity hybridization triggered rolling circle amplification

In this paper, we developed a label-free homogeneous electrochemical sensor for detection of apolipoprotein A4 based on proximity hybridization triggered rolling circle amplification induced G-quadruplex formation. The presence of apolipoprotein A4 promoted the formation of a proximate 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 RCA 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 apolipoprotein A4. Thus, using this "signal-off" mode, label-free homogeneous electrochemical strategy for sensitive apolipoprotein A4 assay with a wide range from 1 pg mL^-1 to 100 ng mL^-1, with a low detection limit of 0.51 pg mL^-1. And it rendered satisfactory analytical performance for the determination of apolipoprotein A4 in serum samples. Furthermore, this method also exhibits additional advantages of simplicity and low cost, since both expensive labeling and sophisticated probe immobilization processes are avoided. The satisfactory results indicated that the proposed sensor had promising potential in the clinical diagnosis of depression.

Dynamically elongated associative toehold for tuning DNA circuit kinetics and thermodynamics

Associative toehold is a powerful concept enabling efficient combinatorial computation in DNA circuit. A longer association length boosts circuit kinetics and equilibrium signal but results in higher leak rate. We reconcile this trade-off by using a hairpin lock design to dynamically elongate the effective associative toehold length in response to the input target. Design guidelines were established to achieve robust elongation without incurring additional leakages. Three hairpin initiators with different combinations of elongated associative toehold (4 → 6 nt, 5 → 8 nt and 6 → 9 nt) were shortlisted from the design framework for further discussion. The circuit performance improved in terms of reaction kinetics, equilibrium signal generated and limit of detection. Overall, the elongated associative toehold served as a built-in function to stabilize and favour the forward, desired reaction when triggered.

Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement

The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.

Proximity hybridization triggered rolling-circle amplification for sensitive electrochemical homogeneous immunoassay

A new homogeneous electrochemical immunoassay strategy was developed for ultrasensitive detection of carcinoembryonic antigen (CEA) based on target-induced proximity hybridization coupled with rolling circle amplification (RCA). The immobilization-free detection of CEA was realized by the use of an uncharged peptide nucleic acid (PNA) probe labeled with ferrocene (Fc) as the electroactive indicator on a negatively charged indium tin oxide (ITO) electrode. In the presence of a target protein and two DNA-labeled antibodies, the proximate complex formed in homogeneous solution could unfold the molecular beacon, and a part of the unfolded molecular beacon as a primer hybridized with the RCA template to initiate the RCA process. Subsequently, the detection probe modified Fc (Fc-PNAs) hybridized with the long amplified DNA products. The consumption of freely diffusible Fc-PNAs (neutrally charged) resulted in a significant reduction of the Fc signal due to the fact that long amplified DNA/Fc-PNA products were electrostatically repelled from the ITO electrode surface. The reduction of the electrochemical signal (signal-off) could indirectly provide the CEA concentration. Under the optimal conditions, CEA detection was implemented in a wide range from 1 pg mL^-1 to 10 ng mL^-1, with a low detection limit of 0.49 pg mL^-1. The proposed strategy exhibited advantages of good selectivity, high sensitivity, acceptable accuracy, and favorable versatility of analytes. Moreover, the practical application value of the system was confirmed by the assay of CEA in human serums with satisfactory results.

Competitive horseradish peroxidase-linked aptamer assay for sensitive detection of Aflatoxin B1

Aflatoxin B1 (AFB1) is one of highly toxic mycotoxins and a known human carcinogen. The frequent contamination of AFB1 in food products and large health risk of AFB1 have raised global concerns. Sensitive detection of AFB1 is of vital importance and highly demanded. Herein, we reported a competitive horseradish peroxidase (HRP)-linked aptamer assay for AFB1, combining the advantages of aptamer for affinity binding and enzyme label for signal amplification. In this assay, free AFB1 in solution competed with a covalent conjugate of bovine serum albumin-AFB1 (BSA-AFB1) coated on the wells of microplate in binding to the HRP-labeled aptamer probe. HRP attached on BSA-AFB1 in the wells catalyzed the conversion of substrates into products, allowing the final detection of AFB1 through measurement of the generated products. When TMB (3,3',5,5'-tetramethylbenzidine dihydrochloride) was used as substrate, absorbance analysis of the product of enzyme reaction enabled the detection of AFB1 at 0.2nM. We further lowered the detection limit of AFB1 to 0.01nM through chemiluminescence analysis by using chemiluminescence substrate of HRP. This assay enabled the detection of AFB1 in complex sample matrix, such as diluted white wine and maize flour. This assay provides a simple, sensitive and rapid method for AFB1 determination.

