Label-free electrochemical detection of protein based on a ferrocene-bearing cationic polythiophene and aptamer

Recent Advances in DNA Nanomaterials

Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.

A dual-blocker aided and dual-label-free electrochemical biosensor based on mbHCR/rGO nanocomplexes for ultrasensitive DNA detection

Heterogeneous electrochemical DNA biosensors have attracted huge attention due to their enhanced signal sensitivity, compared to homogeneous biosensors. However, the high cost of probe labeling and the reduced recognition efficiency associated with current heterogeneous electrochemical biosensors confine their potential applications. In the present work, a dual-blocker assisted and dual-label-free heterogeneous electrochemical strategy based on multi-branched hybridization chain reaction (mbHCR) and reduced graphene oxide (rGO) was fabricated for ultrasensitive detection of DNA. The target DNA could trigger the mbHCR of two DNA hairpin probes, resulting in the generation of multi-branched long chain of DNA duplexes with bidirectional arms. One direction of the multi-branched arms in the mbHCR products were then bound to the label-free capture probe on the gold electrode through multivalent hybridization with enhanced recognition efficiency. The other direction of multi-branched arms in mbHCR product could adsorb rGO via π-π stacking interactions. Two DNA blockers were ingeniously designed to block the binding of excessive H1-pAT on electrode and to prevent the adsorption of rGO by residual unbound capture probes. As a result, with the electrochemical reporter methylene blue selectively intercalated into the long chain of DNA duplex and absorbed on rGO, a remarkable electrochemical signal rise was observed. Thus, a dual-blocker aided and dual-label-free electrochemical strategy for ultrasensitive DNA detection is readily realized with the merit of cost-effective. The as-developed dual-label-free electrochemical biosensor has great potential to be employed in nucleic acid related medical diagnostics.

Target-Synergized Biologically Mediated RAFT Polymerization for Electrochemical Aptasensing of Femtomolar Thrombin

The assay of thrombin levels is integral to the assessment of coagulation function and clinical screening of coagulation disorder-related diseases. In this work, we illustrate the ingenious use of the target-synergized biologically mediated reversible addition-fragmentation chain transfer (RAFT) polymerization (tsBMRP) as a novel amplification strategy for the electrochemical aptamer-based biosensing of thrombin at the femtomolar levels. Briefly, the tsBMRP-based strategy relies on the boronate affinity-mediated decoration of the glycan chain(s) of the target itself with RAFT agents and the subsequent recruitment of signal labels via BMRP, mediated by the direct reduction of RAFT agents by NADH into initiating/propagating radicals. Obviously, the tsBMRP-based strategy is biologically friendly, low-cost, and simple in operation. As thrombin is a glycoconjugate, its electrochemical aptasensing involves the use of the thrombin-binding aptamer (TBA) as the recognition receptor, the site-specific decoration of RAFT agents to the glycan chain of thrombin via boronate affinity, and further the recruitment of ferrocene signal labels via the BMRP of ferrocenylmethyl methacrylate (FcMMA). As boronate affinity results in the decoration of each glycan chain with tens of RAFT agents while BMRP recruits hundreds of signal labels to each RAFT agent-decorated site, the tsBMRP-based strategy allows us to detect thrombin at a concentration of 35.3 fM. This electrochemical aptasensor is highly selective, and its applicability to thrombin detection in serum samples has been further demonstrated. The merits of high sensitivity and selectivity, low cost, good anti-interference capability, and simple operation make the tsBMRP-based electrochemical thrombin aptasensor great promise in biomedical and clinical applications.

Analytical methods for microplastics in the environment: a review

Microplastic pollution is a recently discovered threat to ecosystems requiring the development of new analytical methods. Here, we review classical and advanced methods for microplastic analysis. Methods include visual analysis, laser diffraction particle, dynamic light scattering, scanning electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, thermal analysis, mass spectrometry, aptamer and in vitro selection, and flow cytometry.

Electrochemical Detection of Femtomolar DNA via Boronate Affinity-Mediated Decoration of Polysaccharides with Electroactive Tags

In view of their high efficiency and cost-effectiveness, polymers are of great promise as carriers for signal tags in amplified detection. Herein, we present a polysaccharide-amplified method for the electrochemical detection of a BRCA1 breast cancer gene-derived DNA target at the femtomolar levels. Briefly, peptide nucleic acid (PNA) with a complementary sequence was tethered as the capture probe for the DNA target, to which carboxyl group-containing polysaccharides were then attached via facile phosphate-Zr(IV)-carboxylate crosslinking, followed by the decoration of polysaccharide chains with electroactive ferrocene (Fc) signal tags via affinity coupling between a cis-diol site and phenylboronic acid (PBA) group. As the polysaccharide chain contains hundreds of cis-diol sites, boronate affinity can enable the site-specific decoration of each polysaccharide chain with hundreds of Fc signal tags, efficiently transducing each target capture event into the decoration of many Fc signal tags. As polysaccharides are cheap, renewable, ubiquitous, and biodegradable natural biopolymers, the use of polysaccharides for signal amplification offers the benefits of high efficiency, cost-effectiveness, excellent biocompatibility, and environmental friendliness. The linear range of the polysaccharide-amplified method for DNA detection was demonstrated to be from 10 fM to 10 nM (R² = 0.996), with the detection limit as low as 2.9 fM. The results show that this method can also discriminate single base mismatch with satisfactory selectivity and can be applied to DNA detection in serum samples. In view of these merits, the polysaccharide-amplified PNA-based electrochemical method holds great promise in DNA detection with satisfactory sensitivity and selectivity.

Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: advances, challenges, and opportunities

Clinical diagnostic tests should be quick, reliable, simple to perform, and affordable for diagnosis and treatment of diseases. In this regard, owing to their novel properties, biosensors have attracted the attention of scientists as well as end-users. They are efficient, stable, and relatively cheap. Biosensors have broad applications in medical diagnosis, including point-of-care (POC) monitoring, forensics, and biomedical research. The electrochemical nucleic acid (NA) biosensor, the latest invention in this field, combines the sensitivity of electroanalytical methods with the inherent bioselectivity of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The NA biosensor exploits the affinity of single-stranded DNA/RNA for its complementary strand and is used to detect complementary sequences of NA based on hybridization. After the NA component in the sensor detects the analyte, a catalytic reaction or binding event that generates an electrical signal in the transducer ensues. Since 2000, much progress has been made in this field, but there are still numerous challenges. This critical review describes the advances, challenges, and prospects of NA-based electrochemical biosensors for clinical diagnosis. It includes the basic principles, classification, sensing enhancement strategies, and applications of biosensors as well as their advantages, limitations, and future prospects, and thus it should be useful to academics as well as industry in the improvement and application of EC NA biosensors.

Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: Advances, challenges, and opportunities

Clinical diagnostic tests should be quick, reliable, simple to perform, and affordable for diagnosis and treatment of diseases. In this regard, owing to their novel properties, biosensors have attracted the attention of scientists as well as end-users. They are efficient, stable, and relatively cheap. Biosensors have broad applications in medical diagnosis, including point-of-care (POC) monitoring, forensics, and biomedical research. The electrochemical nucleic acid (NA) biosensor, the latest invention in this field, combines the sensitivity of electroanalytical methods with the inherent bioselectivity of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The NA biosensor exploits the affinity of single-stranded DNA/RNA for its complementary strand and is used to detect complementary sequences of NA based on hybridization. After the NA component in the sensor detects the analyte, a catalytic reaction or binding event that generates an electrical signal in the transducer ensues. Since 2000, much progress has been made in this field, but there are still numerous challenges. This critical review describes the advances, challenges, and prospects of NA-based electrochemical biosensors for clinical diagnosis. It includes the basic principles, classification, sensing enhancement strategies, and applications of biosensors as well as their advantages, limitations, and future prospects, and thus it should be useful to academics as well as industry in the improvement and application of EC NA biosensors.

Using Aptamers as a Novel Method for Determining GnRH/LH Pulsatility

Aptamers are a novel technology enabling the continuous measurement of analytes in blood and other body compartments, without the need for repeated sampling and the associated reagent costs of traditional antibody-based methodologies. Aptamers are short single-stranded synthetic RNA or DNA that recognise and bind to specific targets. The conformational changes that can occur upon aptamer–ligand binding are transformed into chemical, fluorescent, colour changes and other readouts. Aptamers have been developed to detect and measure a variety of targets in vitro and in vivo. Gonadotropin-releasing hormone (GnRH) is a pulsatile hypothalamic hormone that is essential for normal fertility but difficult to measure in the peripheral circulation. However, pulsatile GnRH release results in pulsatile luteinizing hormone (LH) release from the pituitary gland. As such, LH pulsatility is the clinical gold standard method to determine GnRH pulsatility in humans. Aptamers have recently been shown to successfully bind to and measure GnRH and LH, and this review will focus on this specific area. However, due to the adaptability of aptamers, and their suitability for incorporation into portable devices, aptamer-based technology is likely to be used more widely in the future.

Subsecond-Resolved Molecular Measurements Using Electrochemical Phase Interrogation of Aptamer-Based Sensors

Recent years have seen the development of a number of biosensor architectures that rely on target binding-induced changes in the rate of electron transfer from an electrode-bound receptor. Most often, the interrogation of these sensors has relied on voltammetric methods, such as square-wave voltammetry, which limit their time resolution to a few seconds. Here, we describe the use of an impedance-based approach, which we have termed electrochemical phase interrogation, as a means of collecting high time resolution measurements with sensors in this class. Specifically, using changes in the electrochemical phase to monitor target binding in an electrochemical-aptamer based (EAB) sensor, we achieve subsecond temporal resolution and multihour stability in measurements performed directly in undiluted whole blood. Electrochemical phase interrogation also offers improved insights into EAB sensors' signaling mechanism. By modeling the interfacial resistance and capacitance using equivalent circuits, we find that the only parameter that is altered by target binding is the charge-transfer resistance. This confirms previous claims that binding-induced changes in electron-transfer kinetics drive signaling in this class of sensors. Considering that a wide range of electrochemical biosensor architectures rely on this signaling mechanism, we believe that electrochemical phase interrogation may prove generalizable toward subsecond measurements of molecular targets.

Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations

Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.

