Label-free aptamer biosensor for selective detection of thrombin

Nano-bio convergence unveiled: Systematic review on quantum dots-protein interaction, their implications, and applications

Quantum dots (QDs) are semiconductor nanocrystals (2-10 nm) with unique optical and electronic properties due to quantum confinement effects. They offer high photostability, narrow emission spectra, broad absorption spectrum, and high quantum yields, making them versatile in various applications. Due to their highly reactive surfaces, QDs can conjugate with biomolecules while being used, produced, or unintentionally released into the environment. This systematic review delves into intricate relationship between QDs and proteins, examining their interactions that influence their physicochemical properties, enzymatic activity, ligand binding affinity, and stability. The research utilized electronic databases like PubMed, WOS, and Proquest, along with manual reviews from 2013 to 2023 using relevant keywords, to identify suitable literature. After screening titles and abstracts, only articles meeting inclusion criteria were selected for full text readings. This systematic review of 395 articles identifies 125 articles meeting the inclusion criteria, categorized into five overarching themes, encompassing various mechanisms of QDs and proteins interactions, including adsorption to covalent binding, contingent on physicochemical properties of QDs. Through a meticulous analysis of existing literature, it unravels intricate nature of interaction, significant influence on nanomaterials and biological entities, and potential for synergistic applications harnessing both specific and nonspecific interactions across various fields.

Molecularly imprinted electrochemical biosensor for thrombin detection by comparing different monomers

Aim: Investigating molecularly imprinted polymers (MIPs) in electrochemical biosensors for thrombin detection, an essential protein biomarker. Comparing different monomers to showcase distinct sensitivity, specificity and stability advantages. Materials & methods: Dopamine, thionine and ethanolamine serve as monomers for MIP synthesis. Electrochemical methods and atomic force microscopy characterize sensor surfaces. Performance is evaluated, emphasizing monomer-specific electrochemical responses. Results: Monomer-specific electrochemical responses highlight dopamine's superior signal change and stability over 30 days. Notably, a low 5 pg/ml limit of detection, a broad linear range (5-200 pg/ml) and enhanced selectivity against interferents are observed. Conclusion: Dopamine-based MIPs show promise for high-performance electrochemical thrombin biosensors, suggesting significant applications in clinical diagnostics.

Ultrasensitive covalently-linked Aptasensor for cocaine detection based on electrolytes-induced repulsion/attraction of colloids

A quick and easy colorimetric sensor based on gold nanoparticles (GNPs) and aptamers for the detection of cocaine was developed. The sensor was named as 'GAPTA' and showed extremely interesting results regarding cocaine detection with a sensitivity to doses of 0.2 nM. The experimental approach consisted of creating a conjugate between GNPs (10 nm size) and aptamers as a sensing base with the addition of an electrolyte (NaCl) that plays the role of aggregation inducer. In the absence of the aptamer, the electrolyte was able to induce aggregation of the GNPs turning the color of the solution from red to blue while the presence of the aptamer is able to hinder the charges attraction and protects the GNPs from aggregating. The optimization of the aptamer and electrolyte concentration was determined to be 118 nM and 55 mM, respectively, and the resultant GAPTA sensor had a detection limit of 0.97 nM. Furthermore, the selectivity of the platform was tested in the presence of different interferents and showed a specific response towards cocaine while interference ranged between 20 and 40%. The applicability of the GAPTA biosensor was tested on synthetic saliva and demonstrated a sensitivity range between 0.2 and 25 nM. These results suggest the potential of the current colorimetric sensor in abuse drugs screening and creates a stable base for new routine platforms for biomedical and toxicology applications. Graphical abstract.

A ratiometric fluorescent probe for detection of uric acid based on the gold nanoclusters-quantum dots nanohybrid

Herein, we developed a simple strategy for the preparation of dual-emission fluorescent nanohybrid constructed of gold nanoclusters (Au NCs) and quantum dots (QDs). The bovine serum albumin-capped Au NCs can be directly used as the stabilizers to prepare CdS QDs. The synthesized bovine serum albumin-capped Au NCs and CdS QDs nanohybrid (BSA-Au NCs/QDs) displayed dual emission bands respectively at 490 nm and 685 nm. An obvious fluorescence quenching around 685 nm was detected with the addition of hydrogen peroxide (H₂O₂) in the presence of Fe²⁺ ions, and the fluorescence emission peak at 490 nm was not affected. Uricase can break down uric acid to produce H₂O₂, and we further used the BSA-Au NCs/QDs as a ratiometric fluorescent probe for determination of uric acid with the linear range from 0.67 to 60 μmol·L^-1 and the detection limit of 0.21 μmol·L^-1.