A Target-Triggered DNAzyme Motor Enabling Homogeneous, Amplified Detection of Proteins

We report here the concept of a self-powered, target-triggered DNA motor constructed by engineering a DNAzyme to adapt into binding-induced DNA assembly. An affinity ligand was attached to the DNAzyme motor via a DNA spacer, and a second affinity ligand was conjugated to the gold nanoparticle (AuNP) that was also decorated with hundreds of substrate strands serving as a high-density, three-dimensional track for the DNAzyme motor. Binding of a target molecule to the two ligands induced hybridization between the DNAzyme and its substrate on the AuNP, which are otherwise unable to spontaneously hybridize. The hybridization of DNAzyme with the substrate initiates the cleavage of the substrate and the autonomous movement of the DNAzyme along the AuNP. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of the DNAzyme motor in real time. A simple addition or depletion of the cofactor Mg²⁺ allows for fine control of the DNAzyme motor. The motor can translate a single binding event into cleavage of hundreds of substrates, enabling amplified detection of proteins at room temperature without the need for separation.

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.

Highly sensitive chemiluminescence biosensor for protein detection based on the functionalized magnetic microparticles and the hybridization chain reaction

An ultrasensitive chemiluminescence (CL) biosensor for the detection of protein is developed in this study based on the functionalized magnetic microparticles (MMPs) and the hybridization chain reaction (HCR). First, the primer hybridized with the thrombin aptamer conjugated on the surface of MMPs. Then the HCR was triggered by part of the primer and its products were assembled on the surface of the MMPs. Through the interaction between streptavidin and biotin, the streptavidin-horseradish peroxidase (SA-HRP) was coupled with the HCR products. In the presence of thrombin, the HCR products conjugating with SA-HRP were released from the surface of MMPs after the aptamer recognized and bound to its target molecule. So the released SA-HRP in the supernatant produced a significant chemiluminescence imaging signal after the addition of H₂O₂-luminol. The detection limit of thrombin with this method could be as low as 9.7fM. Besides, the sensing strategy was modified by changing the adding order of reagents that was then successfully applied in the detection of thrombin in complex sample. What's more, the DNA detection also could be carried out with this method, which demonstrated the universality of the proposed sensing strategy.

Thrombin-linked aptamer assay for detection of platelet derived growth factor BB on magnetic beads in a sandwich format

Here we describe a thrombin-linked aptamer assay (TLAA) for protein by using thrombin as an enzyme label, harnessing enzyme activity of thrombin and aptamer affinity binding. TLAA converts detection of specific target proteins to the detection of thrombin by using a DNA sequence that consists of two aptamers with the first aptamer binding to the specific target protein and the second aptamer binding to thrombin. Through the affinity binding, the thrombin enzyme is labeled on the protein target, and thrombin catalyzes the hydrolysis of small peptide substrate into product, generating signals for quantification. As a proof of principle, we show a sandwich TLAA for platelet derived growth factor BB (PDGF-BB) by using anti-PDGF-BB antibody coated on magnetic beads and an oligonucleotide containing the aptamer for PDGF-BB and the aptamer for thrombin. The binding of PDGF-BB to both the antibody and the aptamer results in labeling the complex with thrombin. We achieved detection of PDGF-BB at 16 pM. This TLAA contributes a new application of thrombin and its aptamer in bioanalysis, and shows potentials in assay developments.

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.

Amplified binding-induced homogeneous assay through catalytic cycling of analyte for ultrasensitive protein detection

Amplified binding-induced homogeneous assay through catalytic cycling of analytes for ultrasensitive protein detection.

Constructing real-time, wash-free, and reiterative sensors for cell surface proteins using binding-induced dynamic DNA assembly

Cell surface proteins are an important class of biomarkers for fundamental biological research and for disease diagnostics and treatment. In this communication, we report a universal strategy to construct sensors that can achieve rapid imaging of cell surface proteins without any separation by using binding-induced dynamic DNA assembly. As a proof-of-principle, we developed a real-time and wash-free sensor for an important breast cancer biomarker, human epidermal growth factor receptor-2 (HER2). We then demonstrated that this sensor could be used for imaging and sensing HER2 on both fixed and live breast cancer cells. Additionally, we have also incorporated toehold-mediated DNA strand displacement reactions into the HER2 sensor, which allows for reiterating (switching on/off) fluorescence signals for HER2 from breast cancer cells in real-time.

A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA

A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.