A novel optical thrombin aptasensor based on magnetic nanoparticles and split DNAzyme

Metallic nanostructure-based aptasensors for robust detection of proteins

There is a significant need for fast, cost-effective, and highly sensitive protein target detection, particularly in the fields of food, environmental monitoring, and healthcare. The integration of high-affinity aptamers with metal-based nanomaterials has played a crucial role in advancing the development of innovative aptasensors tailored for the precise detection of specific proteins. Aptamers offer several advantages over commonly used molecular recognition methods, such as antibodies. Recently, a variety of metal-based aptasensors have been established. These metallic nanomaterials encompass noble metal nanoparticles, metal oxides, metal-carbon nanotubes, carbon quantum dots, graphene-conjugated metallic nanostructures, as well as their nanocomposites, metal-organic frameworks (MOFs), and MXenes. In general, these materials provide enhanced sensitivity through signal amplification and transduction mechanisms. This review primarily focuses on the advancement of aptasensors based on metallic materials for the highly sensitive detection of protein targets, including enzymes and growth factors. Additionally, it sheds light on the challenges encountered in this field and outlines future prospects. We firmly believe that this review will offer a comprehensive overview and fresh insights into metallic nanomaterials-based aptasensors and their capabilities, paving the way for the development of innovative point-of-care (POC) diagnostic devices.

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.

Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors

In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.

Cancer-Specific MicroRNA Analysis with a Nonenzymatic Nucleic Acid Circuit

Sensitive detection of gastric cancer-related biomarkers in human serum provides a promising means for early cancer diagnosis. Herein, we report the design of a nucleic acid circuit for gastric cancer-related microRNA-27a (miRNA-27a) detection based on dual toehold-mediated circular strand displacement amplification (CSDA). In the presence of miRNA-27a, the hybridization between miRNA-27a and probe DNA on magnetic beads through toehold 1 leads to the release of fluorescent DNA and the exposure of a new toehold 2 on linker DNA. After hybridization with catalytic DNA, CSDA is initiated and target miRNA-27a is released to participate in the next cyclic reaction; therefore, a greatly enhanced fluorescence signal is produced. The efficient magnetic separation makes the sensitive detection of miRNA-27a be accomplished within 45 min. With the efficient CSDA, the detection limit of the system (0.8 pM) is ∼100 folds lower than that of the system based on strand displacement without CSDA (79.3 pM). Furthermore, the system also showed good stability and sensitivity to discriminate single-base mismatch, which allows the detection of miRNA-27a in human serum samples. This study provides a novel platform and approach for the rapid quantitative determination of miRNA, which has great potential in clinical diagnosis and disease treatment.

A sensitive colorimetric aptasensor based on trivalent peroxidase-mimic DNAzyme and magnetic nanoparticles

In this study, a novel colorimetric aptasensor was prepared by coupling trivalent peroxidase-mimic DNAzyme and magnetic nanoparticles for highly sensitive and selective detection of target proteins. A three G-quadruplex (G4) DNA-hemin complex was employed as the trivalent peroxidase-mimic DNAzyme, in which hemin assisted the G4-DNA to fold into a catalytic conformation and act as an enzyme. The design of the aptasensor includes magnetic nanoparticles (MNPs), complementary DNA (cDNA) modified with biotin, and a label-free single strand DNA (ssDNA) including the aptamer and trivalent peroxidase-mimic DNAzyme. The trivalent DNAzyme, which has the highest catalytic activity among multivalent DNAzymes, catalyzed the H₂O₂-mediated oxidation of ABTS. The colorless ABTS was oxidized to produce a blue-green product that can be clearly distinguished by the naked eye. The aptamer and trivalent peroxidase-mimic DNAzyme promote the specificity and sensitivity of this detection method, which can be generalized for other targets by simply replacing the corresponding aptamers. To demonstrate the feasible use of the aptasensor for target detection, a well-known tumor biomarker MUC1 was evaluated as the model target. The limits of detection were determined to be 5.08 and 5.60 nM in a linear range of 50-1000 nM in a buffer solution and 10% serum system, respectively. This colorimetric and label-free aptasensor with excellent sensitivity and strong anti-interference ability has potential application in disease diagnoses, prognosis tracking, and therapeutic evaluation.

