Aptamer proximity recognition-dependent strand translocation for enzyme-free and amplified fluorescent detection of thrombin via catalytic hairpin assembly

Highly efficient photoelectrochemical aptasensor based on CdS/CdTe QDs co-sensitized TiO2 nanoparticles designed for thrombin detection

A photoelectrochemical (PEC) sensor for the sensitive detection of thrombin (TB) was established. Co-sensitized combination of TiO2 nanoparticles combined with modified cadmium sulfide and cadmium telluride quantum dots (CdS/CdTe QDs) was utilized as a photoactive material. Successful growth of CdS/CdTe quantum dots on mesoporous TiO2 films occured by successive ion-layer adsorption and reaction. This interesting formation of co-sensitive structure is conducive to enhancing the photocurrent response by improving the use rate of light energy. Additionally, the step-level structure of CdS/CdTe QDs and TiO2 NPs shows a wide range of visible light absorption, facilitating the dissociation of excitons into free electrons and holes. Consequently, the photoelectric response of the PEC analysis platform is significantly enhanced. This constructed PEC aptasensor shows good detection of thrombin with a low detection limit (0.033 pM) and a wide linear range (0.0001-100 nM) in diluted actual human serum samples. In addition, this PEC aptasensor also has the characteristics of good stability and good reproducibility, which provides a novel insight for the quantitative measurement of other similar analytes.

Homogeneous protein assays mediated by dynamic DNA nanotechnology

Driven by recent advances in DNA nanotechnology, analytical methods have been greatly improved for designing simple and homogeneous assays for proteins. The translation from target proteins to DNA outputs dramatically enhances the sensitivity of protein assays. More importantly, the protein-responsive DNA nanotechnology has offered diverse assay mechanisms, allowing flexible assay designs and high sensitivity without the need for sophisticated operational procedures. This review will focus on the design principles and mechanistic insight of analytical assays mediated by protein-responsive DNA nanotechnology, which will serve a general guide for assay design and applications.

Aptamer-Based Sensors for Thrombin Detection Application

Thrombin facilitates the aggregation of platelet in hemostatic processes and participates in the regulation of cell signaling. Therefore, the development of thrombin sensors is conducive to comprehending the role of thrombin in the course of a disease. Biosensors based on aptamers screened by SELEX have exhibited superiority for thrombin detection. In this review, we summarized the aptamer-based sensors for thrombin detection which rely on the specific recognitions between thrombin and aptamer. Meanwhile, the unique advantages of different sensors including optical and electrochemical sensors were also highlighted. Especially, these sensors based on electrochemistry have the potential to be miniaturized, and thus have gained comprehensive attention. Furthermore, concerns about aptamer-based sensors for thrombin detection, prospects of the future and promising avenues in this field were also presented.

Construction and bioapplications of aptamer-based dual recognition strategy

Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2ⁿ. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.

Target-Catalyzed Assembly of Pyrene-Labeled Hairpins for Exponentially Amplified Biosensing

Rapid and sensitive detection of nucleic acids is vital for disease diagnosis. This work designed an enzyme-free isothermal strategy for rapid exponential signal amplification through target-triggered catalytic hairpin assembly (CHA) to induce the spatially sensitive fluorescent signal of the pyrene excimer. Functionally, this system consisted of three pyrene labelled hairpins (H1, H2, and H3) and one catalyst DNA C. In the presence of C, the CHA was activated to generate intermediate I, which contained a single-stranded region identical to the C sequence for initiating the second cycle of CHA to obtain 2I and thus achieved the exponential formation of I along with the switching of pyrene excimer. The fluorescent signal of the pyrene excimer could be further enhanced via the inclusion of γ-cyclodextrin and showed a linear increase upon increasing logarithm of C concentration. Through the introduction of a helping hairpin H4-containing C sequence and a region specific to the target, this strategy could be extended to realize the quick and sensitive detection of different analytes. Using dengue virus RNA as an analyte model, the proposed fluorescent method showed a linear range from 0.1 to 50 nM with a limit of detection of 0.048 nM at 3σ and good selectivity. The excellent performance and convenient operation demonstrated its promising application in clinical disease diagnosis.

A Rapid and Ultrasensitive Thrombin Biosensor Based on a Rationally Designed Trifunctional Protein

Rapid and sensitive detection of thrombin is imperative for the early diagnosis, prevention, and treatment of thrombin-related diseases. Here, an ultrasensitive and rapid thrombin biosensor is developed based on rationally designed trifunctional protein HTs, comprising three functional units, including a far-red fluorescent protein smURFP, hydrophobin HGFI, and a thrombin cleavage site (TCS). smURFP is used as a detection signal to eliminate any interference from the autofluorescence of sample matrix to increase detection sensitivity. HGFI serve as an adhesive unit to allow rapid immobilization of HTs on a multiwall plate. The TCS linking HGFI and smURFP function as a sensing element to recognize and detect thrombin. HTs immobilization is symmetrically optimized and characterized. Thrombin assay reveals the specific recognition of active thrombin in samples and the hydrolysis of the immobilized HTs, resulting in a decrease in the fluorescence intensity of the sample in a thrombin concentration-dependent manner. The limit of detection (LOD) is as low as 0.2 am in the serum. To the authors' knowledge, this is the lowest LOD ever reported for any thrombin biosensor. This study sheds light on the engineering of multifunctional proteins for biosensing.

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.

