A voltammetric aptamer-based thrombin biosensor exploiting signal amplification via synergetic catalysis by DNAzyme and enzyme decorated AuPd nanoparticles on a poly(o-phenylenediamine) support

Nanopillar array-based electrochemical aptamer sensor for STX sensitivity detection

Saxitoxin (STX) is a cyanotoxin with high toxicity, and therefore, there is an urgent need to develop a facile detection method for STX. In this study, an ordered nanopillar array-based electrochemical aptasensor was fabricated for the high-performance detection of STX. The anti-STX aptamer with methylene blue (MB) incorporated at the 3'-end (MB-Apt) was immobilized at the surface of an Au@PAN nanopillar array electrode and used as the recognition element. The proposed aptasensor demonstrated highly sensitive and selective STX detection because of synergistic catalysis effects of MB and ordered nanopillar arrays along with the selection of MB-Apt. The nanopillar array-based electrochemical aptasensor exhibited high sensitivity over a wide linear concentration range of 1 pM-3 nM with a linear regression equation of ΔI (μA) = 28.0 + 6.9 × log[STX] (R2 = 0.98079) and 3-100 nM with a linear regression equation of ΔI (μA) = 10.7 + 43.4 × log[STX] (R2 = 0.98772), where R is the correlation coefficient. In addition, the limit of detection (LOD) was as low as 1 pM. Furthermore, the designed aptasensor demonstrated excellent selectivity toward STX, preventing interference from neo-STX, okadaic acid, and common metal ions. The presented orderly nanopillar array-based strategy to develop an electrochemical aptasensor for STX detection offers a promising method for developing high-performance electrochemical sensors, and the presented aptasensor should find useful application in the detection of shellfish poison.

Conjugated Polymers for Aptasensing Applications

Rapid and specific assaying of molecules that report on a pathophysiological condition, environmental pollution, or drug concentration is pivotal for establishing efficient and accurate diagnostic systems. One of the main components required for the construction of these systems is the recognition element (receptor) that can identify target analytes. Oligonucleotide switching structures, or aptamers, have been widely studied as selective receptors that can precisely identify targets in different analyzed matrices with minimal interference from other components in an antibody-like recognition process. These aptasensors, especially when integrated into sensing platforms, enable a multitude of sensors that can outperform antibody-based sensors in terms of flexibility of the sensing strategy and ease of deployment to areas with limited resources. Research into compounds that efficiently enhance signal transduction and provide a suitable platform for conjugating aptamers has gained huge momentum over the past decade. The multifaceted nature of conjugated polymers (CPs), notably their versatile electrical and optical properties, endows them with a broad range of potential applications in optical, electrical, and electrochemical signal transduction. Despite the substantial body of research demonstrating the enhanced performance of sensing devices using doped or nanostructure-embedded CPs, few reviews are available that specifically describe the use of conjugated polymers in aptasensing. The purpose of this review is to bridge this gap and provide a comprehensive description of a variety of CPs, from a historical viewpoint, underpinning their specific characteristics and demonstrating the advances in biosensors associated with the use of these conjugated polymers.

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.

Inorganic nanoparticles coupled to nucleic acid enzymes as analytical signal amplification tools

Nucleic acid enzymes (NAzymes) are a class of nucleic acid molecules with catalytic activity, which can be modulated by the presence of different species such as metal ions, genetic biomarkers, small molecules or proteins, among others. NAzymes offer several important advantages for development of novel bioanalytical strategies, resulting from their functionality as specific recognition elements and as amplified analytical signal generators, making them ideal candidates for developing highly specific bioanalytical strategies for the detection of a wide variety of targets. When coupled with the exceptional features of inorganic nanoparticles (NPs), the sensitivity of the assays can be significantly improved, allowing the detection of targets using many different detection techniques including visual readout, spectrophotometry, fluorimetry, electrochemiluminescence, voltammetry, and single-particle inductively coupled plasma-mass spectrometry. Here we provide an overview of the fundamentals of novel strategies developed to achieve analytical signal amplification based on the use of NAzymes coupled with inorganic NPs. Some representative examples of such strategies for the highly sensitive detection of different targets will be presented, including metal ions, proteins, DNA- or RNA-based biomarkers, and small molecules or microorganisms. Furthermore, future prospective challenges will be discussed.