DNAzyme-based biosensors and nanodevices

DNAzymes, screened through in vitro selection, have shown great promise as molecular tools in the design of biosensors and nanodevices. The catalytic activities of DNAzymes depend specifically on cofactors and show multiple enzymatic turnover properties, which make DNAzymes both versatile recognition elements and outstanding signal amplifiers. Combining nanomaterials with unique optical, magnetic and electronic properties, DNAzymes may yield novel fluorescent, colorimetric, surface-enhanced Raman scattering (SERS), electrochemical and chemiluminescent biosensors. Moreover, some DNAzymes have been utilized as functional components to perform arithmetic operations or as "walkers" to move along DNA tracks. DNAzymes can also function as promising therapeutics, when designed to complement target mRNAs or viral RNAs, and consequently lead to down-regulation of protein expression. This feature article focuses on the most significant achievements in using DNAzymes as recognition elements and signal amplifiers for biosensors, and highlights the applications of DNAzymes in logic gates, DNA walkers and nanotherapeutics.

A structure-switchable aptasensor for aflatoxin B1 detection based on assembly of an aptamer/split DNAzyme

An ultrasensitive, colorimetric and homogeneous strategy for aflatoxin B1 (AFB1) detection, which uses a DNA aptamer and two split DNAzyme halves, has been developed. Split halves of a hemin-binding DNAzymes is combined with an AFB1 aptamer to generate a homogeneous colorimetric sensor that undergoes an AFB1 induced DNA structural change. In the absence of AFB1, the split probes have peroxidase mimicking DNAzyme activity associated with catalysis of a color change reaction. Specific recognition of AFB1 by the aptamer component leads to structural deformation of the aptamer-DNAzyme complex, which causes splitting of the DNAzyme halves and a reduction in peroxidase mimicking activity. Therefore, a decrease of colorimetric signal arising from the catalytic process takes place upon in the presence of AFB1 in a concentration dependent manner in the 0.1-1.0 × 10(4) ng/mL range and with a colorimetric detection limit of 0.1 ng/mL. The new assay system exhibits high selectivity for AFB1 over other mycotoxins and can be employed detect the presence of AFB1 in ground corn samples. Overall, the strategy should serve as the basis for the development of rapid, simple and low-cost methods for detection of mycotoxins.

Terminal protection of small molecule-linked ssDNA for label-free and highly sensitive colorimetric detection of folate receptor biomarkers

Protection of ssDNA from digesting by Exo I generates amplified color transition for label-free and sensitive detection of folate receptors.

An amplified electrochemical aptasensor for thrombin detection based on pseudobienzymic Fe3O4-Au nanocomposites and electroactive hemin/G-quadruplex as signal enhancers

A sensitive and selective electrochemical aptasensor for thrombin detection was constructed based on hemin/G-quadruplex as the signal label and Fe3O4-Au nanocomposites with glucose oxidase (GOx-) and peroxide-mimicking enzyme activity as the signal enhancers. Due to their large surface area and good biocompatibility, Fe3O4-Au nanocomposites were employed to immobilize electroactive hemin/G-quadruplex, which was formed by the conjugation between a single-stranded guanine-rich nucleic acid and hemin. Based on the GOx-mimicking enzyme activity, Au nanoparticles on the surface of the Fe3O4-Au nanocomposites effectively catalyzed the oxidization of glucose in the presence of dissolved O2, accompanied by the production of H2O2. Both the Fe3O4 cores of Fe3O4-Au nanocomposites and hemin/G-quadruplex with H2O2-mimicking enzyme activity could catalyze the reduction of the generated H2O2, which promoted the electron transfer of hemin and amplified the electrochemical signal. The proposed electrochemical aptasensor had a wide dynamic linear range of 0.1 pM to 20 nM with a lower detection limit of 0.013 pM, which provided a promising method for a sensitive assay for the detection of proteins in electrochemical aptasensors.

