Proximity ligation assay induced and DNAzyme powered DNA motor for fluorescent detection of thrombin

Triblock PolyA-Mediated Protein Biosensor Based on a Size-Matching Proximity Hybridization Analysis

The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.

A novel magneto-mediated electrochemical biosensor integrated DNAzyme motor and hollow nanobox-like Pt@Ni-Co electrocatalyst as dual signal amplifiers for vanilla detection

Herein, a novel magneto-mediated electrochemical aptasensor using the signal amplification technologies of DNAzyme motor and electrocatalyst for vanilla (VAN) detection was fabricated. The D/B duplex, formed by the DNAzyme motor that was each silenced by a blocker, and hairpin DNA1 (H1) containing adenosine ribonucleotide (rA) site were tethered on the sites of the gold nanoparticles@hollow porphyrinic-Metal-organic framework/polyethyleneimine-reduced graphene oxide (AuHPCN-222/PEI-rGO)-modified gold electrode (AuE). Then, after homogeneous and specific recognition in the presence of the VAN, trigger DNA was released and enriched by magnetic separation technique and introduced to the sensing platform to activate the DNAzyme motor, which efficiently improved target recognition capability and avoided the obstacle of multiple DNA strands tangling. More interestingly, the activated DNAzyme motor could repeatedly bind to and cleave H1 in the presence of Mg2+, leading to the exposure of a plethora of capture probes. The thionine (Thi) functionalized hairpin DNA2 (H2)-Pt@Ni-Co as signal probes could hybridize with capture probes. Additionally, the Pt@Ni-Co electrocatalysts presented catalytic activity towards Thi to obtain stronger electrochemical signals. VAN with concentrations ranging from 1 × 10-6 to 10 μM was determined and a detection limit was down to 0.15 pM. The designed electrochemical sensor was highly selective with specificity, stability, reproducibility, and reliable capability for monitoring the VAN in real samples.

Construction and application of thrombin-activated fluorescence-SERS dual-mode optical nanoprobes

Thrombin (TB) plays a key role in the pathological and physiological coagulation of diseases. In this work, a TB-activated fluorescence-surface-enhanced Raman spectroscopy (SERS) dual-mode optical nanoprobe (MRAu) was constructed by linking rhodamine B (RB)-modified magnetic fluorescent nanospheres with AuNPs through TB-specific recognition peptides. In the presence of TB, the polypeptide substrate could specifically be cleaved by TB, resulting in the weakening of SERS hotspot effect and the reduction of Raman signal. Meanwhile, the fluorescence resonance energy transfer (FRET) system was destroyed, and the RB fluorescence signal originally quenched by AuNPs was recovered. Using MRAu, SERS and fluorescence methods were combined to extend the TB detection range to 1-150 pM, and the detection limit was as low as 0.35 pM. In addition, the ability to detect TB in human serum also verified the effectiveness and practicality of the nanoprobe. The probe was also successfully employed to evaluate the inhibitory effect against TB of active components in Panax notoginseng. This study provides a new technical means for the diagnosis and drug development of abnormal TB-related diseases.

AuNPs-DNAzyme motor triggered two colors DNA tweezer for fluorescent amplified detection of bisphenol A

An AuNPs-DNAzyme motor triggered ultrasensitive, two colors DNA tweezer was developed for fluorescent detection of bisphenol A (BPA). BPA can bind with its aptamer on the gold nanoparticles (AuNPs) and reactivate the Pb²⁺ enzyme strands. Thus, Pb²⁺ enzyme strands can cleave the substrate strand on AuNPs and release a DNA fragment from AuNPs. The released DNA fragment can bind with the loop of the Y shaped DNA tweezer to form Mg²⁺-specific DNAzyme, the following cleavage causing the leaving of another two DNA fragments. Then, these two DNA fragments can open the two ends of the Y shaped DNA tweezer, causing the recovery of fluorescent signals. This strategy shows a good linear relationship for BPA detection from 0.44 to 2.2 × 10³ pM. The sensitivity has been significantly improved by the two levels of amplification strategy DNAzyme motor and cyclic cleavage of the loop. Importantly, it also can significantly reduce the false positive result by two colors signals. Moreover, it also exhibits satisfactory performance in practical sample detection.

