Ultrasensitive Norovirus Detection Using DNA Aptasensor Technology

DNA aptamers were developed against murine norovirus (MNV) using SELEX (Systematic Evolution of Ligands by EXponential enrichment). Nine rounds of SELEX led to the discovery of AG3, a promising aptamer with very high affinity for MNV as well as for lab-synthesized capsids of a common human norovirus (HuNoV) outbreak strain (GII.3). Using fluorescence anisotropy, AG3 was found to bind with MNV with affinity in the low picomolar range. The aptamer could cross-react with HuNoV though it was selected against MNV. As compared to a non-specific DNA control sequence, the norovirus-binding affinity of AG3 was about a million-fold higher. In further tests, the aptamer also showed nearly a million-fold higher affinity for the noroviruses than for the feline calicivirus (FCV), a virus similar in size and structure to noroviruses. AG3 was incorporated into a simple electrochemical sensor using a gold nanoparticle-modified screen-printed carbon electrode (GNPs-SPCE). The aptasensor could detect MNV with a limit of detection of approximately 180 virus particles, for possible on-site applications. The lead aptamer candidate and the aptasensor platform show promise for the rapid detection and identification of noroviruses in environmental and clinical samples.     

Determination of glucose and uric acid with bienzyme colorimetry on microfluidic paper-based analysis devices

An aptamer is an artificial functional oligonucleic acid, which can interact with its target molecule with high affinity and specificity. Enzyme linked aptamer assay (ELAA) is developed to detect cocaine using aptamer fragment/cocaine configuration based on the affinity interaction between aptamer fragments with cocaine. The aptasensor was constructed by cleaving anticocaine aptamer into two fragments: one was assembled on a gold electrode surface, while the other was modified with biotin at 3'-end, which could be further labelled with streptavidin-horseradish peroxidase (SA-HRP). Upon binding with cocaine, the HRP-labelled aptamer fragment/cocaine complex formed on the electrode would increase the reduction current of hydroquinone (HQ) in the presence of H(2)O(2). The sensitivity and the specificity of the proposed electrochemical aptasensor were investigated by differential pulse voltammetry (DPV). The results indicated that the DPV signal change could be used to sensitively detect cocaine with the dynamic range from 0.1 μM to 50 μM and the detection limit down to 20 nM (S/N=3). The proposed aptasensor has the advantages of high sensitivity and low background current. Furthermore, a new configuration for ELAA requiring only a single aptamer sequence is constructed, which can be generalized for detecting different kinds of targets by cleaving the aptamers into two suitable segments.     

Aptasensor for amplified IgE sensing based on fluorescence quenching by graphene oxide

Water‐soluble graphene oxide (GO) with a two‐dimensional layered nanostructure was synthesized and used as a quencher to construct a highly sensitive and selective fluorescence resonance energy transfer (FRET) aptasensor for sensing Immunoglobulin E (IgE). The fluorescein isothiocyanate (FITC)‐labeled aptamer could be adsorbed stably onto the surface of GO via π → π stacking interaction, which led to the occurrence of FRET from FITC to GO, and the fluorescence of FITC‐labeled aptamer was quenched by GO via energy transfer. In the presence of IgE, the fluorescence was recovered due to a higher affinity between the aptamer and IgE compared with interactions between GO and the aptamer, leading to a high signal‐to‐background ratio. The fluorescence intensity of the aptamer increased in proportion to the amount of IgE in the sample,so that IgE could be detected with a linear range of 60–225 pM and a detection limit of 22 pM. The assay was highly selective because the aptamer was unaffected by the presence of immunoglobulin G (IgG), human serum albumin (HSA) and bovine serum albumin (BSA). The practical application of the proposed aptasensor was successfully carried out for the determination of IgE in human serum samples. Copyright © 2012 John Wiley & Sons, Ltd.     

