Aptamers as Recognition Elements for Electrochemical Detection of Exosomes

Exosome analysis is emerging as an attractive noninvasive approach for disease diagnosis and treatment monitoring in the field of liquid biopsy. Aptamer is considered as a promising molecular probe for exosomes detection because of the high binding affinity, remarkable specificity, and low cost. Recently, many approaches have been developed to further improve the performance of electrochemical aptamer based(E-AB) sensors with a lower limit of detection. In this review, we focus on the development of using aptamer as a specific recognition element for exosomes detection in electrochemical sensors. We first introduce recent advances in evolving aptamers against exosomes. Then, we review methods of immobilization aptamers on electrode surfaces, followed by a summary of the main strategies of signal amplification. Finally, we present the insights of the challenges and future directions of E-AB sensors for exosomes analysis.     

Label free,highly sensitive and selective recognition of small molecule using gold surface confined aptamers

A highly sensitive and selective small molecule detection platform has been developed using aptamers immobilized on electrode surface. In our system, two aptamers were used – one of which is for ATP recognition and the other is for signal produce. We designed two probes L1 (containing ATP aptamer and a part of hemin aptamer) and L2 (containing the complementary strand of ATP aptamer and the rest of hemin aptamer) and immobilized L1 on electrode surface. L2 was used to hybridize to L1 and form L1–L2 duplex which brought the two parts of hemin aptamer into close proximity. Then hemin can be captured by this duplex and detected by electrochemical methods. When we introduced ATP into the system, the ATP binding destroyed the duplex and L2 diffused into the solution. As a result, hemin cannot be captured to bring electrochemical signal.     

Aptamer-based electrochemical sensors that are not based on the target binding-induced conformational change of aptamers

This study describes a new kind of aptamer-based electrochemical sensor that is not based on the target binding-induced conformational change of the aptamers by using a 15-mer thrombin-binding aptamer (5'-GGTTGGTGTGGTTGG-3') as the model oligonucleotide. The sensors are developed by first self-assembling the aptamer (i.e. a thrombin-binding aptamer) onto an Au electrode and then hybridizing the assembled aptamer with a ferrocene (Fc)-labeled short aptamer-complementary DNA oligonucleotide to form an electroactive double-stranded DNA (ds-DNA) oligonucleotide onto the Au electrode. The binding of the target (i.e. thrombin) towards the aptamer essentially destroys the Watson-Crick helix structure of the ds-DNA oligonucleotide assembled onto the electrode and leads to the dissociation of the Fc-labeled short complementary DNA oligonucleotide from the electrode surface to the solution, resulting in a decrease in the current signal obtained at the electrode, which can be used for the determination of the target. With the thrombin-binding aptamer as the model oligonucleotide, the current decrease obtained with the aptamer-based electrochemical sensors is linear with the concentration of thrombin within the concentration range from 0 to 10 nM (DeltaI/nA = 6.7C(thrombin)/nM + 2.8, gamma = 0.975). Unlike most kinds of existing aptamer-based electrochemical sensor, the electrochemical aptasensors demonstrated here are not based on the conformational change of the aptamers induced by the specific target binding. Moreover, the aptasensors are essentially label-free and are very responsive toward the targets. This study may pave a facile and general way to the development of aptamer-based electrochemical sensors.     

Optimization of electrochemical aptamer-based sensors via optimization of probe packing density and surface chemistry