G-quadruplex DNAzyme molecular beacon for amplified colorimetric biosensing of Pseudostellaria heterophylla

With an internal transcribed spacer of 18 S, 5.8 S and 26 S nuclear ribosomal DNA (nrDNA ITS) as DNA marker, we report a colorimetric approach for authentication of Pseudostellaria heterophylla (PH) and its counterfeit species based on the differentiation of the nrDNA ITS sequence. The assay possesses an unlabelled G-quadruplex DNAzyme molecular beacon (MB) probe, employing complementary sequence as biorecognition element and 1:1:1:1 split G-quadruplex halves as reporter. In the absence of target DNA (T-DNA), the probe can shape intermolecular G-quadruplex structures capable of binding hemin to form G-quadruplex-hemin DNAzyme and catalyze the oxidation of ABTS²⁻ to blue-green ABTS^•− by H₂O₂. In the presence of T-DNA, T-DNA can hybridize with the complementary sequence to form a duplex structure, hindering the formation of the G-quadruplex structure and resulting in the loss of the catalytic activity. Consequently, a UV-Vis absorption signal decrease is observed in the ABTS²⁻-H₂O₂ system. The “turn-off” assay allows the detection of T-DNA from 1.0 × 10⁻⁹ to 3.0 × 10⁻⁷ mol·L⁻¹ (R² = 0.9906), with a low detection limit of 3.1 × 10⁻¹⁰ mol·L⁻¹. The present study provides a sensitive and selective method and may serve as a foundation of utilizing the DNAzyme MB sensor for identifying traditional Chinese medicines.

Magnetic particle-based ultrasensitive biosensors for diagnostics

The process of sensitive and accurate detection of small quantities of disease biomarkers is critical for the clinical diagnosis of disease. In this regard, magnetic particles (MPs) have been widely used because of their unique magnetic properties allowing for efficient target capture, enrichment and convenient separation. These properties, coupled with great signal amplification, have enabled MP-based biosensors to achieve ultrasensitivities. Over the past few years, several ultrasensitive MP-based biosensors suitable for early clinical diagnostics have been reported. This article highlights some of the most recent developments, with a focus on MP-based ultrasensitive assays that use an antibody or aptamer as the target-binding agent, and that utilize efficient signal amplification/readout strategies.

Enzyme-free colorimetric bioassay based on gold nanoparticle-catalyzed dye decolorization

A novel, enzyme-free and aptamer-based colorimetric platform for protein detection has been developed, which takes advantage of aptamer-functionalized magnetic beads (MBs) for target capture, concentration and separation, and aptamer-conjugated gold nanoparticle (AuNP)-catalyzed color bleaching reaction of methyl orange (MO) to generate the colorimetric signals. It was demonstrated that the proposed colorimetric sensing strategy enables simple, cost-effective, sensitive and specific thrombin detection without the use of any enhancing solutions and enzymes. Herein, by naked eye observation, we can detect the human thrombin with a detection limit of approximately 320 pM, which can be further decreased to 30 pM with the help of a UV-vis instrument. In addition, this method also works for targets with two or more binding sites.

Pulsed-laser desorption/ionization of clusters from biofunctional gold nanoparticles: implications for protein detections

In this paper, we describe a pulsed-laser desorption/ionization mass spectrometry (LDI-MS) approach for the detection of proteins with femtomolar sensitivity through the analysis of gold (Au) clusters desorbed from aptamer-modified gold nanoparticles (Apt-AuNPs) on a nitrocellulose membrane (NCM). After the target protein (thrombin) was selectively captured by the surface-bound 29-mer thrombin-binding aptamer (TBA(29)), the thrombin/TBA(29)-AuNP complexes were concentrated and deposited onto the NCM to form a highly efficient background-free surface-assisted LDI substrate. Under pulsed laser irradiation (355 nm), the binding of thrombin decreased the desorption and/or ionization efficiencies of the Au atoms from the AuNP surfaces. The resulting decreases in the intensities of the signals for Au clusters in the mass spectra provided a highly amplified target-labeling indicator for the targeted protein. Under optimized conditions, this probe was highly sensitive (limit of detection: ca. 50 fM) and selective (by at least 1000-fold over other proteins) toward thrombin; it also improved reproducibility (<5%) of ion production by presenting a more-homogeneous substrate surface, thereby enabling LDI-based measurements for the accurate and precise quantification of thrombin in human serum. This novel LDI-MS approach allows high-speed analyses of low-abundance thrombin with ultrahigh sensitivity; decorating the AuNP surfaces with other aptamers also allowed amplification of other biological signals.