An aptasensor for rapid and sensitive detection of estrogen receptor alpha in human breast cancer

The analysis of estrogen receptor (ER) expression in breast carcinomas plays a crucial role in determining the endocrine responsiveness of tumors for systemic adjuvant therapy. Conventionally, the ER levels in breast carcinomas had been detected using the dextran-coated charcoal assay and radioimmunoassay, which are now substituted with safer and economic antibody-based assays such as immunohistochemistry (IHC) and enzyme-linked immunosorbent assay (ELISA). Despite a gold (Au) standard method, the IHC has been criticized for factors such as tissue fixation, antibody selection, and threshold staining for result interpretation that could falsify test accuracy and reproducibility. The quest for alternative methods of ER quantification in tissue samples paved the way for aptamer-based diagnostics. Previously, we have isolated a DNA aptamer against human ER alpha (ERα) using an in vitro evolution system. In this study, we developed an electrochemical sensor using the 76-nucleotide DNA ERα- aptamer for rapid, precise, and cost-effective detection of ERα expression in human breast cancer patients. The aptasensor was constructed by covalently immobilizing the thiolated ERα- aptamer onto a screen-printed Au electrode. Construction of aptasensors was confirmed through atomic force microscopy and differential pulse voltammetry measurements. A detection limit of 0.001 ng/ml was calculated for full-length ERα (66.2 kDa) in a detection time of 10 min. Analysis of the cancerous breast tissue samples using the ELISA and aptasensor methods enabled distinctive classification of samples into the categories of ER −ve, weak ER +ve, and strong ER +ve samples. The current change of this aptasensor lies within 5% after a storage of 60 days at 4°C. Further studies on a reasonably large sample size are required to realize the clinical potential of the sensor.     

Graphene oxide based fluorescent aptasensor for adenosine deaminase detection using adenosine as the substrate

We present a novel fluorescent aptasensor for simple and accurate detection of adenosine deaminase (ADA) activity and inhibition on the basis of graphene oxide (GO) using adenosine (AD) as the substrate. This aptasensor consists of a dye-labeled single-stranded AD specific aptamer, GO and AD. The fluorescence intensity of the dye-labeled AD specific aptamer is quenched very efficiently by GO as a result of strong π-π stacking interaction and excellent electronic transference of GO. In the presence of AD, the fluorescence of the GO-based probe is recovered since the competitive binding of AD and GO with the dye-labeled aptamer prevents the adsorption of dye-labeled aptamer on GO. When ADA was introduced to this GO-based probe solution, the fluorescence of the probe was quenched owing to ADA can convert AD into inosine which has no affinity to the dye-labeled aptamer, thus allowing quantitative investigation of ADA activity. The as-proposed sensor is highly selective and sensitive for the assay of ADA activity with a detection limit of 0.0129U/mL in clean buffer, which is more than one order of magnitude lower than the previous reports. Meanwhile, a good linear relationship with the correlation coefficient of R=0.9922 was obtained by testing 5% human serum containing a series of concentrations of ADA. Additionally, the inhibition effect of erythro-9-(2-hydroxy-3-nonyl) adenine on ADA activity was investigated in this design. The GO-based fluorescence aptasensor not only provides a simple, cost-effective and sensitive platform for the detection of ADA and its inhibitor but also shows great potential in the diagnosis of ADA-relevant diseases and drug development.     

基于HT-SELEX筛选的节球藻毒素-R适配体的鉴定

节球藻毒素-R（nodularin-R,NOD-R）是具有强烈肝毒性的蓝藻毒素。然而,现有的NOD-R检测技术均存在一定的局限性,亟待开发一种新的检测方法。本文利用指数富集的配基系统进化（systematic evolution of ligands by exponential enrichment,SELEX）技术结合高通量测序（HT-SELEX）,筛选出NOD-R特异的高亲和力适配体。生物膜干涉（biolayer interferometry,BLI）技术对适配体的鉴定结果表明,适配体H62与NOD-R之间的亲和力最高,达到了168 nM。而且,该适配体不与其他毒素结合,具有较高的特异性。以上结果表明,适配体H62有望作为NOD-R检测新方法——适配体生物传感器的分子识别元件。     

Electrochemical aptasensor for tetracycline detection

An electrochemical aptasensor was developed for the detection of tetracycline using ssDNA aptamer that selectively binds to tetracycline as recognition element. The aptamer was highly selective for tetracycline which distinguishes minor structural changes on other tetracycline derivatives. The biotinylated ssDNA aptamer was immobilized on a streptavidin-modified screen-printed gold electrode, and the binding of tetracycline to aptamer was analyzed by cyclic voltammetry and square wave voltammetry. Our results showed that the minimum detection limit of this sensor was 10 nM to micromolar range. The aptasensor showed high selectivity for tetracycline over the other structurally related tetracycline derivatives (oxytetracycline and doxycycline) in a mixture. The aptasensor developed in this study can potentially be used for detection of tetracycline in pharmaceutical preparations, contaminated food products, and drinking water.     