Electrochemical, aptamer-based (E-AB) sensors, which are comprised of an electrode modified with surface immobilized, redox-tagged DNA aptamers, have emerged as a promising new biosensor platform. In order to further improve this technology we have systematically studied the effects of probe (aptamer) packing density, the AC frequency used to interrogate the sensor, and the nature of the self-assembled monolayer (SAM) used to passivate the electrode on the performance of representative E-AB sensors directed against the small molecule cocaine and the protein thrombin. We find that, by controlling the concentration of aptamer employed during sensor fabrication, we can control the density of probe DNA molecules on the electrode surface over an order of magnitude range. Over this range, the gain of the cocaine sensor varies from 60% to 200%, with maximum gain observed near the lowest probe densities. In contrast, over a similar range, the signal change of the thrombin sensor varies from 16% to 42% and optimal signaling is observed at intermediate densities. Above cut-offs at low hertz frequencies, neither sensor displays any significant dependence on the frequency of the alternating potential employed in their interrogation. Finally, we find that E-AB signal gain is sensitive to the nature of the alkanethiol SAM employed to passivate the interrogating electrode; while thinner SAMs lead to higher absolute sensor currents, reducing the length of the SAM from 6-carbons to 2-carbons reduces the observed signal gain of our cocaine sensor 10-fold. We demonstrate that fabrication and operational parameters can be varied to achieve optimal sensor performance and that these can serve as a basic outline for future sensor fabrication.     

Aptamer-based competitive electrochemical assay of small biomolecules

A convenient aptamer-based competitive electrochemical biosensor for a small biomolecule,adenosine,was described. The sensing surface was fabricated by self-assembly of an aptamer/mercaptohexanol monolayer on a gold disk electrode. The principle of this aptasensor is based on the competition between an adenosine target molecule and a ferrocene-conjugated signaling DNA strand for the aptamer binding site on the sensing surface. Due to the competitive nature of this assay,the electrochemical responses of the ...     

Reagentless, reusable, ultrasensitive electrochemical molecular beacon aptasensor

A bifunctional derivative of the thrombin-binding aptamer with a redox-active Fc moiety and a thiol group at the termini of the aptamer strand was synthesized. The ferrocene-labeled aptamer thiol was self-assembled through S-Au bonding on a polycrystalline gold electrode surface and the surface was blocked with 2-mercaptoethanol to form a mixed monolayer. By use of a fluorescent molecular beacon, the effect of counterions on quadruplex formation was established. The aptamer-modified electrode was characterized electrochemically by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The modified electrode showed a voltammetric signal due to a one-step redox reaction of the surface-confined ferrocenyl moiety of the aptamer immobilized on the electrode surface in 10 mM N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) buffer of pH 8.0. An increase in the DPV current signal was evident after blocking with 2-mercaptoethanol, effectively removing aptamer nonspecifically absorbed rather than bound to electrode surface or due to the formation of the aptamer-thrombin affinity interaction. The impedance measurement, in agreement with the differential pulse voltammetry (DPV), showed decreased Faradaic resistances in the same sequence. The "signal-on" upon thrombin association could be attributed to a change in conformation from random coil-like configuration on the probe-modified film to the quadruplex structure. The DPV of the modified electrode showed a linear response of the Fc oxidation signal to the increase in the thrombin concentration in the range between 5.0 and 35.0 nM with a linear correlation of r = 0.9988 and a detection limit of 0.5 nM. The molecular beacon aptasensor was amenable to full regeneration by simply unfolding the aptamer in 1.0 M HCl, and could be regenerated 25 times with no loss in electrochemical signal upon subsequent thrombin binding.     

Ultrasensitive electrochemiluminescent aptasensor for ochratoxin A detection with the loop-mediated isothermal amplification