DNAzyme-Based Biosensors: Immobilization Strategies, Applications, and Future Prospective

Since their discovery almost three decades ago, DNAzymes have been used extensively in biosensing. Depending on the type of DNAzyme being used, these functional oligonucleotides can act as molecular recognition elements within biosensors, offering high specificity to their target analyte, or as reporters capable of transducing a detectable signal. Several parameters need to be considered when designing a DNAzyme-based biosensor. In particular, given that many of these biosensors immobilize DNAzymes onto a sensing surface, selecting an appropriate immobilization strategy is vital. Suboptimal immobilization can result in both DNAzyme detachment and poor accessibility toward the target, leading to low sensing accuracy and sensitivity. Various approaches have been employed for DNAzyme immobilization within biosensors, ranging from amine and thiol-based covalent attachment to non-covalent strategies involving biotin-streptavidin interactions, DNA hybridization, electrostatic interactions, and physical entrapment. While the properties of each strategy inform its applicability within a proposed sensor, the selection of an appropriate strategy is largely dependent on the desired application. This is especially true given the diverse use of DNAzyme-based biosensors for the detection of pathogens, metal ions, and clinical biomarkers. In an effort to make the development of such sensors easier to navigate, this paper provides a comprehensive review of existing immobilization strategies, with a focus on their respective advantages, drawbacks, and optimal conditions for use. Next, common applications of existing DNAzyme-based biosensors are discussed. Last, emerging and future trends in the development of DNAzyme-based biosensors are discussed, and gaps in existing research worthy of exploration are identified.

Ultra-sensitive and selective electrochemical biosensor with aptamer recognition surface based on polymer quantum dots and C60/MWCNTs- polyethylenimine nanocomposites for analysis of thrombin protein

In this study, an ultra-sensitive and selective Thrombin biosensor with aptamer-recognition surface is introduced based on carbon nanocomposite. To prepare the this biosensor, screen-printed carbon electrodes (SPCE) were modified with a nanocomposite made from fullerene (C₆₀), multi-walled carbon nanotubes (MWCNTs), polyethylenimine (PEI) and polymer quantum dots (PQdot). The unique characteristics of each component of the C₆₀/MWCNTs-PEI/PQdot nanocomposite allow for synergy between nanoparticles while polymer quantum dots resulted in characteristics such as high stability, high surface to volume ratio, high electrical conductivity, high biocompatibility, and high mechanical and chemical stability. The large number of amine groups in C₆₀/MWCNTs-PEI/PQdot nanocomposite created more sites for better covalent immobilization of amino-linked aptamer (APT) which improved the sensitivity and stability of the aptasensor. Differential Pulse Voltammetry (DPV) method with probe solution was used as the measurment method. Binding of thrombin protein to aptamers immobilized on the transducer resulted in reduced electron transfer at the electrode/electrolyte interface which reduces the peak current (I_P) in DPV. The calibration curve was drawn using the changes in the peak current (ΔI_P),. The proposed aptasensor has a very low detection limit of 6 fmol L^-1, and a large linear range of 50 fmol L^-1 to 20 nmol L^-1. Furthermore, the proposed C₆₀/MWCNTs-PEI/PQdot/APT aptasensor has good reproducibility, great selectivity, low response time and a good stability during its storage. Finally, the application of the proposed aptasensor for measuring thrombin on human blood serum samples was investigated. This aptasensor can be useful in bioengineering and biomedicine applications as well as for clinical studies.

Recent Trends in Electrochemical Sensors for Vital Biomedical Markers Using Hybrid Nanostructured Materials

This work provides a succinct insight into the recent developments in electrochemical quantification of vital biomedical markers using hybrid metallic composite nanostructures. After a brief introduction to the biomarkers, five types of crucial biomarkers, which require timely and periodical monitoring, are shortlisted, namely, cancer, cardiac, inflammatory, diabetic and renal biomarkers. This review emphasizes the usage and advantages of hybrid nanostructured materials as the recognition matrices toward the detection of vital biomarkers. Different transduction methods (fluorescence, electrophoresis, chemiluminescence, electrochemiluminescence, surface plasmon resonance, surface-enhanced Raman spectroscopy) reported for the biomarkers are discussed comprehensively to present an overview of the current research works. Recent advancements in the electrochemical (amperometric, voltammetric, and impedimetric) sensor systems constructed with metal nanoparticle-derived hybrid composite nanostructures toward the selective detection of chosen vital biomarkers are specifically analyzed. It describes the challenges involved and the strategies reported for the development of selective, sensitive, and disposable electrochemical biosensors with the details of fabrication, functionalization, and applications of hybrid metallic composite nanostructures.