Subsecond-Resolved Molecular Measurements in the Living Body Using Chronoamperometrically Interrogated Aptamer-Based Sensors

Electrochemical, aptamer-based (E-AB) sensors support the continuous, real-time measurement of specific small molecules directly in situ in the living body over the course of many hours. They achieve this by employing binding-induced conformational changes to alter electron transfer from a redox-reporter-modified, electrode-attached aptamer. Previously we have used voltammetry (cyclic, alternating current, and square wave) to monitor this binding-induced change in transfer kinetics indirectly. Here, however, we demonstrate the potential advantages of employing chronoamperometry to measure the change in kinetics directly. In this approach target concentration is reported via changes in the lifetime of the exponential current decay seen when the sensor is subjected to a potential step. Because the lifetime of this decay is independent of its amplitude (e.g., insensitive to variations in the number of aptamer probes on the electrode), chronoamperometrically interrogated E-AB sensors are calibration-free and resistant to drift. Chronoamperometric measurements can also be performed in a few hundred milliseconds, improving the previous few-second time resolution of E-AB sensing by an order of magnitude. To illustrate the potential value of the approach we demonstrate here the calibration-free measurement of the drug tobramycin in situ in the living body with 300 ms time resolution and unprecedented, few-percent precision in the determination of its pharmacokinetic phases.

High Surface Area Electrodes Generated via Electrochemical Roughening Improve the Signaling of Electrochemical Aptamer-Based Biosensors

The electrochemical, aptamer-based (E-AB) sensor platform provides a modular approach to the continuous, real-time measurement of specific molecular targets (irrespective of their chemical reactivity) in situ in the living body. To achieve this, however, requires the fabrication of sensors small enough to insert into a vein, which, for the rat animal model we employ, entails devices less than 200 μm in diameter. The limited surface area of these small devices leads, in turn, to low faradaic currents and poor signal-to-noise ratios when deployed in the complex, fluctuating environments found in vivo. In response we have developed an electrochemical roughening approach that enhances the signaling of small electrochemical sensors by increasing the microscopic surface area of gold electrodes, allowing in this case more redox-reporter-modified aptamers to be packed onto the surface, thus producing significantly improved signal-to-noise ratios. Unlike previous approaches to achieving microscopically rough gold surfaces, our method employs chronoamperometric pulsing in a 5 min etching process easily compatible with batch manufacturing. Using these high surface area electrodes, we demonstrate the ability of E-AB sensors to measure complete drug pharmacokinetic profiles in live rats with precision of better than 10% in the determination of drug disposition parameters.

Calibration-Free Electrochemical Biosensors Supporting Accurate Molecular Measurements Directly in Undiluted Whole Blood

The need to calibrate to correct for sensor-to-sensor fabrication variation and sensor drift has proven a significant hurdle in the widespread use of biosensors. To maintain clinically relevant (±20% for this application) accuracy, for example, commercial continuous glucose monitors require recalibration several times a day, decreasing convenience and increasing the chance of user errors. Here, however, we demonstrate a "dual-frequency" approach for achieving the calibration-free operation of electrochemical biosensors that generate an output by using square-wave voltammetry to monitor binding-induced changes in electron transfer kinetics. Specifically, we use the square-wave frequency dependence of their response to produce a ratiometric signal, the ratio of peak currents collected at responsive and non- (or low) responsive square-wave frequencies, which is largely insensitive to drift and sensor-to-sensor fabrication variations. Using electrochemical aptamer-based (E-AB) biosensors as our test bed, we demonstrate the accurate and precise operation of sensors against multiple drugs, achieving accuracy in the measurement of their targets of within better than 20% across dynamic ranges of up to 2 orders of magnitude without the need to calibrate each individual sensor.

A colorimetric aptamer biosensor based on cationic polythiophene derivative as peroxidase mimetics for the ultrasensitive detection of thrombin

A colorimetric assay for the ultrasensitive determination of thrombin was presented, in which the cationic polythiophene derivative was used as catalyst of the 3,3',5,5'-tetramethylbenzidine (TMB)-H₂O₂ reaction and the thrombin-binding aptamer (TBA) was used as inducing polymer's different conformation elements. It was found the cationic polythiophene derivative, poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-t-hiophene hydrochloride] (PMNT), can catalyze the oxidation reaction of TMB in the presence of H₂O₂ to produce a blue color solution. The catalytic activity of PMNT on the TMB-H₂O₂ reaction was closely relevant to the conformation of PMNT. The absorbance of TMB-H₂O₂ was distinctly increased in the presence of TBA. With the addition of thrombin, TBA interacted with thrombin to form a G-quadruplex structure. The conformational change weakened the catalytic activity of PMNT and resulted in a decrease in the absorbance. The colorimetric sensor could detect thrombin down to 4pM with high selectivity against other interfering proteins. This work is not only of importance for a better understanding of the unique properties of cationic polythiophenes derivative but also have great potential for medical diagnostics and therapy for human health.

A new FRET-based ratiometric probe for fluorescence and colorimetric analyses of adenosine 5′-triphosphate

A new ratiometric probe for ATP was designed based on the binding-induced modulation of FRET coupled with the ACQ sensing mechanism.