In this study, we for the first time presented an efficient, accurate, rapid, simple and ultrasensitive detection system for small molecule ochratoxin A (OTA) by using the integration of loop-mediated isothermal amplification (LAMP) technique and subsequently direct readout of LAMP amplicons with a signal-on electrochemiluminescent (ECL) system. Firstly, the dsDNA composed by OTA aptamer and its capture DNA were immobilized on the electrode. After the target recognition, the OTA aptamer bond with target OTA and subsequently left off the electrode, which effectively decreased the immobilization amount of OTA aptamer on electrode. Then, the remaining OTA aptamers on the electrode served as inner primer to initiate the LAMP reaction. Interestingly, the LAMP amplification was detected by monitoring the intercalation of DNA-binding Ru(phen)₃²⁺ ECL indictors into newly formed amplicons with a set of integrated electrodes. The ECL indictor Ru(phen)₃²⁺ binding to amplicons caused the reduction of the ECL intensity due to the slow diffusion of Ru(phen)₃²⁺–amplicons complex to the electrode surface. Therefore, the presence of more OTA was expected to lead to the release of more OTA aptamer, which meant less OTA aptamer remained on electrode for producing LAMP amplicons, resulting in less Ru(phen)₃²⁺ interlaced into the formed amplicons within a fixed Ru(phen)₃²⁺ amount with an obviously increased ECL signal input. As a result, a detection limit as low as 10 fM for OTA was achieved. The aptasensor also has good reproducibility and stability.     

Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor

A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the “signal-off” of Fc and the “signal-on” of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10⁻¹³ to 10⁻⁸ mol L⁻¹ with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.     

Finding the Optimal Surface Density of Aptamer Monolayers by SPR Imaging Detection‐based Aptamer Microarrays

Surface plasmon resonance imaging (SPRi) by enabling label‐free, real time assessment of biomolecular interactions in multiplexed manner is one of the methods of choice for high throughput characterization of large pools of DNA aptamer candidates following in vitro selection. Moreover, with major advances in in situ amplification methods SPRi became also a viable detection platform for aptamer microarrays. In case of aptamer microarrays, commonly prepared by microspotting, the direct assessment of the surface density of aptamer probes, which is essential for both kinetic and sensing measurements is not possible. Therefore, here we introduce a methodology for simple, one‐step determination of surface densities of thiol labelled aptamer monolayers microspotted on gold SPRi chips. Based on this methodology we investigated in detail the effect of the surface density of aptamers on target binding through two aptamer‐target systems, i. e. human immunoglobulin E (hIgE) and six histidine tag 6xHis‐tag. We found that the surface density of the aptamers is indeed critical and shows a sharp maximum in terms of target binding efficiency, which is largely determined by the size of the target. The optimal aptamer surface densities determined, the immobilization chemistry (shared by many detection platforms, e. g., electrochemical, surface acoustic) and the trends identified may be used for rapid rational optimization of aptamer‐target assays.     

A versatile label-free and signal-on electrochemical biosensing platform based on triplex-forming oligonucleotide probe

Nucleic acid and protein assays are very important in modern life sciences, and the recently developed triplex-forming oligonucleotide probes provide a unique means for biological analysis of different kinds of analytes. Herein, we report a label-free and signal-on electrochemical sensor for the detection of specific targets, which is based on the triple-helix structure formation between the hairpin molecular beacon and the capture probe through the intermolecular DNA hybridization induced by Watson-Crick and Hoogsteen base pairings. Upon the introduction of a specific target, the triple-helical stem region is dissembled to liberate the hemin aptamer, and a G-quadruplex− hemin complex can be formed in the presence of K⁺ and hemin on the electrode surface to give an electrochemical response, thus signaling the presence of the target. With the use of Human Immunodeficiency Virus type 1 (HIV-1) as a proof-of-principle analyte, we first demonstrated this approach by using a molecular beacon, which consists of a central section with the DNA sequence complementary to HIV-1, flanked by two arm segments. This newly designed protocol provides an ultrasensitive electrochemical detection of HIV-1 with a limit of detection down to 0.054 nM, and also exhibit good selectivity. Therefore, the as-proposed strategy holds a great potential for early diagnosis in gene-related diseases, and with further development, it could be used as a universal protocol for the detection of various DNA sequences and may be extended for the detection of aptamer-binding molecules.     