G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives

G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

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.

Microfluidic paper-based photoelectrochemical sensing platform with electron-transfer tunneling distance regulation strategy for thrombin detection

This work reports a microfluidic paper-based photoelectrochemical (μ-PEC) sensing platform for thrombin (TB) detection with electron-transfer tunneling distance regulation (ETTDR) and aptamer target-triggering nicking enzyme signaling amplification (NESA) dual strategies. Specifically, paper-based TiO₂ nanosheets (PTNs) were prepared with an efficient hydrothermal process, serving as the direct pathway for the charge carriers transfer. When CeO₂-labeled hairpin DNA 3 (HP3) was closely located at the PTNs, the CeO₂-PTNs heterostructure was formed, which could great facilitate the photogenerated carries separation of CeO₂. In addition, with the aid of aptamer target-triggering NESA strategy, the input TB could be transducted to numerous output target of DNA (tDNA), achieving the goal of desirable signal amplification. In the presence of TB, the output tDNA could be further hybridized with HP3 and unfold its hairpin loop, which forced the CeO₂ away from the surface of PTNs and vanished the CeO₂-PTNs heterostructure, resulting in the obviously reducing of photocurrent signal. The as-designed sensing platform exhibited a linear range from 0.02 pM to 100 pM with a detection limit of 6.7 fM. Importantly, this μ-PEC sensing platform could not only realize the highly efficient TB detection, but also pave a luciferous way for the detection of other protein in bioanalysis.

Investigations on the interface of nucleic acid aptamers and binding targets

Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.

Electrochemiluminescent aptasensor for thrombin using nitrogen-doped graphene quantum dots

An electrochemiluminescent (ECL) aptamer based method is described for the determination of thrombin. Three-dimensional nitrogen-doped graphene oxide (3D-NGO) was placed on a glassy carbon electrode (GCE) to provide an electrode surface that displays excellent electrical conductivity and acts as a strong emitter of ECL. The modified electrode was further coated with chitosan via electrodeposition. Finally, the amino-modified aptamer was immobilized on the modified GCE. The interaction between thrombin and aptamer results in a decrease in ECL. The assay has a linear response in the 1 fM to 1 nM thrombin concentration range and a 0.25 fM lower detection limit (at an S/N ratio of 3). The method was applied to the determination of thrombin in spiked human plasma samples, and recoveries ranged between 94 and 105% (with RSDs of <3.6%). The calibration plot was recorded at potential and wavelength of fluorescence emission (wavelength: 445 nm; potential: 0 to -2 V). Graphical abstract A bare glassy carbon electrode (GCE) does not display electrochemiluminescence (ECL). If, however, nitrogen-doped graphene quantum dots, chitosan, and three-dimensional nitrogen-doped graphene oxide (NGQD-chitosan/3D-NGO) are electrodeposited on the GCE, strong ECL can be observed. The ECL intensity decreased after aptamer and bovine serum albumin (BSA) were dropped onto the electrode (curve a). However, the ECL further decreases after addition of thrombin (TB; curve b).

Current Conjugation Methods for Immunosensors

Recent advances in the development of immunosensors using polymeric nanomaterials and nanoparticles have enabled a wide range of new functions and applications in diagnostic and prognostic research. One fundamental challenge that all immunosensors must overcome is to provide the specificity of target molecular recognition by immobilizing antibodies, antibody fragments, and/or other peptides or oligonucleotide molecules that are capable of antigen recognition on a compact device surface. This review presents progress in the application of immobilization strategies including the classical adsorption process, affinity attachment, random cross-linking and specific covalent linking. The choice of immobilization methods and its impact on biosensor performance in terms of capture molecule loading, orientation, stability and capture efficiency are also discussed in this review.

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.

A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification

Synthetic enzyme-free DNA nanomachine performs quasi-mechanical movements in response to external intervention, suggesting the promise of constructing sensitive and specific biosensors. Herein, a smart DNA nanomachine biosensor for biomolecule (such as nucleic acid, thrombin and adenosine) detection is developed by target-assisted enzyme-free hairpin DNA cascade amplifier. The whole DNA nanomachine system is constructed on gold nanoparticle which decorated with hundreds of locked hairpin substrate strands serving as DNA tracks, and the DNA nanomachine could be activated by target molecule toehold-mediated exchange on gold nanoparticle surface, resulted in the fluorescence recovery of fluorophore. The process is repeated so that each copy of the target can open multiplex fluorophore-labeled hairpin substrate strands, resulted in amplification of the fluorescence signal. Compared with the conventional biosensors of catalytic hairpin assembly (CHA) without substrate in solution, the DNA nanomachine could generate 2-3 orders of magnitude higher fluorescence signal. Furthermore, the DNA nanomachine could be used for nucleic acid, thrombin and adenosine highly sensitive specific detection based on isothermal, and homogeneous hairpin DNA cascade signal amplification in both buffer and a complicated biomatrix, and this kind of DNA nanomachine could be efficiently applied in the field of biomedical analysis.