Sensitive analytical performance of folding based biosensor using methylene blue tagged aptamers

This work demonstrates the development of a folding based electrochemical aptasensor using methylene blue (MB) tagged anti-Ochratoxin A (OTA) aptamers. Different aptamer coupling strategies were tested using Hexamethylenediamine, polyethylene glycol, simple adsorption and diazonium coupling mechanism. The best sensitivity was recorded by oxidation of amines using hexamethylenediamine (HDMA) on screen printed carbon electrode (SPCE). To achieve the direct detection of OTA, aptamer conjugated redox probe was used and detection was demonstrated based on the conformational changes in aptamer structure upon OTA sensing. Signaling in this class of sensors arises from changes in electron transfer efficiency upon target-induced changes in the conformation/flexibility of the aptamer probe. These changes can be readily recorded electrochemically. The developed aptasensor is unique in its own mechanism as redox probe tagged aptamer coupling such as MB has never been tried to immobilize using long carbon chain spacers as, addition of spacers would provide more sensitive detection methods. A good dynamic range 0.01-5ng/ml was obtained for OTA with Limit of detection (LOD) 0.01ng/ml and Limit of quantification (LOQ) of 0.03ng/ml respectively. The good reproducibility was recorded with RSD% of 3.75. The obtained straight line equation was y=0.4035x+0.90311, r=0.9976. We believe that the sensor design guidelines outlined here represents a general strategy for developing new folding-based electrochemical aptasensors. The developed aptasensor was extended to screen cocoa samples for OTA contamination. The cocoa samples were extracted and purified using molecular imprinted polymer (MIP) columns. The aptasensor displayed good recovery values in the range 84-85% thus, exhibited the effectiveness of proposed aptasensor for such complex matrices.

Electroanalysis of pM-levels of urokinase plasminogen activator in serum by phosphorothioated RNA aptamer

Protein biomarkers of cancer allow a dramatic improvement in cancer diagnostics as compared to the traditional histological characterisation of tumours by enabling a non-invasive analysis of cancer development and treatment. Here, an electrochemical label-free assay for urokinase plasminogen activator (uPA), a universal biomarker of several cancers, has been developed based on the recently selected uPA-specific fluorinated RNA aptamer, tethered to a gold electrode via a phosphorothioated dA tag, and soluble redox indicators. The binding properties of the uPA-aptamer couple and interference from the non-specific adsorption of bovine serum albumin (BSA) were modulated by the electrode surface charge. A nM uPA electroanalysis at positively charged surfaces, complicated by the competitive adsorption of BSA, was tuned to the pM uPA analysis at negative surface charges of the electrode, being improved in the presence of negatively charged BSA. The aptamer affinity for uPA displayed via the binding/dissociation constant relationship correspondingly increased, ca. three orders of magnitude, from 0.441 to 367. Under optimal conditions, the aptasensor allowed 10(-12)-10(-9) M uPA analysis, also in serum, being practically useful for clinical applications. The proposed strategy for optimization of the electrochemical protein sensing is of particular importance for the assessment and optimization of in vivo protein ligand binding by surface-tethered aptamers.

Fluorescence and colorimetric detection of ATP based on a strategy of self-promoting aggregation of a water-soluble polythiophene derivative

A sensitive fluorescent and colorimetric dual-modal probe for the detection of ATP has been developed based on a strategy of self-promoting aggregation of a cationic polythiophene derivative bearing anthracene groups in the side chain with a detection limit as low as 10(-9) M.

Real Colorimetric Thrombin Aptasensor by Masking Surfaces of Catalytically Active Gold Nanoparticles

We presented a simple, cost-effective, and ultrasensitive colorimetric approach for visually detecting thrombin by the catalytic amplification of gold nanoparticles (AuNPs) and aptamer-thrombin recognition. Thrombin can be quantified in the presence of catalytic AuNP surface by using color-change time of 4-nitrophenol. Without thrombin, yellow 4-nitrophenol can freely access the surface of AuNP and becomes colorless 4-aminophenol. With the addition of thrombin, aptamer-thrombin with large size interaction masks the partial surfaces of AuNPs, and increases the reduction time of 4-nitrophenol to 4-aminophenol. The maximum number of bound thrombin fully mask the catalytic AuNP surface, and thus 4-nitrophenol cannot approach to AuNP surface, the color of the solution remains yellow. The limit of detection (LOD) of 0.1 nM can be achieved with naked eyes. Of note, the method was further applied for the detection of thrombin in human serum samples, showing the results in agreement with those values obtained in an immobilization buffer by the colorimetric method.

Electrochemical DNA hybridization sensors based on conducting polymers

Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.

A simple and sensitive label-free fluorescent approach for protein detection based on a Perylene probe and aptamer

Highly sensitive detection of proteins is of great importance for effective clinical diagnosis and biomedical research. However, so far most detection methods rely on antibody-based immunoassays and are usually laborious and time-consuming with poor sensitivity. Here, we developed a simple and ultra-sensitive method to detect a biomarker protein-thrombin by taking advantage of the fluorescent probe Perylene tetracarboxylic acid diimide (PTCDI) derivatives and thrombin aptamer. The water-soluble dye PTCDI shows strong fluorescence in buffer solution for the existence of free dye monomer, but becomes weak after aggregation through self-assembly on nucleic acid aptamer. In the presence of thrombin, it specifically binds to thrombin aptamer which causes the conformational transition between aptamer and PTCDI and results in a significant fluorescence recovery. The results showed that as low as 40 pM of thrombin could be detected by this method. The high sensitivity of the developed sensing system mainly attributes to the ultra-sensitivity of the fluorescence intensity changes of PTCDI. With the specificity of aptamer, the assay exhibited high selectivity for thrombin against three other proteins (bovine serum albumin, lysozyme, mouse IgG) and 1% diluted fetal bovine serum. The detection method might be extended to sensitive detection of a variety of proteins for its advantages of isothermal conditions required, simple and rapid without multiple separation and washing steps.