Dual signal amplification coupling with DNA-templated silver nanoclusters for sensitive and label-free detection of thrombin

Sensitive and reliable determination of thrombin is relevant in the realms of medical and biological research as it serves as an essential biomarker of a number of blood-related illnesses. Herein, we integrate allosteric probe-based specific identification of thrombin and dual signal amplification to present an unique fluorescent technique for label-free and sensitive thrombin detection. Based on DNA polymerase and endonuclease-assisted signal amplification, the method exhibits a high sensitivity with a low limit of detection of 2.3 pM, while maintaining an excellent selectivity and stability. More importantly, the approach is successfully applied in analyzing the effect of nalbuphine on coagulation function of mice. Overall, this approach possesses the advantages of high specificity and sensitivity in label-free detection of thrombin, which is promising in the diagnosis of blood-related diseases.

The Recent Progress in DNAzymes-Based Aptasensors for Thrombin Detection

Thrombin (TB) is classified among human blood coagulation proteins with key functions in hemostasis of blood vessels, wound healing, atherosclerosis, tissue adhesion, etc. Moreover, TB is involved as the main enzyme in the conversion of the fibrinogen to fibrin. Given the importance of TB detection in the clinical area, the development of innovative methods can considerably improve TB detection. Newly, aptasensors or aptamer-based biosensors have received special attention for sensitive and facile TB detection. In addition, the aptamer/nanomaterial conjugates have presented new prospects in accurate TB detection as nanoaptasensors. DNA-based enzymes or DNAzymes, as new biocatalysts, have many advantages over protein enzymes and can be used in analytical tools. This article reviews a brief overview of significant progresses regarding the various types of DNAzymes-based aptasensors and nano aptasensors developed for thrombin detection. In the following, challenges and prospects of TB detection by DNAzymes-based aptasensors are discussed.

Aptamer-Based Solution-Gated Graphene Transistors for Highly Sensitive and Real-Time Detection of Thrombin Molecules

Thrombin is an important biomarker for various diseases and biochemical reactions. Rapid and real-time detection of thrombin that quickly neutralizes in early coagulation in the body has gained significant attention for its practical applications. Solution-gated graphene transistors (SGGTs) have been widely studied due to their higher sensitivity and low-cost fabrication for chemical and biological sensing applications. In this paper, the ssDNA aptamer with 29 bases was immobilized on the surface of the gate electrode to specifically recognize thrombin. The SGGT sensor achieved high sensitivity with a limit of detection (LOD) up to fM. The LOD was attributed to the amplification function of SGGTs and the suitable aptamer choice. The ssDNA configuration folding induced by thrombin molecules and the electropositivity of thrombin molecules could arouse the same electrical response of SGGTs, helping the device obtain a high sensitivity. The channel current variation of sensors had a good linear relationship with the logarithm of thrombin concentration in the range of 1 fM to 10 nM. The fabricated device also demonstrated a short response time to thrombin molecules, and the response time to the 1 fM thrombin molecules was about 150 s. In summary, the sensing strategy of aptamer-based SGGTs with high sensitivity and high selectivity has a good prospect in medical diagnosis.

A "turn-on" and proximity ligation assay dependent DNA tweezer for one-step amplified fluorescent detection of DNA

A "turn-on" and proximity ligation assay dependent DNA tweezer was proposed for one-step amplified fluorescent detection of DNA. Target DNA can anneal with capture probe to form an entire long sequence. The formed long sequence can circularly open the hairpin, resulting the "turn-on" of DNA tweezers. A good linear relationship was shown from 40 pM to 20 nM with limit of detection of 10 pM. In addition, it has been successfully utilized to analysis DNA in human serum, representing a great and practical application future.