Polymerization nicking-triggered LAMP cascades enable exceptional signal amplification for aptamer-based label-free detection of trace proteins in human serum

Detecting molecular biomarkers in high sensitivity plays an important role in the diagnosis of various diseases at the early stage. Here, by combining the target-induced polymerization nicking reaction (TIPNR) with the loop-mediated isothermal amplification (LAMP), we describe an ultrasensitive and label-free aptamer-based sensing method for detecting low levels of proteins in human serum by using thrombin as the model target analyte. The target thrombin binds and causes spontaneous assembly of two distinct aptamer probes to form the templates for the polymerization nicking reaction recycling amplification to produce many forward inner primer sequences. Subsequently, downstream LAMP reactions are initiated by these sequences for the generation of tremendous DNA hairpins with various lengths via automated cyclic strand displacement reactions. The SYBR Green I organic dye further binds the many hairpins to show drastically amplified fluorescence for ultrasensitive detection of thrombin down to 3.6 fM in the linear range from 0.01 pM to 10 nM. Such a sensing method based on aptamers has high discrimination capability for the target molecules against other non-specific proteins and is applicable for diluted serum samples. With the successful demonstration of the substantial signal amplification ability and simplicity feature of this assay approach, highly sensitive and convenient detection of other disease biomarkers with this method can be envisioned in the near future.

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.

Aptamer recognition and proximity-induced entropy-driven circuit for enzyme-free and rapid amplified detection of platelet-derived growth factor-BB

Platelet-derived growth factor-BB (PDGF-BB) is currently used as a biomarker protein for cancer early diagnosis and clinical treatment. Herein, we reported a robust and enzyme-free strategy based on aptamer recognition and proximity-induced entropy-driven circuits (AR-PEDC) for homogeneous and rapid detection of platelet-derived growth factor BB (PDGF-BB) without any washing steps or thermocycling. The proximity probes specifically recognize target protein to form the completed trigger (CT). Then, the CT reacts with three-strand complex to form intermediate, which subsequently binds to fuel strand to release reporter strand, assistant strand and the CT. The revised proximity probes exhibit significantly improved signal-to-background ratio and faster association rate. Moreover, target protein/proximity probes interaction can specifically initiate entropy-driven circuits, thus providing immense signal amplification for ultrasensitive detection of PDGF-BB with low detection limit of 9.6 pM. The practical ability of the developed strategy is demonstrated by detection of PDGF-BB in human serum with satisfactory results. In addition, this method is flexible and can be conveniently extended to a variety of targets by simply substituting the target specific sequence. Thus, this strategy presents a rapid, low background and versatile amplification mechanism for the detection of protein biomarkers and offers a promising alternative platform for clinical diagnosis.

C60@C3N4 nanocomposites as quencher for signal-off photoelectrochemical aptasensor with Au nanoparticle decorated perylene tetracarboxylic acid as platform

Herein, a novel signal-off photoelectrochemical (PEC) aptasensor was proposed for sensitive detection of thrombin on the basis of C₆₀@C₃N₄ nanocomposites as quencher and Au nanoparticles (depAu) decorated perylene tetracarboxylic acid (PTCA) as sensing platform. Owing to the excellent membrane-forming of PTCA and superior conductivity of depAu, the PTCA between two depAu layers can simply and effectively produce an extremely high initial photocurrent to afford a precondition for sensitive biodetection. Thereafter, the assembly of C₆₀@C₃N₄ nanocomposites on electrode via typical sandwich reaction enabled the generation of a significantly decreased photocurrent. Here, the C₃N₄ with high surface area not only provided massive binding sites for C₆₀ immobilization, but also partly competed with PTCA in light absorption for producing a significantly smaller photocurrent in the presence of electron donor ascorbic acid (AA). Additionally, both the C₃N₄ and C₆₀ have the poor conductivity, which could inhibit the electron transfer to achieve a further decreased photocurrent, effectively improving the sensitivity of proposed biosensor. As a result, the PEC biosensor in a "signal-off" mode showed an extremely low detection limit down to 1.5 fM, providing a sensitive and universal strategy for protein detection.

Highly stable Ni-MOF comprising triphenylamine moieties as a high-performance redox indicator for sensitive aptasensor construction

Electroactive metal-organic frameworks (MOFs) with large surface area and manipulatable structural properties show promise as a new type of signal probe for electrochemical biosensing application. In this work, an electroactive Ni-MOF, assembled by the redox-active ligands 4,4',4″-Tricarboxytriphenylamine (H₃TCA), a triphenylamine derivatives, as the electroactive source and magnetic ordered Ni₄O₄ clusters as electronic transport nodes, is first designed and applied for electrochemical aptasensing of thrombin (Tb). The designed Ni-MOF probe realizes a stable and sensitive electrochemical signal output based on simple sandwich-type aptasensing because the high-content TCA active sites and good magnetic ordered intermediate of Ni₄O₄ clusters are periodically arranged in well-defined porous structure of the MOF. The Ni-MOF probe assembled by redox-active ligand presents the high stability and can be directly applied in electrochemical aptasensor, avoiding any post-modification and the addition of redox mediators. As a result, the constructed electrochemical aptasensor shows a wide linear relationship for Tb from 0.05 pM to 50 nM and a detection limit of 0.016 pM (S/N = 3). Furthermore, the proposed aptasensor is successfully applied to analysis of target Tb in real serum sample with satisfactory results. The present work indicates that fabricating a redox-active organic molecule in functionalized MOFs offer a feasible strategy to design high-stable electroactive MOFs for construction of electrochemical biosensors with simplicity, high selectivity and sensitivity.