A highly sensitive electrochemical biosensor for protein based on a tetrahedral DNA probe, N- and P-co-doped graphene, and rolling circle amplification

A tetrahedral DNA probe can effectively overcome the steric effects of a single-stranded probe to obtain well-controlled density and minimize nonspecific adsorption. Herein, a highly sensitive electrochemical biosensor is fabricated for determination of protein using a tetrahedral DNA probe and rolling circle amplification (RCA). N- and P-co-doped graphene (NP-rGO) is prepared, and AuNPs are then electrodeposited on it for DNA probe immobilization. Benefitting from the synergistic effects of the excellent electrical conductivity of NP-rGO, the stability of the tetrahedral DNA probe and the signal amplification of RCA, the biosensor achieves a low limit of 3.53 × 10^-14 M for thrombin and a wide linear range from 1 × 10^-13 to 1 × 10^-7 M. This study provides a sensitive and effective method for the detection of protein in peripheral biofluids, and paves the way for future clinical diagnostics and treatment of disease. Graphical abstract.

Electrochemiluminescence methods using CdS quantum dots in aptamer-based thrombin biosensors: a comparative study

The detection of thrombin by using CdS nanocrystals (CdS NCs), gold nanoparticles (AuNPs) and luminol is investigated in this work. Thrombin is detected by three methods. One is called the quenching method. It is based on the quenching effect of AuNPs on the yellow fluorescence of CdS NCs (with excitation/emission wavelengths of 355/550 nm) when placed adjacent to CdS NCs. The second method (called amplification method) is based on an amplification mechanism in which the plasmonics on the AuNPs enhance the emission of CdS NCs through distance related Förster resonance energy transfer (FRET). The third method is ratiometric and based on the emission by two luminophores, viz. CdS NCs and luminol. In this method, by increasing the concentration of thrombin, the intensity of CdS NCs decreases, while that of luminol increases. The results showed that ratiometric method was most sensitive (with an LOD of 500 fg.mL^-1), followed by the amplification method (6.5 pg.mL^-1) and the quenching method (92 pg.mL^-1). Hence, the latter is less useful. Graphical abstract Schematic representation of three different methods (quenching, amplification and ratiometric) were applied for detection of thrombin via aptasensor. The CdS nanocrystals, streptavidin (Str) coated AuNPs and also Str-luminol coated AuNPs were used for the construction steps of the electrochemiluminescence (ECL)-based biosensor.

DNA nanotetrahedron linked dual-aptamer based voltammetric aptasensor for cardiac troponin I using a magnetic metal-organic framework as a label

An ultrasensitive voltammetric aptasensor was constructed to analyze cardiac troponin I (cTnI). It is based on DNA nanotetrahedron (NTH) linked dual-aptamer (dAPT) and magnetic metal organic frameworks (mMOFs) of type Fe₃O₄@UiO-66. Firstly, the DNA NTH linked dAPT (Tro4 and Tro6) were immobilized on a gold electrode for improving the capture efficiency of cTnI. The novel mMOFs Fe₃O₄@UiO-66 was then decorated by Au@Pt nanoparticles (Au@PtNPs), horseradish peroxidase (HRP), G-quadruplex/hemin (GQH) DNAzyme, and two types of aptamers to form signaling nanoprobes. In the presence of cTnI, an aptamer-protein-nanoprobe sandwich-type structure is formed. Afterward, the nanoprobes including enzyme, GQH DNAzyme and Fe₃O₄@UiO-66/Au@PtNP were utilized to catalyze the oxidation of hydroquinone by hydrogen peroxide for the electrochemical signals amplification, typically at a working potential of -0.1 V (vs. Ag/AgCl). The voltammetric signal increases linearly in the 0.01 to 100 ng·mL^-1 cTnI concentration range, and the detection limit is 5.7 pg·mL^-1. Graphical abstract An ultrasensitive voltammetric aptasensor was constructed to analyze cardiac troponin I (cTnI) based on DNA nanotetrahedron linked dual-aptamer and magnetic metal organic frameworks of type Fe₃O₄@UiO-66. The results indicated the aptasensor has a wide linear response range (0.01 to 100 ng/mL) and low detection limit (5.74 pg/mL) for cTnI. GE: gold electrode; MCH: 6-Mmercapto-1-hexanol; HRP: horseradish peroxidase; HQ: hydroquinone; BQ: benzoquinone.