Technology Advancements in Blood Coagulation Measurements for Point-of-Care Diagnostic Testing

In recent years, blood coagulation monitoring has become crucial to diagnosing causes of hemorrhages, developing anticoagulant drugs, assessing bleeding risk in extensive surgery procedures and dialysis, and investigating the efficacy of hemostatic therapies. In this regard, advanced technologies such as microfluidics, fluorescent microscopy, electrochemical sensing, photoacoustic detection, and micro/nano electromechanical systems (MEMS/NEMS) have been employed to develop highly accurate, robust, and cost-effective point of care (POC) devices. These devices measure electrochemical, optical, and mechanical parameters of clotting blood. Which can be correlated to light transmission/scattering, electrical impedance, and viscoelastic properties. In this regard, this paper discusses the working principles of blood coagulation monitoring, physical and sensing parameters in different technologies. In addition, we discussed the recent progress in developing nanomaterials for blood coagulation detection and treatments which opens up new area of controlling and monitoring of coagulation at the same time in the future. Moreover, commercial products, future trends/challenges in blood coagulation monitoring including novel anticoagulant therapies, multiplexed sensing platforms, and the application of artificial intelligence in diagnosis and monitoring have been included.

One-step sensitive thrombin detection based on a nanofibrous sensing platform

Convenient and time-saving one-step strategies for detecting ultralow concentrations of protein biomarkers play key roles in rapid disease diagnosis. In this study, we report a one-step detection method based on a nanofibrous sensing platform via the combination of proximity-induced DNA strand displacement (PiDSD), catalytic hairpin assembly (CHA) amplification and thioflavin T (ThT) binding. The interface behaviors on the nanofibrous membrane were studied to promote interface reaction kinetics and thermodynamics. Thrombin was used as a model biomarker, and the nanofibrous sensing platform achieved a limit of detection as low as 1.0 pM, a wide linear range of 50 pM to 5 nM, excellent specificity and good long-term stability. Compared with previous one-step thrombin detection methods, our one-step detection method is label-free, convenient and much more sensitive; it has potential applications for protein detection in point-to-care testing (POCT) and early diagnosis.

Target-induced structure switching of aptamers facilitates strand displacement for DNAzyme recycling amplification detection of thrombin in human serum

To monitor the thrombin concentration under the condition of abnormal blood coagulation is of clinical significance for the diagnosis of various diseases. Here, on the basis of the aptamer structure switching induced by the target molecules and the signal amplification strategy via recycling of metal-ion dependent DNAzymes, we have established a sensitive and simple fluorescent aptasensor for detecting thrombin in human serum. The thrombin target specifically binds to the aptamer sequence and causes a corresponding conformational structure switching, which leads to the formation of a toehold sequence to facilitate the strand migration displacement reaction for the generation of functional metal-ion dependent DNAzymes. These DNAzymes further cleave the fluorescently quenched hairpin substrates cyclically to yield substantially amplified fluorescence recovery for sensitively detecting thrombin in the dynamic range from 0.01 nM to 50 nM. Such an aptasensor shows a detection limit of 6.9 pM and can achieve the monitoring of thrombin in diluted human serum with high selectivity, offering a universal sensing strategy for the construction of various sensitive and simple aptasensors to detect different biomarker molecules.

Quenched sandwich-type photoelectrochemical aptasensor for protein detection based on exciton energy transfer

This work proposes a quenched photoelectrochemical sensing method for highly selective and sensitive detection of protein via Energy Transfer (ET) effect between the AuNPs and CdS:Mn quantum dots. This detection was performed on a sandwich-type aptamer sensing interface. Chitosan modified CdS:Mn/TiO₂/ITO electrode was used to immobilize capture DNA (S1) via -CONH- bond. In the presence of target protein, AuNPs labeled DNA (AuNPs-S2) was further bonded to the protein to fabricate sandwich sensing platform, which forced the AuNPs away from the electrode surface. In this state, the photocurrent was greatly depressed, mainly due to two factors: (a) the ET effect produced by interparticle distance between CdS:Mn and AuNPs; (b) the steric hindrance of AuNPs-S2 partly obstructs the diffusion of the electron donor. The photocurrent decreased with the increasing concentration of the target protein. Using thrombin as a target, this sensitized method showed a detectable range of 0.1 pM to 8 nM and a detection limit of 30 fM. It possessed high selectivity and good stability for detection of thrombin. This method is extremely flexible and can be extended to varieties of protein targets.