Thrombin-linked aptamer assay for detection of platelet derived growth factor BB on magnetic beads in a sandwich format

Aptamer-based sensing of breast cancer biomarkers: a comprehensive review of analytical figures of merit

INTRODUCTION

Accurate determination of the aberrantly expressed biomarkers such as human epidermal growth factor receptor 2 (HER2), carcinoembryonic antigen (CEA), platelet-derived growth factor (PDGF), mucin 1 (MUC1), and vascular endothelial growth factor VEGF₁₆₅ have played an essential role in the clinical management of the breast cancer. Assessment of these cancer-specific biomarkers has conventionally relied on time-taking methods like the enzyme-linked immunosorbent assay and immunohistochemistry. However, recent development in the aptamer-based diagnostics has allowed developing tools that may substitute the conventional means of biomarker assessment in breast cancer. Adopting the aptamer-based diagnostic tools (aptasensors) to clinical practices will depend on their analytical performance on clinical samples.

AREAS COVERED

In this review, we provide an overview of the analytical merits of HER2, CEA, PDGF, MUC1, and VEGF₁₆₅ aptasensors. Scopus and Pubmed databases were searched for studies reporting aptasensor development for the listed breast cancer biomarkers in the past one decade. Linearity, detection limit, and response time are emphasized.

EXPERT OPINION

In our opinion, aptasensors have proven to be on a par with the antibody-based methods for detection of various breast cancer biomarkers. Though robust validation of the aptasensors on significant sample size is required, their ability to detect pathophysiological range of biomarkers suggest the possibility of future clinical adoption.

The application of antibody-aptamer hybrid biosensors in clinical diagnostics and environmental analysis

The growing number of various diseases and the increase of environmental contamination are the causes for the development of novel methods for their detection. The possibility of the application of affinity-based biosensors for such purposes seems particularly promising as they provide high selectivity and low detection limits. Recently, the usage of hybrid antibody-aptamer sandwich constructs was shown to be more advantageous in terms of working parameters in comparison to aptamer-based and immune-based biosensors. This review is focused on the usage of hybrid antibody-aptamer receptor layers for the determination of clinically and environmentally important target molecules. In this work, antibodies and aptamer molecules are characterized and the methods of their immobilization as well as analytical signal generation are shown. This is followed by the critical presentation of examples of hybrid sandwich biosensors that have been elaborated in the past 12 years.

A sensitive thrombin-linked sandwich immunoassay for protein targets using high affinity phosphorodithioate modified aptamer for thrombin labeling

Thrombin and its aptamers have been well studied and widely used as models in aptamer based assays and sensors. Here we reported a thrombin-linked sandwich immunoassay for proteins to demonstrate new applications of thrombin and the aptamers, converting protein detection to analysis of thrombin label. In this assay, target protein was sandwiched by the capture antibody on a microplate and the biotinylated detection antibody. Thrombin bound to one biotinylated aptamer, and then the thrombin-labeled aptamer was attached on the sandwich complex through streptavidin-biotin interaction by using streptavidin as a linker. Thrombin catalyzed cleavage of fluorogenic peptide substrates, generating fluorescence signals for target detection. Among a few different anti-thrombin aptamers, the use of one nuclease resistant RNA aptamer having phosphorodithioate (PS2) modification on a specific backbone position enabled higher assay sensitivity due to its much higher affinity. This thrombin-linked sandwich immunoassay allowed detection of prostate-specific antigen (PSA) at 2 pM, an important protein related cancer disease, with high sensitivity and specificity. The strategy was general, and also enabled sensitive detection of botulinum neurotoxin type A (BoNTA) light chain, one toxin protein causing risk to human health. This assay combines advantages of antibody recognition, aptamer affinity labeling, high affinity of aptamers, and enzyme activity of thrombin. Labeling thrombin on the immunosandwich complex through simple affinity binding overcomes limitations of covalent conjugating enzyme on antibody in conventional immunoassay. This assay is promising in applications for protein detection.