A label-free and high sensitive aptamer biosensor based on hyperbranched polyester microspheres for thrombin detection

In this paper, we have synthesized hyperbranched polyester microspheres with carboxylic acid functional groups (HBPE-CA) and developed a label-free electrochemical aptamer biosensor using thrombin-binding aptamer (TBA) as receptor for the measurement of thrombin in whole blood. The indium tin oxide (ITO) electrode surface modified with HBPE-CA microspheres was grafted with TBA, which has excellent binding affinity and selectivity for thrombin. Binding of the thrombin at the modified ITO electrode surface greatly restrained access of electrons for a redox probe of [Fe(CN)6](3-/4-). Moreover, the aptamer biosensor could be used for detection of thrombin in whole blood, a wide detection range (10fM-100nM) and a detection limit on the order of 0.90fM were demonstrated. Control experiments were also carried out by using bull serum albumin (BSA) and lysozyme in the absence of thrombin. The good stability and repeatability of this aptamer biosensor were also proved. We expect that this demonstration will lead to the development of highly sensitive label-free sensors based on aptamer with lower cost than current technology. The integration of the technologies, which include anticoagulant, sensor and nanoscience, will bring significant input to high-performance biosensors relevant to diagnostics and therapy of interest for human health.

Target-induced conjunction of split aptamer fragments and assembly with a water-soluble conjugated polymer for improved protein detection

Rapid and sensitive detection of proteins is crucial to biomedical research as well as clinical diagnosis. However, so far, most detection methods rely on antibody-based assays and are usually laborious and time-consuming, with poor sensitivity. Herein, we developed a simple and sensitive fluorescence-based strategy for protein detection by using split aptamer fragments and a water-soluble polycationic polymer (poly{[9,9-bis(6'-(N,N,N-diethylmethylammonium)hexyl)-2,7-fluorenylene ethynylene]-alt-co-[2,5-bis(3'-(N,N,N-diethylmethylammonium)-1'-oxapropyl)-1,4-phenylene] tetraiodide} (PFEP)). The thrombin-binding DNA aptamer was split into two fragments for target recognition. The PFEP with high fluorescence emission was used as energy donor to amplify the signal of dye-labeled DNA probe. In the absence of target, three DNA/PFEP complexes were formed via strong electrostatic interactions, resulting in efficient Föster resonance energy transfer (FRET) between two fluorophores. While the presence of target induces a conjunction of two split aptamer fragments to form G-quadruplex, and subsequent assemble with PFEP leading to the formation of G-quadruplex/thrombin/PFEP complex. The distance between the PFEP and dye increased due to protein's large size, leading to a remarkable decrease of the FRET signal. Compared with the intact aptamer, the use of shorter split aptamer fragments increases the possibility of forming G-quadruplex upon target. Thus, the rate of change of FRET signal before and after the addition of target improved significantly and a higher sensitivity (limit of detection (LOD) = 2 nM) was obtained. This strategy is superior in that it is rapid, has low cost and homogeneous detection, and does not need heating to avoid an unfavorable secondary structure of DNA probe. With further efforts, this method could be extended to a universal way for simple and sensitive detection of a variety of biomolecules.

Vascular Endothelial Growth Factor (VEGF) Detection Using an Aptamer and PNA-Based Bound/Free Separation System

We have developed a bound/free separation system using a vascular endothelial growth factor (VEGF) aptamer and a peptide nucleic acid (PNA) to detect VEGF. In this system, we designed capture PNA (CaPNA), which hybridizes with the aptamer in the absence of the target protein, but does not hybridize with the aptamer in the presence of the target protein due to steric hindrance and/or stabilization of the aptamer's structure. By removing the aptamers not bound to the target protein using CaPNA immobilized beads, we can detect the target protein by measuring signals labeled with the aptamer in the supernatant. In this study, we detected VEGF using CaPNA-immobilized beads without the time-consuming washing step. This simple and rapid system can detect 25 nM of VEGF in 15 min.

Novel homogeneous label-free electrochemical aptasensor based on functional DNA hairpin for target detection

We first developed a label-free and immobilization-free homogeneous electrochemical aptasensor, which combined a smart functional DNA hairpin and a designed miniaturized electrochemical device. Cocaine was chosen as a model target. The anticocaine aptamer and peroxidase-mimicking DNAzyme were integrated into one single-stranded DNA hairpin. Both aptamer and G-quadruplex were elaborately blocked by the stem region. The conformation switching induced by the affinity interaction between aptamer and cocaine released G-quadruplex part and turned on DNAzyme activity. The designed electrochemical device, constructed by a disposable micropipet tip and a reproducible carbon fiber ultramicroelectrode, was applied to the detection of homogeneous DNAzyme catalytic activity at the microliter level. The aptasensor realized the quantification of cocaine ranging from 1 to 500 μM with high specificity. The clever combination of the functional DNA hairpin and the novel device achieved an absolutely label-free electrochemical aptasensor, which showed excellent performance like low cost, easy operation, rapid detection, and high repeatability.