Novel application of fluorescence coupled capillary electrophoresis to resolve the interaction between the G-quadruplex aptamer and thrombin

The dynamic binding status between the thrombin and its G-quadruplex aptamers and the stability of its interaction partners were probed using our previously established fluorescence-coupled capillary electrophoresis method. A 29-nucleic acid thrombin binding aptamer was chosen as a model to study its binding affinity with the thrombin ligand. First, the effects of the cations on the formation of G-quadruplex from unstructured 29-nucleic acid thrombin binding aptamer were examined. Second, the rapid binding kinetics between the thrombin and 6-carboxyfluorescein labeled G-quadruplex aptamer was measured. Third, the stability of G-quadruplex aptamer-thrombin complex was also examined in the presence of the interfering species. Remarkably, it was found that the complementary strand of 29-nucleic acid thrombin binding aptamer could compete with G-quadruplex aptamer and thus disassociated the G-quadruplex structure into an unstructured aptamer. These data suggest that our in-house established fluorescence-coupled capillary electrophoresis assay could be applied to binding studies of the G-quadruplex aptamers, thrombin, and their ligands, while overcoming the complicated and costly approaches currently available.

Silver Nanoclusters Beacon as Stimuli-Responsive Versatile Platform for Multiplex DNAs Detection and Aptamer-Substrate Complexes Sensing

An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved. Additionally, with the introduction of aptamer for the design of the molecular beacon, the detections of small molecule adenosine triphosphate (ATP) and biomacromolecule thrombin have also been realized. This is the first time that an activatable fluorescent silver nanoclusters (Ag NCs)-based probe and the target recognition have been integrated into a single process, which provides a versatile platform for different analytes in a facile way. The successful application of our proposed ASNCB in real sample analysis and ATP imaging in living cells further displayed its promising potential for fluorescence sensing.

Polypeptide Functional Surface for the Aptamer Immobilization: Electrochemical Cocaine Biosensing

Electroanalytical technologies as a beneficial subject of modern analytical chemistry can play an important role for abused drug analysis which is crucial for both legal and social respects. This article reports a novel aptamer-based biosensing procedure for cocaine analysis by combining the advantages of aptamers as selective recognition elements with the well-known advantages of biosensor systems such as the possibility of miniaturization and automation, easy fabrication and modification, low cost, and sensitivity. In order to construct the aptasensor platform, first, polythiophene bearing polyalanine homopeptide side chains (PT-Pala) was electrochemically coated onto the surface of an electrode and then cocaine aptamer was attached to the polymer via covalent conjugation chemistry. The stepwise modification of the surface was confirmed by electrochemical characterization. The designed biosensing system was applied for the detection of cocaine and its metabolite, benzoylecgonine (BE), which exhibited a linear correlation in the range from 2.5 up to 10 nM and 0.5 up to 50 μM for cocaine and BE, respectively. In order to expand its practical application, the proposed method was successfully tested for the analysis of synthetic biological fluids.

Sandwich Immunoassays of Multicomponent Subtrace Pathogenic DNA Based on Magnetic Fluorescent Encoded Nanoparticles

A novel magnetic fluorescent encoded nanoimmunoassay system for multicomponent detection and separation of the subtrace pathogenic DNA (hepatitis B virus surface gene, HBV; hepatitis A virus poly the protein gene, HAV) was established based on new type of magnetic fluorescent encoded nanoparticles and sandwich immunoassay principle. This method combines multifunctional nanoparticles, immunoassay technique, fluorescence labeling, and magnetic separation of multicomponent technology. It has many advantages such as high sensitivity, low detection limit, easy operation, and great potential for development. The results of this work show that, based on nanoimmunoassay system, it could quantitatively detect the multicomponent trace pathogenic HAV and HBV DNA, as well as detection limit up to 0.1 pM and 0.12 pM. Furthermore, with the improvement of the performances of magnetic fluorescent encoded nanoparticles, the sensitivity will be further improved. In this experiment, a new nanoimmunoassay system based on magnetic fluorescent encoded nanoparticles was established, which will provide a new way for the immunoassay and separation of multicomponent biomolecules.