A competitive thrombin-linked aptamer assay for small molecule: aflatoxin B1

We described a competitive thrombin-linked aptamer assay for small molecule, using aflatoxin B₁ (AFB₁) as a model, taking advantage of aptamer affinity binding and enzymatic activity of thrombin. We designed a dual functional DNA probe that contained the aptamer sequence for thrombin and the aptamer sequence for AFB₁. Thrombin was labeled on the DNA probe by affinity binding between thrombin and anti-thrombin aptamer. This thrombin-labeled DNA probe was attached on AFB₁-bovine serum albumin conjugate (BSA-AFB₁) coated on a microplate through the affinity interaction between AFB₁ and anti-AFB₁ aptamer. The thrombin attached on the microplate catalyzed the cleavage of peptide substrate into detectable product, generating signal for detection. In the presence of AFB₁, free AFB₁ competed with BSA-AFB₁ in the binding to the limited amount of DNA probe, leading to signal decrease. Detection of AFB₁ was achieved by measuring the signal change. Under optimized conditions, AFB₁ was successfully detected in the range from 0.5 nM to 1 μM when fluorogenic peptide substrate of thrombin and fluorescence analysis were applied. The use of chromogenic peptide substrate in the assay allowed the detection of AFB₁ ranging from 0.5 to 125 nM by simple absorbance analysis. The thrombin-linked aptamer assay showed good selectivity towards AFB₁, and enabled the detection of AFB₁ spiked in diluted beer and corn flour. This TLAA strategy extends the analytical application of thrombin and aptamers in detection of small molecules. Graphical abstract.

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.

An electrochemical tyrosinamide aptasensor using a glassy carbon electrode modified by N-acetyl-l-cysteine-capped Ag-In-S QDs

This paper reports an aptamer-based green approach for the electrochemical evaluation of tyrosinamide (Tyr-NH₂). In this regard, at the first step, an aqueous synthetic strategy for preparing N-acetyl-l-cysteine (NAC)-capped Ag-In-S (AIS) quantum dots (QDs) with bright yellow/orange emission was developed. The conjugation of AIS QDs to NAC-biomolecules provides opportunities for using them as luminescent contrast agents for living cell tracking and labeling or sensing studies. In the next step, the design stage of the aptasensor, the glassy carbon electrode (GCE) was modified with the AIS QDs and then the Tyr-NH₂ special aptamer, which has an amine group at its end, interacts with silver and indium ions at the surface of the AIS QDs and through the formation of covalent bonding of AgN and InN, attaches to the GCE surface modified with the AIS QDs. In this approach, for the first time, NAC-capped AIS QDs have been used to modify the electrode surface in the aptamer-based electrochemical sensor. The response changes of the [Fe(CN)₆]^4-/3- as redox probe, during the modification of GCE surface, the fabrication and assessment of proposed aptasensing, using the cyclic voltammetry, differential pulse voltammetry and electrochemical impedance spectroscopy were recorded. The designed aptasensor for the Tyr-NH₂ evaluation showed good linearity from 0.01 to 2.81 nM and 2.81-10.81 nM, and low detection limit of 3.34 pM. The obtained results of the stability, reproducibility and selectivity investigations implying that the reported aptasensor as the first aptamer-based electrochemical assay for Tyr-NH₂, can be reliable for the determination of Tyr-NH₂ in serum samples.

Sensitive aptamer-based fluorescene assay for ochratoxin A based on RNase H signal amplification

A new assay for the selective and sensitive aptamer-based fluorescent biosensor for ochratoxin A (OTA) detection is proposed. It consists of a ribonuclease H (RNase H)-assisted cycle response that leads to a significant amplification of the signal, which allow for a low limit of detection (LOD) of 0.08 ng/mL. By using this technique, a high selectivity for OTA against ochratoxin B and aflatoxin B₁ (AFB₁) was noticed. The quantitative determination in real samples has been verified using red wine samples spiked with a series of OTA concentrations (0.4, 4, and 12 ng/mL), and the recoveries ranged from 96.1 to 107.5%. This aptasensor has great practical applications in food industry and moreover, can be extended for the detection of other toxins by replacing the sequence of the recognition aptamer.

Recent advances on aptamer-based biosensors to detection of platelet-derived growth factor