Signal enhancement in a lateral flow immunoassay based on dual gold nanoparticle conjugates

OBJECTIVE

In order to amplify signal of lateral flow immunoassay for specific detection of thrombin.

DESIGN AND METHODS

A new, simple method of amplifying signals using two gold nanoparticle conjugates (GNP) in gold-nanoparticle-based lateral flow immunoassay without an additional step was developed. The first conjugates were prepared by labeling DNA1 with 30 nm GNPs, and the second conjugates were prepared by immobilizing both DNA2 and thrombin aptamer on the surfaces of 16 nm GNPs.

RESULTS

The detection limit was improved 30 times. The lateral flow immunoassay developed in this study was applied to detect thrombin concentration in the range of 0.5-120 nM with a detection limit of 0.25 nM.

CONCLUSIONS

The lateral flow immunoassay developed in this study was used to detect thrombin concentrations within a range of 0.5-120 nM with a detection limit of 0.25 nM. This assay is very versatile and can be easily extended to other proteins.

Electrokinetic characterization of superparamagnetic nanoparticle-aptamer conjugates: design of new highly specific probes for miniaturized molecular diagnostics

With the view of designing new nanoparticle (NP)-aptamer conjugates and proving their suitability as biorecognition tools for miniaturized molecular diagnostics, new maghemite-silica core-shell NP-aptamer conjugates were characterized for the first time in terms of grafting rate and colloidal stability under electrophoretic conditions using capillary electrophoresis. After the grafting rate (on the order of six to 50) of the lysozyme-binding aptamer had been estimated, the electrophoretic stability and peak dispersion of the resulting oligonucleotide-NP conjugates were estimated so as to determine the optimal separation conditions in terms of buffer pH, ionic strength and nature, as well as temperature and electric field strength. The effective surface charge density of the NPs was close to zero for pH lower than 5, which led to some aggregation. The NPs were stable in the pH range from 5 to 9, and an increase in electrophoretic mobility was evidenced with increasing pH. Colloidal stability was preserved at physiological pH for both non-grafted NPs and grafted NPs in the 10-100 mM ionic strength range and in the 15-60 °C temperature range. A strong influence of the nature of the buffer counterion on NP electrophoretic mobility and peak dispersion was evidenced, thus indicating some interactions between buffer components and NP-aptamer conjugates. Whereas an electric field effect (50-900 V cm(-1)) on NP electrophoretic mobility was evidenced, probably linked to counterion dissociation, temperature seems to have an appreciable effect on the zeta potential and aptamer configuration as well. This information is crucial for estimating the potentialities of such biorecognition tools in electrophoretic systems.

Aptamer-linked biosensor for thrombin based on AuNPs/thionine-graphene nanocomposite

A novel protocol of electrochemical thrombin aptasensor based on a goldnanoparticles/thionine-graphene (AuNPs/Th-G) nanocomposite modified glassy carbon electrode was presented. Graphene was non-covalently functionalized by thionine viaπ-stacking interaction, and then AuNPs were electrodeposited onto the Th-G surface. The morphology and conductivity of the AuNPs/Th-G nanocomposite were characterized by scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. The ethanethiol-substituted oligonucleotide probe was immobilized onto the surface of the AuNPs/Th-G nanocomposite to prepare an electrochemical biosensing platform. The aptamer-thrombin reaction was monitored by differential pulse voltammetry. Under optimum conditions, the proposed biosensor exhibits high sensitivity and a low detection limit for thrombin determination. The thrombin could be quantified in a wide range of 0.5 to 40 nM and with a low detection limit of 0.093 nM (S/N = 3).

Coffee ring aptasensor for rapid protein detection

We introduce a new biosensing platform for rapid protein detection that combines one of the simplest methods for biomolecular concentration, coffee ring formation, with a sensitive aptamer-based optical detection scheme. In this approach, aptamer beacons are utilized for signal transduction where a fluorescence signal is emitted in the presence of the target molecule. Signal amplification is achieved by concentrating aptamer-target complexes within liquid droplets, resulting in the formation of coffee ring "spots". Surfaces with various chemical coatings were utilized to investigate the correlation among surface hydrophobicity, concentration efficiency, and signal amplification. On the basis of our results, we found that the increase in the coffee ring diameter with larger droplet volumes is independent of surface hydrophobicity. Furthermore, we show that highly hydrophobic surfaces produce enhanced particle concentration via coffee ring formation, resulting in signal intensities 6-fold greater than those on hydrophilic surfaces. To validate this biosensing platform for the detection of clinical samples, we detected α-thrombin in human serum and 4-fold-diluted whole blood. Coffee ring spots from serum and blood produced detection signals up to 40 times larger than those from samples in liquid droplets. Additionally, this biosensor exhibits a lower limit of detection of 2 ng/mL (54 pM) in serum, and 4 ng/mL (105 pM) in blood. On the basis of its simplicity and high performance, this platform demonstrates immense potential as an inexpensive diagnostic tool for the detection of disease biomarkers, particularly for use in developing countries that lack the resources and facilities required for conventional biodetection practices.