Recent Advances in Aptamer Discovery and Applications

Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection 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).

Core-shell assay based aptasensor for sensitive and selective thrombin detection using dark-field microscopy

In this work, we developed a robust and ultrasensitive bio-sensor based on the target-aptamer recognition strategy and microscopic enumeration of gold nanoparticles (AuNPs) using dark field microscopy (DFM). The aptasensor with a core-shell structure consisting of a magnetic bead (MB), aptamer and AuNPs was fabricated by complementary hybridization of the DNA probe on the AuNPs surface to the aptamer coupled to the MB. Upon addition of the target molecule, the strong interaction between the aptamer and the target molecule, thrombin, results in the release of the AuNPs from the MB. The quantities of thrombin is therefore linearly correlated to the number of the released AuNPs, which can be digitally counted using DFM. To demonstrate the feasible use of the aptasensor for target detection, thrombin was evaluated as the model target. The limit of detection was determined to be 2.54 fM with dynamic range of 6 fM-100 fM. When the concentration of thrombin exceeded 100 fM, the counted number of AuNPs didn't correlate linearly to molecules of thrombin anymore, as the nanoparticles aggregated partly due to high concentration. However, the color of the solution changes to purple and the concentration of free AuNPs can be conveniently quantified by UV-Vis spectroscopy for up to 100 nM. It is noteworthy that our aptasensor is very easy to operate and requires neither complex isolation and amplification processes nor expensive instruments and consumables. Furthermore, this strategy can be easily generalized to other targets by replacing the corresponding aptamers and show great potential for the detection of biomarkers in clinical samples.

A cascade amplification strategy of catalytic hairpin assembly and hybridization chain reaction for the sensitive fluorescent assay of the model protein carcinoembryonic antigen

A cascade nucleic acid amplification strategy is presented for fluorometric aptamer based determination of the model protein carcinoembryonic antigen (CEA). Amplification is accomplished by combining catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR). In this assay, a specially designed single-stranded DNA containing the aptamer sequence (AS) specific for CEA is hybridized with an inhibitor strand (IS) to form a double-stranded DNA (IS@AS). In the presence of CEA, it will recognize and bind to the AS strand which causes the release of IS. By introducing two DNA hairpins (H1 and H2; these containing complementary sequences) CHA will be activated via the hybridization reactions of H1 and H2. This is accompanying by the formation of a double-stranded DNA (H1-H2) and the release of CEA@AS. The liberated CEA@AS further drives successive recycling of the CHA, thereby generating further copies of H1-H2. The resultant H1-H2 hybrids act as primers and trigger HCR with the help of other two DNA hairpins (H3 and H4) containing G-rich toehold at the 5'-terminus and 3'-terminus of H3 and H4, respectively. The fluorescent probe N-methyl mesoporphyrin IX (NMM) is finally intercalated into the G-rich domains of the long DNA nanostructures due to formation of G-quadruplex structures. This generates a fluorescent signal (best measured at excitation/emission wavelengths of 399/610 nm) that increases with the concentration of target (CEA). This aptamer-based fluorescence assay is highly sensitive and has a linear range that covers the 1 pg·mL^-1 to 2 ng·mL^-1 CEA concentration range, with a 0.3 pg·mL^-1 detection limit. Graphical abstract By integrating catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) for effective signal enhancement, a novel cascade amplification strategy is presented to develop a sensitive and selective fluorescent method for the assay of the model protein carcinoembryonic antigen (CEA).