Ru(bpy)3<Superscript>2+</Superscript>/β-cyclodextrin-Au nanoparticles/nanographene functionalized nanocomposites-based thrombin electrochemiluminescence aptasensor

In this study, a functionalized nanocomposite-based electrochemiluminescence (ECL) sensor for detecting thrombin was developed. First, Ru(bpy)₃²⁺/β-cyclodextrin-Au nanoparticles (β-CD-AuNPs)/nanographene (NGP) composites were used to modify the glassy carbon electrode (GCE) surface, and then aptamers (TBA1 and TBA2 with a 1:1 M ratio) were labeled with ferrocene (Fc) acting as the probes and were attached to the composite via the host–guest recognition between β-CD and Fc. In the absence of thrombin, the quenching of Fc to [Ru(bpy)₃]²⁺ was maintained, and “signal-off” ECL was observed. However, because of the specific combination of the aptamer probes and thrombin, the configuration of aptamer probes changed and escaped from the electrode surface once thrombin appears, which results in the quenching disappearance, and the ECL signal was changed from “off” to “on.” Meanwhile, the application of nanocomposites amplified the effect of “signal-on.” By this strategy, thrombin was detected with high sensitivity and with a detection limit down to 0.23 pM. Moreover, the relatively simple ECL sensor exhibited excellent reproducibility with at least 6 cycles of recovering the original signal.     

Electrochemical detection of thrombin by sandwich approach using antibody and aptamer

The goal of this work was to introduce a modified electrochemical sandwich model for target protein detection, exploiting antibody as the capturing probe, aptamer as the detection probe and methylene blue as the electrochemical active marker intercalating in the probing aptamer without previous labeling. With appropriate design of the sequence of the aptamer, the aptamer was successfully utilized instead of antibody for obtaining the electrochemical detection. A special immobilization interface consisting of nanogold-chitosan composite film was used to improve the conductivity and performance characteristics of the electrode. The capturing antibody was linked to the glassy carbon electrodes modified with composite film via a linker of glutaraldehyde. Differential pulse voltammetry was performed to produce the response signal. Thrombin was taken as the model target analyte to demonstrate the feasibility of proposed methodology. The sensor shows the linear response for thrombin in the range 1-60 nM with a detection limit of 0.5 nM. The proposed approach provides an alternative approach for sandwich protein assay using aptamers.     

Specific detection of oxytetracycline using DNA aptamer-immobilized interdigitated array electrode chip

An electrochemical sensing system for oxytetracycline (OTC) detection was developed using ssDNA aptamer immobilized on gold interdigitated array (IDA) electrode chip. A highly specific ssDNA aptamer that bind to OTC with high affinity was employed to discriminate other tetracyclines (TCs), such as doxycycline (DOX) and tetracycline (TET). The immobilized thiol-modified aptamer on gold electrode chip served as a biorecognition element for the target molecules and the electrochemical signals generated from interactions between the aptamers and the target molecules was evaluated by cyclic voltammetry (CV) and square wave voltammetry (SWV). The current decrease due to the interference of bound OTC, DOX or TET was analyzed with the electron flow produced by a redox reaction between ferro- and ferricyanide. The specificity of developed EC-biosensor for OTC was highly distinguishable from the structurally similar antibiotics (DOX and TET). The dynamic range was determined to be 1-100 nM of OTC concentration in semi-logarithmic coordinates.     

A new aptameric biosensor for cocaine based on surface-enhanced Raman scattering spectroscopy

The present study reports the proof of principle of a reagentless aptameric sensor based on surface-enhanced Raman scattering (SERS) spectroscopy with "signal-on" architecture using a model target of cocaine. This new aptameric sensor is based on the conformational change of the surface-tethered aptamer on a binding target that draws a certain Raman reporter in close proximity to the SERS substrate, thereby increasing the Raman scattering signal due to the local enhancement effect of SERS. To improve the response performance, the sensor is fabricated from a cocaine-templated mixed self-assembly of a 3'-terminal tetramethylrhodamine (TMR)-labeled DNA aptamer on a silver colloid film by means of an alkanethiol moiety at the 5' end. This immobilization strategy optimizes the orientation of the aptamer on the surface and facilitates the folding on the binding target. Under optimized assay conditions, one can determine cocaine at a concentration of 1 muM, which compares favorably with analogous aptameric sensors based on electrochemical and fluorescence techniques. The sensor can be readily regenerated by being washed with a buffer. These results suggest that the SERS-based transducer might create a new dimension for future development of aptameric sensors for sensitive determination in biochemical and biomedical studies.     