Selected ssDNA aptamers–graphene oxide-based fluorescent biosensor to detect sulfameter in milk

The abuse of sulfameter (SME) in animal husbandry can cause drug resistance and toxic or allergic reactions in humans. Therefore, it is very important to establish a simple, inexpensive, and efficient method for detecting SME in food. In this work, we propose a single fluorescent aptamer/graphene oxide (GO)-based biosensor to detect SME residues in milk. Aptamers that specifically bind to SME were screened using capture-SELEX and a ssDNA library immobilized on magnetic beads. The 68 active candidate aptamers were chemically synthesized for specificity and affinity characterization. Among the aptamers, the aptamer sulf-1 revealed the highest affinity (K_d = 77 ± 15 nM) to SME and was selected to construct a GO-based fluorescent biosensor for real milk sample detection. Under optimal conditions, the single fluorescent aptasensor had a wide linear range (R² was 0.997) from 7 to 336 ng/ml and a low detection limit of 3.35 ng/ml that was calculated with a 3SD/slope. The single fluorescent method was also validated using SME-fortified milk samples, showing average recoveries ranging from 99.01% to 104.60% with a relative standard deviation of less than 3.88%. These results demonstrate that this novel aptamer sensor provides an opportunity for sensitive, convenient, and accurate detection of SME residues in milk.     

4-(dimethylamino)butyric acid@PtNPs as enhancer for solid-state electrochemiluminescence aptasensor based on target-induced strand displacement

A solid-state electrochemiluminescence (ECL) aptasensor based on target-induced aptamer displacement for highly sensitive detection of thrombin was developed successfully using 4-(dimethylamino)butyric acid (DMBA)@PtNPs labeling as enhancer. Such a special aptasensor included three main parts: ECL substrate, ECL intensity amplification and target-induced aptamer displacement. The ECL substrate was made by modifying the complex of Pt nanoparticles (PtNPs) and tris(2,2-bipyridyl) ruthenium (II) (Ru(bpy)(3)(2+)) (Ru-PtNPs) onto nafion@multi-walled carbon nanotubes (nafion@MWCNTs) modified electrode surface. A complementary thrombin aptamer labeled by DMBA@PtNPs (Aptamer II) acted as the ECL intensity amplification. The thrombin aptamer (TBA) was applied to hybridize with the labeled complementary thrombin aptamer, yielding a duplex complex of TBA-Aptamer II on the electrode surface. The introduction of thrombin triggered the displacement of Aptamer II from the self-assembled duplex into the solution and the association of inert protein thrombin on the electrode surface, decreasing the amount of DMBA@PtNPs and increasing the electron transfer resistance of the aptasensor and thus resulting large decrease in ECL signal. With the synergistic amplification of DMBA and PtNPs to Ru(bpy)(3)(2+) ECL, the aptasensor showed an enlarged ECL intensity change before and after the detection of thrombin. As a result, the change of ECL intensity has a direct relationship with the logarithm of thrombin concentration in the range of 0.001-30 nM. The detection limit of the proposed aptasensor is 0.4 pM. Thus, the approach is expected to open new opportunities for protein diagnostics in clinical as well as bioanalysis in general.     