Characterization of a modified gold platform for the development of a label-free anti-thrombin aptasensor

This work reports the characterization of a modified gold surface as a platform for the development of a label free aptasensor for thrombin detection. The biorecognition platform was obtained by the self-assembly of 4-mercaptobenzoic acid onto a gold surface, covalent attachment of streptavidin and further immobilization of the biotinylated anti-thrombin aptamer. The biosensing platform was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation monitoring. The biorecognition event aptamer-thrombin was detected from changes in the SPR angle produced as a consequence of the molecular interaction between the aptasensor and the target protein. The biosensing platform demonstrated to be highly selective for human thrombin even in the presence of large excess of bovine thrombin, bovine serum albumin, cytochrome C, lysozyme and myoglobin. The relationship between the changes in the SPR angle and thrombin concentration was linear up to 0.19 μmol L(-1) (R(2)=0.992) while the detection limit was of 12.0 nmol L(-1) (240 fmol in the sample). This new sensing approach represents an interesting and promising alternative for the SPR-based quantification of thrombin.

Optical aptasensors for the analysis of the vascular endothelial growth factor (VEGF)

The vascular endothelial growth factor, VEGF, is an important biomarker for different diseases and clinical disorders. We present a series of optical aptasensor-based sensing platforms for VEGF that include the following: (i) A FRET-based sensor that involves the VEGF-induced separation of aptamer-functionalized quantum dots blocked by a quencher nucleic acid (detection limit 1 nM). (ii) A FRET-based sensor based on the VEGF-induced assembly of the aptamer subunits functionalized with QDs and a dye acceptor (Cy5), respectively (detection limit 12 nM). (iii) A chemiluminescence aptasensor based on VEGF-induced assembly of a hemin/G-quadruplex catalyst (detection limit 18 nM). (iv) A chemiluminescence aptasensor based on the VEGF-stimulated assembly of two aptamer subunits into the hemin/G-quadruplex catalyst (detection limit 2.6 nM). (v) A chemiluminescence resonance energy transfer (CRET) aptasensor based on the VEGF-induced assembly of a semiconductor QDs-hemin/G-quadruplex supramolecular structure (detection limit 875 pM). Furthermore, an amplified optical aptasensor system based on the Exonuclease III (Exo III) recycling of the VEGF analyte was developed. In this system, one aptamer subunit is modified at its 5' and 3' ends with QDs and a black hole quencher, respectively. The VEGF-induced self-assembly of the aptamer subunits result in the digestion of the quencher units and the autonomous recycling of the analyte, while triggering-on the luminescence of the QDs (detection limit 5 pM). The system was implemented to analyze VEGF in human sera samples.

Hierarchical dendritic gold microstructure-based aptasensor for ultrasensitive electrochemical detection of thrombin using functionalized mesoporous silica nanospheres as signal tags

A sensitive electrochemical approach for the detection of thrombin was designed by using densely packed hierarchical dendritic gold microstructures (HDGMs) with secondary and tertiary branches as matrices, and thionine-functionalized mesoporous silica nanospheres as signal tags. To prepare the signal tags, the positively charged thionine (as an indicator) was initially adsorbed onto the mesoporous silica nanoparticles (MSNs). Then [AuCl(4)](-) ions were in situ reduced on the thionine-modified MSNs by ascorbic acid to construct nanogold-decorated MSNs (GMSNs). The formed GMSNs were employed as label of the aminated aptamers. The assay was carried out in PBS, pH 7.4 with a sandwich-type assay mode by using the assembled thionine in the GMSNs as indicators. Compared with the pure silica nanoparticles, mesoporous silica could provide a larger surface for the immobilization of biomolecules and improve the sensitivity of the aptasensor. Under optimal conditions, the electrochemical aptasensors exhibited a wide linear range from 0.001 to 600 ng mL(-1) (i.e. 0.03 pM to 0.018 μM thrombin) with a low detection limit (LOD) of 0.5 pg mL(-1) (≈15 fM) thrombin at 3σ. No obvious non-specific adsorption was observed during a series of analyses to detect target analyte. The precision, selectivity and stability of the aptasensors were acceptable. Importantly, the methodology was evaluated with thrombin spiked samples in blank fetal calf serum, and the recoveries were 94.2-112%, indicating an exciting potential for thrombin detection.