DNA aptamer folding on gold nanoparticles: from colloid chemistry to biosensors

We have investigated the effect of the folding of DNA aptamers on the colloidal stability of gold nanoparticles (AuNPs) to which an aptamer is tethered. On the basis of the studies of two different aptamers (adenosine aptamer and K+ aptamer), we discovered a unique colloidal stabilization effect associated with aptamer folding: AuNPs to which folded aptamer structures are attached are more stable toward salt-induced aggregation than those tethered to unfolded aptamers. This colloidal stabilization effect is more significant when a DNA spacer was incorporated between AuNP and the aptamer or when lower aptamer surface graft densities were used. The conformation that aptamers adopt on the surface appears to be a key factor that determines the relative stability of different AuNPs. Dynamic light scattering experiments revealed that the sizes of AuNPs modified with folded aptamers were larger than those of AuNPs modified with unfolded (but largely collapsed) aptamers in salt solution. From both the electrostatic and steric stabilization points of view, the folded aptamers that are more extended from the surface have a higher stabilization effect on AuNP than the unfolded aptamers. On the basis of this unique phenomenon, colorimetric biosensors have been developed for the detection of adenosine, K+, adenosine deaminase, and its inhibitors. Moreover, distinct AuNP aggregation and redispersion stages can be readily operated by controlling aptamer folding and unfolding states with the addition of adenosine and adenosine deaminase.     

Electrochemical aptasensor for the cancer biomarker CEA based on aptamer induced current due to formation of molybdophosphate

The authors describe a method for signal amplification in electrochemical aptasensors. It is based on the induction of an increased electrochemical current by the aptamer captured on a glassy carbon electrode (GCE). The phosphate groups on the aptamer backbone are brought to reaction with added molybdate to form a redox-active molybdophosphate precipitate on the surface of the GCE that generates a strong electrochemical current. To further enhance sensitivity, gold nanorods (GNRs) were selected as a support for the immobilization of aptamers. The aptasensor was applied to the determination of the cancer biomarker carcinoembryonic antigen (CEA) in a sandwich format. Antibody against CEA, CEA (antigen) and GNRs modified with CEA aptamer  were sequentially captured on the GCE. The resulting aptasensor, best operated at a voltage as low as 0.18 V vs. Ag/AgCl, is highly sensitive and has a wide linear range that extends from 0.1 pg·mL^?1 to 10 ng·mL^?1 of CEA. This amplification strategy uses an aptamer as both the recognition probe and signal probe and therefore simplifies signal transduction. Conceivably, this detection scheme may be adapted to numerous other electrochemical bioassays if respective antibodies and aptamers are available.

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Graphical abstract Schematic presentation of an electrochemical aptasensor based on aptamer induced electrochemical current for the detection of cancer biomarker carcinoembryonic antigen (CEA). Gold nanorods (GNR) are chosen for the immobilization of aptamers to increase the loading of aptamers.

     

Nanometric layers for direct, signal-on, selective, and sensitive electrochemical detection of oligonucleotides hybridization

We report a signal-on, reagentless electrochemical DNA biosensor, based on an electroactive self-assembled naphthoquinone derivative (JUG(thio)) monolayer. This system achieves highly sensitive (approximately 300 pM) and selective signal-on detection. Before hybridization, the single strand can interact with JUG(thio) and slow down the redox reaction. When the complementary target is added, the formation of the double helix eliminates the single strand/JUG(thio) interactions and the JUG(thio) redox rate, and hence the current increase.     