Label-free and sensitive faradic impedance aptasensor for the determination of lysozyme based on target-induced aptamer displacement

A label-free and sensitive faradic impedance spectroscopy (FIS) aptasensor based on target-induced aptamer displacement was developed for the determination of lysozyme as a model system. The aptasensor was fabricated by self-assembling the partial complementary single strand DNA (pcDNA)–lysozyme binding aptamer (LBA) duplex on the surface of a gold electrode. To measure lysozyme, the change in interfacial electron transfer resistance of the aptasensor using a redox couple of [Fe(CN)₆]^3−/4− as the probe was monitored. The introduction of target lysozyme induced the displacement of the LBA from the pcDNA–LBA duplex on the electrode into the solution, decreasing the electron transfer resistance of the aptasensor. The decrease in the FIS signal is linear with the concentration of lysozyme in the range from 0.2 nM to 4.0 nM, with a detection limit of 0.07 nM. The fabricated aptasensor shows a high sensitivity, good selectivity and satisfactory regeneration. This work demonstrates that a high sensitivity of the fabricated aptasensor can be obtained using a relatively short pcDNA. This work also demonstrates that the target-induced aptamer displacement strategy is promising in the design of an electrochemical aptasensor for the determination of lysozyme with good selectivity and high sensitivity.     

Colorimetric Aptasensor Using Unmodified Gold Nanoparticles for Homogeneous Multiplex Detection

Colorimetric aptasensors using unmodified gold nanoparticles (AuNPs) have attracted much attention because of their low cost, simplicity, and practicality, and they have been developed for various targets in the past several years. However, previous research has focused on developing single-target assays. Here, we report the development of a homogeneous multiplex aptasensor by using more than one class of aptamers to stabilize AuNPs. Using sulfadimethoxine (SDM), kanamycin (KAN) and adenosine (ADE) as example targets, a KAN aptamer (750 nM), an SDM aptamer (250 nM) and an ADE aptamer (500 nM) were mixed at a 1∶1∶1 volume ratio and adsorbed directly onto the surface of unmodified AuNPs by electrostatic interaction. Upon the addition of any of the three targets, the conformation of the corresponding aptamer changed from a random coil structure to a rigid folded structure, which could not adsorb and stabilize AuNPs. The AuNPs aggregated in a specific reaction buffer (20 mM Tris-HCl containing 20 mM NaCl and 5 mM KCl), which led to a color change from red to purple/blue. These results demonstrate that the multiplex colorimetric aptasensor detected three targets simultaneously while maintaining the same sensitivity as a single-target aptasensor for each individual target. The multiplex aptasensor could be extended to other aptamers for various molecular detection events. Due to its simple design, easy operation, fast response, cost effectiveness and lack of need for sophisticated instrumentation, the proposed strategy provides a powerful tool to examine large numbers of samples to screen for a small number of potentially positive samples containing more than one analyte, which can be further validated using sophisticated instruments.     

Enzyme-free fluorescence aptasensor for amplification detection of human thrombin via target-catalyzed hairpin assembly

Aptamers have many advantages, such as simple synthesis, good stability, high binding affinity and wide applicability, making them suitable candidates for protein detection. Since the disease-related protein may be present in very small amounts in biological samples, the development of amplification paths for aptasensors is essential. In this paper, we develop a simple and enzyme-free amplified aptasensor for protein detection via target-catalyzed hairpin assembly. This aptasensor contains two DNA hairpins termed as H1 and H2. H1, which is modified at its 5' and 3' ends with a fluorophore and a quencher respectively, consists of the aptamer sequence of human thrombin. Meanwhile, H2 is partially complementary to H1. These two hairpins H1 and H2 interact slowly with each other. Upon the addition of target protein, it can facilitate the opening of the hairpin structure of H1 and thus accelerate the hybridization between H1 and H2, resulting in the significant fluorescence enhancement of the system. By monitoring the change in fluorescence intensity, we could detect the target protein with high sensitivity. The detection limit of this aptasensor is 20 pM, which is more than two orders of magnitude lower than that of reported unamplified aptasensors. Furthermore, this amplified aptasensor shows high selectivity toward its target protein. Thus, the proposed aptasensor could be used as a simple, sensitive and selective platform for target protein detection.     