Thrombin aptasensing with inherently electroactive graphene oxide nanoplatelets as labels

Graphene and its associated materials are commonly used as the transducing platform in biosensing. We propose a different approach for the application of graphene in biosensing. Here, we utilized graphene oxide nanoplatelets as the inherently electroactive labels for the aptasensing of thrombin. The basis of detection lies in the ability of graphene oxide to be electrochemically reduced, thereby providing a well-defined reduction wave; one graphene oxide nanoplatelet of dimension 50 × 50 nm can provide a reduction signal by accepting ~22,000 electrons. We demonstrate that by using graphene oxide nanoplatelets as an inherently electroactive label, we can detect thrombin in the concentration range of 3 pM-0.3 μM, with good selectivity of the aptamer towards interferences by bovine serum albumin, immunoglobulin G and avidin. Therefore, the inherently electroactive graphene oxide nanoplatelets are a material which can serve as an electroactive label, in a manner similar to metallic nanoparticles.

A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification

In this work, a novel signal amplification electrochemical aptasensor for the sensitive and selective detection of thrombin was successfully fabricated. The amplification method was based on the hybridization chain reaction (HCR) and a pseudobienzyme electrocatalytic system. HCR-based double-stranded DNA (dsDNA) polymers not only constructed an effective carrier for anchoring larger amounts of electron mediator methylene blue (MB) into the DNA duplexes to produce a strong differential pulse voltammetry (DPV) signal, but also resulted in the formation of hemin/G-quadruplex DNAzymes nanowires by intercalating hemin into two induced single-stranded DNA (ssDNA). With the addition of NADH into the electrolytic cell, the hemin/G-quadruplex acting as an NADH oxidase and HRP-mimicking DNAzyme for the pseudobienzyme amplifying system could in situ biocatalyze the formation of H₂O₂ with local concentrations and low transfer loss resulting in dramatic signal enhancements. The binding event can be detected by a decrease in the integrated charge of MB which electrostatically absorbed onto dsDNA polymers. In the presence of thrombin, the dsDNA polymers associated with MB and hemin/G-quadruplex structures were removed from the electrode surface, leading to a significant decrease of redox current. DPV signals of MB provided quantitative measures of the concentrations of thrombin, with a linear calibration range of 0.01-50 nM and a detection limit of 2 pM. Moreover, the resulting aptasensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay and various protein analyses.

Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors

Aptamers are single-stranded nucleic acids that can be selected in vitro with special folding structures to bind to many different small-molecule, protein, and cellular targets. Over the past two decades, aptamers have become novel promising recognition elements for the fabrication of biosensors. These ‘aptasensors’ have several advantages over antibodies in that they are relatively easy to synthesise or modify in vitro, and can be appended with linkers and reporters for adaptation to various sensing strategies. In this chapter, we introduce the various electrochemical techniques that can be used as powerful readout methods for aptasensors, providing a brief introduction to aptamers and related electrochemical techniques, and then a detailed description of various branches within the field, including labelled strategies, unlabelled strategies, and enzyme-amplified strategies. For each type of approach, several basic and improved design principles will be addressed. It is hoped that, through this discussion, readers will get a sense of how several variables (aptamers, targets and redox reporters) are successfully combined with electrochemical techniques in order to produce a series of sensing platforms with high selectivity and sensitivity.

Immunoassays with protein misfolding cycle amplification: a platform for ultrasensitive detection of antigen

Protein misfolding cycle amplification (PMCA), a novel technology on amplifying cyclically misfolded proteins in vitro, is conceptually analogous to DNA amplification by polymerase chain reaction (PCR) and has tremendous implications for the researches and diagnosis. Here we first introduce the protein amplification technology into the classic immunoassay and develop a PMCA-based immunoassay (immuno-PMCA) for highly sensitive detection of antigen. This method takes advantage of sandwich binding of two affinity aptamers for increased specificity, magnetic nanoparticles for fast magnetic separation, PMCA for signal amplification, and conjugated polyelectrolytes for visual detection, allowing the detection limit of antigen by colorimetry down to femtomolar level with a wide linear range from 10 to 10(4) fM. More importantly, no specialized facilities or enzymes are needed either in the amplification reaction or the evaluation of results, which indicates its great potential application in immunological research and clinical diagnostics.

Towards understanding of protein adsorption behavior on plasma polymerized pyrrole film

Plasma polymerized pyrrole-like (PPpy) films exhibit good environmental stability and offer high reactivity with biomolecules. The present paper follows on from previous work on PPpy films applied as DNA immobilization/hybridization and describes the adsorption kinetics of bovine serum albumin (BSA) on PPpy films. Atom force microscopy was used to detect the surface roughness of PPpy surfaces obtained at different input powers or for different polymerization time, including the surface roughness before and after BSA adsorption. The influence of experimental conditions (i.e., the plasma input power, the polymerization time, the concentration of BSA, and the pH values of buffer solutions) on protein adsorption was investigated in situ by Surface plasmon resonance spectroscopy (SPR). SPR analysis confirmed the differently dynamic adsorption behavior of BSA on PPpy films under various experimental conditions. The adsorption constant, K a , was deduced from Langmuir isotherm equations, which were simulated using experimental data collected by SPR and electrochemical impedance spectroscopy (EIS). Analysis of the combination data of SPR and EIS indicates that PPpy films under various conditions show completely different adsorption behaviors and could be applied as biomaterials for electrochemical protein sensing or as protein-resistant.

Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development

Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.