Platelet-derived growth factor (PDGF-BB), a significant serum cytokine, is an important protein biomarker in diagnosis and recognition of cancer, which straightly rolled in proceeding of various cell transformations, including tumor growth and its development. Fibrosis, atherosclerosis are certain appalling diseases, which PDGF-BB is near to them. Generally, the expression amount of PDGF-BB increases in human life-threatening tumors serving as an indicator for tumor angiogenesis. Thus, identification and quantification of PDGF-BB in biomedical fields are particularly important. Affinity chromatography, immunohistochemical methods and enzyme-linked immunosorbent assay (ELISA), conventional methods for PDGF-BB detection, requiring high-cost and complicated instrumentation, take too much time and offer deficient sensitivity and selectivity, which restrict their usage in real applications. Hence, it is essential to design and build enhanced systems and platforms for the recognition and quantification of protein biomarkers. In the past few years, biosensors especially aptasensors have been received noticeable attention for the detection of PDGF-BB owing to their high sensitivity, selectivity, accuracy, fast response, and low cost. Since the role and importance of developing aptasensors in cancer diagnosis is undeniable. In this review, optical and electrochemical aptasensors, which have been applied by many researchers for PDGF-BB cancer biomarker detection, have been mentioned and merits and demerits of them have been explained and compared. Efforts related to design and development of aptamer-based biosensors using nanoparticles for sensitive and selective detection of PDGF-BB have been reviewed considering: Aptamer importance as recognition elements, principal, application and the recent improvements and developments of aptamer based optical and electrochemical methods. In addition, commercial biosensors and future perspectives for rapid and on-site detection of PDGF-BB have been summarized.

Proximity hybridization-mediated isothermal exponential amplification for ultrasensitive electrochemical protein detection

In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR) for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes. As a consequence, the output DNA was displaced, which can hybridize with the duplex probes immobilized on the electrode surface subsequently, leading to the initiation of the EXPAR as well as the cleavage of duplex probes. Each cleavage will release the gold nanoparticles (AuNPs) binding sequence. With the modification of G-quadruplex sequence, electrochemical signals were yielded by the AuNPs through oxidizing 3,3',5,5'-tetramethylbenzidine in the presence of H₂O₂. The study we proposed exhibited high sensitivity toward platelet-derived growth factor BB (PDGF-BB) with the detection limit of 52 fM. And, this method also showed great selectivity among the PDGF isoforms and performed well in spiked human serum samples.

Quantitative determination of VEGF165 in cell culture medium by aptamer sandwich based chemiluminescence assay

In this work, we have developed a sensitive and selective chemiluminescence (CL) assay for vascular endothelial growth factor (VEGF165) quantitative detection based on two specific VEGF165 binding aptamers (Apt). VEGF is a predominant biomarker in cancer angiogenesis, and sensitive detection method of VEGF are highly demanded for both academic study and clinical diagnosis of multiple cancers. In our experiment, VEGF165 was captured in a sandwich structure assembled by two binding aptamers, one capture aptamer was immobilized on streptavidin-coated magnetic beads (MBs) and another VEGF-binding aptamer was labeled by biotin for further phosphatase conjunction. After Apt-VEGF-Apt sandwich was formed on MBs surface, alkaline phosphatase (ALP) was modified to the second aptamer to catalyze CL reaction. By applying 4-methoxy-4-(3-phosphatephenyl)-spiro-(1,2-dioxetane-3,2-adamantane) (AMPPD) as CL substrate, strong signal intensity was achieved. VEGF165 content as low as 1ng/mL was detected in standard spiked samples by our assay, and linear range of working curve was confirmed from 1 to 20ng/mL. Then our method was successfully applied for cell culture medium analysis and on-chip hypoxic HepG2-HUVEC co-culture model study with excellent accuracy equal to ELISA Kit. Our developed assay demonstrated an outstanding performance in VEGF165 quantification and may be further extended to clinical testing of important biomarkers as well as probing microchip cell culture model.

Nuclease-aided target recycling signal amplification strategy for ochratoxin A monitoring

Ochratoxin A (OTA), a toxin produced by Aspergillus ochraceus and Penicillium verrucosum, is one of the most abundant food-contaminating mycotoxins worldwide. OTA mainly exerts nephrotoxicity, immunotoxicity, mutagenicity, carcinogenicity, teratogenicity, and neurotoxicity. This paper describes a simple and sensitive aptamer/single-walled carbon nanohorn (SWCNH)-based assay for OTA detection. SWCNHs can protect DNA from DNase I cleavage. However, aptamers can be detached from the surface of SWCNHs through specific target binding, exposing them to enzymatic cleavage and releases the target for a new cycle. Cycling of targets leads to significant signal amplification and low limit of detection (LOD), resulting in a nearly 20-fold reduction in LOD for OTA assay compared with non-target recycling under the same experimental parameters. This technique responded specifically to OTA without interference from other analogues (Ochratoxin B, Ochratoxin C, warfarin, and N-acetyl-l-phenylalanine). Moreover, the application of this technique in real sample has been verified using red wine samples spiked with a series of OTA concentrations. This aptasensor offers a great practical importance in food safety and can be widely extended for detection of other toxins by replacing the sequence of the recognition aptamer.