莱克多巴胺核酸适配体电化学生物传感器的研制

莱克多巴胺(RAC)被大量非法用于畜牧生产,易在动物组织残留,对人体造成危害。因此,研发灵敏、快捷的检测RAC的新方法是有效控制RAC滥用的关键环节之一。通过等温滴定量热法筛选到了一条对莱克多巴胺有高亲和力(Kd=1.66×10-6mol/L)的核酸适配体,利用该适配体作为识别分子成功的构建了莱克多巴胺适配体电化学生物传感器。差分脉冲伏安法分析,在0.5~1.0×102ng/ml浓度范围内,峰电流值的差值ΔIp与莱克多巴胺浓度的对数呈现良好的线性关系,相关系数R2=0.977 0,检测限达到0.1 ng/ml,反应时间为15 min。对同一浓度的莱克多巴胺重复检测7次,其峰电流值的RSD值为3.8%;说明该传感电极具有良好的检测重现性。不仅如此,该适配体传感器还具有良好的选择性。     

Highly sensitive electrochemical aptasensor for immunoglobulin E detection based on sandwich assay using enzyme-linked aptamer

Here, we describe the fabrication of an electrochemical immunoglobulin E (IgE) aptasensor using enzyme-linked aptamer in the sandwich assay method and thionine as redox probe. In this protocol, 5′-amine-terminated IgE aptamer and thionine were covalently attached on glassy carbon electrode modified with carbon nanotubes/ionic liquid/chitosan nanocomposite. Furthermore, another IgE aptamer was modified with biotin and enzyme horseradish peroxidase (HRP), which attached to the aptamer via biotin–streptavidin interaction. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry were performed at each stage of the chemical modification process to confirm the resulting surface changes. The presence of IgE induces the formation of a double aptamer sandwich structure on the electrode, and the electrocatalytic reduction current of thionine in the presence of hydrogen peroxide was measured as the sensor response. Under optimized conditions and using differential pulse voltammetry as the measuring technique, the proposed aptasensor showed a low detection limit (6 pM) and high sensitivity (1.88 μA nM⁻¹). This aptasensor also exhibited good stability and high selectivity for IgE detection without an interfering effect of some other proteins such as bovine serum albumin (BSA) and lysozyme. The application of the aptasensor for IgE detection in human serum sample was also investigated. The proposed protocol is quite promising as an alternative sandwich approach for various protein assays.     

Ultrasensitive one-step rapid visual detection of bisphenol A in water samples by label-free aptasensor

A simple, one-step, rapid method to detect bisphenol A (BPA) using a label-free aptasensor is presented. A high selective anti-BPA aptamer was added to gold nanoparticles (GNPs) to prepare the label-free aptasensor for BPA, which maintains good tolerance of GNPs under aqueous conditions with high salt concentrations. With the presence of BPA in the aptasensor system, the GNPs would aggregate by competitive binding of BPA and aptamer. Detection results can be visualized by the aggregation-induced color change of GNPs without the use of any instrumentation. The limit of visual detection (LOD) was found to be 0.1ng/mL by naked-eye observation, which was competitive to some current rapid BPA detection methods, even some instrumental based methods. Besides the obvious advantages, including reduced detection time and operation procedures, the results of this method meet the various detection requirements for BPA and are comparable to the traditional ELISA and instrument-based methods. The proposed one-step, label-free method was successfully used to determine BPA in actual water samples.     

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

A new fluorimetric aptasensor was designed for the determination of adenosine triphosphate (ATP) based on magnetic nanoparticles (MNPs) and carbon dots (CDs). In this analytical strategy, an ATP aptamer was conjugated on MNPs and a complementary strand of the aptamer (CS) was labeled with CDs. The aptamer and its CS were hybridized to form a double helical structure. The hybridized aptamers could be used for the specific recognition of ATP in a biological complex matrix using a strong magnetic field to remove the interfering effect. In the absence of ATP, no CDs–CS could be released into the solution and this resulted in a weak fluorescence signal. In the presence of ATP, the target binds to its aptamer and causes the dissociation of the double helical structure and liberation of the CS, such that a strong fluorescence signal was generated. The increased fluorescence signal was proportional to ATP concentration. The limit of detection was estimated to be 1.0 pmol L^–1 with a dynamic range of 3.0 pmol L^–1 to 5.0 nmol L^–1. The specific aptasensor was applied to detect ATP in human serum samples with satisfactory results. Moreover, molecular dynamic simulation (MDS) studies were used to analyze interactions of the ATP molecule with the aptamer.     