General colorimetric detection of proteins and small molecules based on cyclic enzymatic signal amplification and hairpin aptamer probe

In this work, we developed a simple and general method for highly sensitive detection of proteins and small molecules based on cyclic enzymatic signal amplification (CESA) and hairpin aptamer probe. Our detection system consists of a hairpin aptamer probe, a linker DNA, two sets of DNA-modified AuNPs, and nicking endonuclease (NEase). In the absence of a target, the hairpin aptamer probe and linker DNA can stably coexist in solution. Then, the linker DNA can assemble two sets of DNA-modified AuNPs, inducing the aggregation of AuNPs. However, in the presence of a target, the hairpin structure of aptamer probe is opened upon interaction with the target to form an aptamer probe-target complex. Then, the probe-target complex can hybridize to the linker DNA. Upon formation of the duplex, the NEase recognizes specific nucleotide sequence and cleaves the linker DNA into two fragments. After nicking, the released probe-target complex can hybridize with another intact linker DNA and the cycle starts anew. The cleaved fragments of linker DNA are not able to assemble two sets of DNA-modified AuNPs, thus a red color of separated AuNPs can be observed. Taking advantage of the AuNPs-based sensing technique, we are able to assay the target simply by UV-vis spectroscopy and even by the naked eye. Herein, we can detect the human thrombin with a detection limit of 50 pM and adenosine triphosphate (ATP) with a detection limit of 100 nM by the naked eye. This sensitivity is about 3 orders of magnitude higher than that of traditional AuNPs-based methods without amplification. In addition, this method is general since there is no requirement of the NEase recognition site in the aptamer sequence. Furthermore, we proved that the proposed method is capable of detecting the target in complicated biological samples.

An aptamer-based fluorescence biosensor for multiplex detection using unmodified gold nanoparticles

A novel aptamer-based fluorescence biosensor for multiplex detection using unmodified AuNPs is developed to detect adenosine, thrombin and cocaine. Besides, this strategy can be applied to detect other small molecule substances.

Highly sensitive detection of platelet-derived growth factor on a functionalized diamond surface using aptamer sandwich design

Aptamer-based fluorescence detection of platelet-derived growth factor (PDGF) on a functionalized diamond surface was demonstrated. In this work, a sandwich design based on the ability of PDGF to bind with aptamers at its two available binding sites was employed. It was found that this sandwich design approach significantly increases the fluorescence signal intensity, and thereby a very low detection limit of 4 pM was achieved. The effect of the ionic strength of MgCl(2) buffer solution was also investigated, and the most favourable binding for PDGF-BB occurred at a Mg(2+) concentration of 5.5 mM. Since the aptamers bind to the target PDGF with high affinity, fluorescence detection exhibited high selectivity towards different biomolecules. The high reproducibility of detection was confirmed by performing three cycles of measurements over a period of three days.

A label-free aptasensor for the sensitive and specific detection of cocaine using supramolecular aptamer fragments/target complex by electrochemical impedance spectroscopy

A simple and label-free aptasensor for sensitive and specific detection of cocaine was developed by measuring the change in electrochemical impedance spectra (EIS), based on the formation of a supramolecular aptamer fragments/substrate complex. An anticocaine aptamer was divided into two fragments, Cx and Cy. Three different sensing interfaces, called Au/Cx5S/MCE, Au/Cy3S/MCE and Au/Cy5S/MCE, were fabricated by immobilizing Cx or Cy on a gold electrode through modifying their 5' or 3' end with a thiolated group followed by the treatment with mercaptoethanol (MCE). The formation of the corresponding supramolecular aptamer fragments/cocaine complex was investigated via monitoring electrochemical impedance spectra in the presence of [Fe(CN)(6)](3-/4-). The interfacial electron transfer resistance (R(et)) was found to depend strongly on the cocaine concentration. Since the supramolecular aptamer fragments/cocaine complex was formed on the electrode surface, the sensing interface strongly affected the sensitivity of the aptasensor. Au/Cx5S/MCE was shown to have good sensitivity within a cocaine detection range of 0.1-20 μM. Moreover, MCE was shown to improve the sensitivity of the aptasensor greatly. Even without the help of amplification or labeling, cocaine concentrations as low as 100 nM could be easily detected by the impedimetric aptasensor developed. The specificity and regeneration of the cocaine aptasensor were also investigated and satisfactory results were obtained. The developed aptasensor was successfully applied to detect the cocaine in biological fluids.

Aptamers and their biological applications

Recently, aptamers have attracted the attention of many scientists, because they not only have all of the advantages of antibodies, but also have unique merits, such as thermal stability, low cost, and unlimited applications. In this review, we present the reasons why aptamers are known as alternatives to antibodies. Furthermore, several types of in vitro selection processes, including nitrocellulose membrane filtration, affinity chromatography, magnetic bead, and capillary electrophoresis-based selection methods, are explained in detail. We also introduce various applications of aptamers for the diagnosis of diseases and detection of small molecules. Numerous analytical techniques, such as electrochemical, colorimetric, optical, and mass-sensitive methods, can be utilized to detect targets, due to convenient modifications and the stability of aptamers. Finally, several medical and analytical applications of aptamers are presented. In summary, aptamers are promising materials for diverse areas, not just as alternatives to antibodies, but as the core components of medical and analytical equipment.