A Rapid and Sensitive Aptamer‐Based Electrochemical Biosensor for Direct Detection of Escherichia Coli O111

A sensitive and specific electrochemical biosensor based on target‐induced aptamer displacement was developed for direct detection of Escherichia coli O111. The aptamer for Escherichia coli O111 was immobilized on a gold electrode by hybridization with the capture probe anchored on the electrode surface through Au‐thiol binding. In the presence of Escherichia coli O111, the aptamer was dissociated from the capture probe‐aptamer duplex due to the stronger interaction between the aptamer and the Escherichia coli O111. The consequent single‐strand capture probe could be hybridized with biotinylated detection probe and tagged with streptavidin‐alkaline phosphatase, producing sensitive enzyme‐catalyzed electrochemical response to Escherichia coli O111. The designed biosensor showed weak electrochemical signal to Salmonella typhimurium, Staphylococcus aureus and common non‐pathogenic Escherichia coli, indicating high specificity for Escherichia coli O111. Under the optimal conditions, the proposed strategy could directly detect Escherichia coli O111 with the detection limit of 112 CFU mL^?1 in phosphate buffer saline and 305 CFU mL^?1 in milk within 3.5 h, demonstrated the sensitive and accurate quantification of target pathogenic bacteria. The designed biosensor could become a powerful tool for pathogenic microorganisms screening in clinical diagnostics, food safety, biothreat detection and environmental monitoring.     

Target-Dependent Protection of DNA Aptamers against Nucleolytic Digestion Enables Signal-On Biosensing with Toehold-Mediated Rolling Circle Amplification

We report a generalizable strategy for biosensing that takes advantage of the resistance of DNA aptamers against nuclease digestion when bound with their targets, coupled with toehold mediated strand displacement (TMSD) and rolling circle amplification (RCA). A DNA aptamer containing a toehold extension at its 5′-end protects it from 3′-exonuclease digestion by phi29 DNA polymerase (phi29 DP) in a concentration-dependent manner. The protected aptamer can participate in RCA in the presence of a circular template that is designed to free the aptamer from its target via TMSD. The absence of the target leads to aptamer digestion, and thus no RCA product is produced, resulting in a turn-on sensor. Using two different DNA aptamers, we demonstrate rapid and quantitative real-time fluorescence detection of two human proteins: platelet-derived growth factor (PDGF) and thrombin. Sensitive detection of PDGF was also achieved in human serum and human plasma, demonstrating the selectivity of the assay.     

DNA Electrochemical Aptasensor for Detecting Fumonisins B1 Based on Graphene and Thionine Nanocomposite

In this paper, a novel aptasensor was designed by with the dual amplification of Au nanoparticles (AuNPs) and graphene/thionine nanocomposites (GS‐TH) for sensitive determination of fumonisins B₁ (FB₁). AuNPs is modified at the electrode surface to increase the electrical conductivity and fabricate specific recognition interface for FB₁ through the hybridization of capture DNA and its aptamer. Large number of TH molecules were loaded at the surface of graphene sheet to served as electrochemical probe and increase its electrochemical signal due to the excellent conductivity and large surface area of graphene sheet. This type of nanocomposites is then assembled to the single strand section of FB₁ aptamer at electrode surface by π–π stacking interactions between them, leading to an enhanced electrochemical signal. After the specific combination between FB₁ aptamer and its target (FB₁) in solution, GS–TH was released from electrode surface, resulting in a decreased electrochemical signal. The result demonstrated that the decreased currents were proportional to the FB₁ concentration in the range of 1–10⁶ pg/mL with a detection limit of 1 pg/mL. Besides, the developed aptasensor was also applied successfully for the determination of FB₁ in feed samples. The result shows this aptasensor has a higher sensitivity and selectivity.