Detection of lysozyme with aptasensor based on fluorescence resonance energy transfer from carbon dots to graphene oxide

A photoluminescent aptasensor has been developed for the detection of lysozyme based on fluorescence resonance energy transfer (FRET) between the carbon dots (CDs) and graphene oxide (GO). In the sensing system, the CDs‐labeled aptamer is adsorbed onto the GO surface and the photoluminescence (PL) signal of the CDs is effectively quenched by GO. Addition of lysozyme can cause a significant FRET inhibition and recover the PL signal of the CDs due to the specific combination of lysozyme and its aptamer and the removal of the CDs‐labeled aptamer from GO surface. Under optimal conditions, the ratio of PL intensity change at 440 nm of the sensing system before and after the addition of lysozyme shows a good linear relationship against the concentration of lysozyme in the range of 0.01–2 μg/mL, with a low detection limit of 1 × 10^?3 μg/mL. In addition, the aptasensor has good selectivity so it can distinguish lysozyme with no or little interference by many other biomolecules. It was applied to the detection of lysozyme in human sera with satisfactory recoveries. The results demonstrate the applicability of the aptasensor for monitoring lysozyme in real samples. Copyright © 2016 John Wiley & Sons, Ltd.     

The affinity ratio--its pivotal role in gold nanoparticle-based competitive colorimetric aptasensor

We present an important role of the ratio of affinities in unmodified gold nanoparticles-based colorimetric aptasensor reactions. An affinity ratio, representing the competitive interactions among aptamers, targets, and unmodified gold nanoparticles (umAuNPs), was found to be an important factor for the sensitivity (the performance), where the affinity ratio is the affinity of the aptamer to targets divided by the affinity to umAuNPs (K(dAuNP)/K(dTarget)). In this study, the five different aptamers having different affinity ratios to both umAuNPs and targets are used, and the degree of color change is well correlated with its affinity ratio. This result is verified by using a tetracycline binding aptamer (TBA) showing different affinities to its three derivatives, tetracycline, oxytetracycline and doxycycline. Based on this model, the sensitivity of umAuNPs based colorimetric detection for ibuprofen can be enhanced simply through reducing the ibuprofen binding aptamer's affinity to umAuNP by using bis (p-sulfonatophenyl) phenylphosphine as an AuNP-capping ligand, instead of using the citrate. As a result, a clear color change is observed even at a 20-fold less amount of ibuprofen. This study presents that the performance (detection sensitivity) of umAuNPs-based colorimetric aptasensors could be improved by simply adjusting the affinity ratio of the aptamers to targets and umAuNPs, without knowing the conformational changes of aptamers upon the target binding or needing any modification of aptamer sequences.     

An Aptamer-Based Biosensor for Colorimetric Detection of Escherichia coli O157:H7

Background

An aptamer based biosensor (aptasensor) was developed and evaluated for rapid colorimetric detection of Escherichia coli (E. coli) O157:H7.

Methodology/Principal Findings

The aptasensor was assembled by modifying the truncated lipopolysaccharides (LPS)-binding aptamer on the surface of nanoscale polydiacetylene (PDA) vesicle using peptide bonding between the carboxyl group of the vesicle and the amine group of the aptamer. Molecular recognition between E. coli O157:H7 and aptamer at the interface of the vesicle lead to blue-red transition of PDA which was readily visible to the naked eyes and could be quantified by colorimetric responses (CR). Confocal laser scanning microscope (CLSM) and transmission electron microscopy (TEM) was used to confirm the specific interactions between the truncated aptamer and E. coli O157:H7. The aptasensor could detect cellular concentrations in a range of 10⁴∼ 10⁸ colony-forming units (CFU)/ml within 2 hours and its specificity was 100% for detection of E. coli O157:H7. Compared with the standard culture method, the correspondent rate was 98.5% for the detection of E. coli O157:H7 on 203 clinical fecal specimens with our aptasensor.

Conclusions

The new aptasensor represents a significant advancement in detection capabilities based on the combination of nucleic acid aptamer with PDA vesicle, and offers a specific and convenient screening method for the detection of pathogenic bacteria. This technic could also be applied in areas from clinical analysis to biological terrorism defense, especially in low-resource settings.