Ultrasensitive aptamer-based protein detection via a dual amplified biocatalytic strategy

Conjugated Polymers for Aptasensing Applications

Rapid and specific assaying of molecules that report on a pathophysiological condition, environmental pollution, or drug concentration is pivotal for establishing efficient and accurate diagnostic systems. One of the main components required for the construction of these systems is the recognition element (receptor) that can identify target analytes. Oligonucleotide switching structures, or aptamers, have been widely studied as selective receptors that can precisely identify targets in different analyzed matrices with minimal interference from other components in an antibody-like recognition process. These aptasensors, especially when integrated into sensing platforms, enable a multitude of sensors that can outperform antibody-based sensors in terms of flexibility of the sensing strategy and ease of deployment to areas with limited resources. Research into compounds that efficiently enhance signal transduction and provide a suitable platform for conjugating aptamers has gained huge momentum over the past decade. The multifaceted nature of conjugated polymers (CPs), notably their versatile electrical and optical properties, endows them with a broad range of potential applications in optical, electrical, and electrochemical signal transduction. Despite the substantial body of research demonstrating the enhanced performance of sensing devices using doped or nanostructure-embedded CPs, few reviews are available that specifically describe the use of conjugated polymers in aptasensing. The purpose of this review is to bridge this gap and provide a comprehensive description of a variety of CPs, from a historical viewpoint, underpinning their specific characteristics and demonstrating the advances in biosensors associated with the use of these conjugated polymers.

Sensitive electrochemical immunosensor using a bienzymatic system consisting of β-galactosidase and glucose dehydrogenase

Bienzymatic systems are often used with electrochemical affinity biosensors to achieve high signal levels and/or low background levels. It is important to select two enzymes whose reactions do not exhibit mutual interference but have similar optimal conditions. Here, we report a sensitive electrochemical immunosensor based on a bienzymatic system consisting of β-galactosidase (Gal, a hydrolase enzyme) and flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH, a redox enzyme). Both enzymes showed high activities at neutral pH, the reactions catalyzed by them did not exhibit mutual interference, and the electrochemical-enzymatic redox cycling based on FAD-GDH coupled with enzymatic amplification by Gal enabled high signal amplification. Among the three amino-hydroxy-naphthalenes and 4-aminophenol (potential Gal products), 4-amino-1-naphthol showed the highest signal amplification. Glucose, as an electro-inactive, stable reducing agent for redox cycling, helped in achieving low background levels. Our bienzymatic system could detect parathyroid hormone at a detection limit of ∼0.2 pg mL-1, implying that it can be used for highly sensitive electrochemical detection of parathyroid hormone and other biomarkers in human serum.

Nucleic Acid Aptamers as Emerging Tools for Diagnostics and Theranostics

Aptamers are ssDNA or RNA sequences (20-80 nucleotides) generated in vitro by SELEX (Systematic Evolution of Ligands using EXponential enrichment) against diverse range of targets from small molecules to bacteria, viruses, and even eukaryotic cells. Aptamers, also known as chemical bodies, bind to their respective targets with tunable affinity and specificity, making aptamers as potent probes for diagnostics and excellent ligands for drug delivery in therapeutics. In this chapter, we have described the methods for generating DNA aptamers against proteins and their use in theranostics.

Label-free detection of cytochrome C by a conducting polymer-based impedimetric screen-printed aptasensor

In this study we have introduced a new sensitive and selective biosensor for the determination of cytochrome C (Cyt C) as a biomarker for cell apoptosis.

Enzyme linking to DNA aptamers via a zinc finger as a bridge

We propose a novel enzyme-labeling method for DNA aptamers using enzyme-fused zinc finger proteins. We achieved thrombin detection and vascular endothelial growth factor detection using zinc finger-fused firefly luciferase.

Detection of thrombin based on aptamer isothermal exponential signal amplification technique

In this report, a strategy based on an aptameric molecule switch to realize homogeneous and isothermal signal exponential amplification and protein detection has been described. This method was simple and sensitive, allowing detection of as low as 2.6 × 10(-12) M thrombin.

A label-free amperometric immunosensor for the detection of carcinoembryonic antigen based on novel magnetic carbon and gold nanocomposites

In this work, a novel label-free electrochemical immunosensor was developed for the quantitative detection of carcinoembryonic antigen (CEA).

Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification

Loop-mediated isothermal amplification (LAMP) is an outstanding DNA amplification procedure, in which the reaction can accumulate 10(9) copies from less than 10 copies of input template within an hour. While the amplification reaction is extremely powerful, the quantitative detection of LAMP products is still analytically difficult. Besides, the type of targets that LAMP can detect is also less, which to some extent limited the application of LAMP. In this study, we are reporting for the first time an efficient and accurate detection system which employs the integration of LAMP, aptamer and the electrochemical method for the sensitive detection of Ochratoxin A (OTA). Aptamers were designed as the forward outer primer to trigger the LAMP reaction, and then the LAMP amplification products were combined with a redox active molecule methylene blue (MB) and analyzed by an electrode using differential pulse voltammograms (DPV). As the reaction progresses, the MB intercalated into double-stranded regions of LAMP amplicons reduces the free MB concentration. Hence, the peak current of reaction mixture decreased with the amplification because of the slow diffusion of MB-amplified DNA complex to the electrode surface. The peak height of the current was related to the input amount of the aptamers, providing a ready means to detection the concentration of OTA. With such design, the proposed assay showed a good linear relationship within the range of 0.001-50 nM with a detection limit of 0.3 pM (defined as S/N = 3) for OTA.

A new hybrid signal amplification strategy for ultrasensitive electrochemical detection of DNA based on enzyme-assisted target recycling and DNA supersandwich assemblies

A highly sensitive electrochemical sequence-specific DNA detection strategy is demonstrated by coupling N.BstNB I (a nicking endonuclease)-assisted target recycling amplification with DNA supersandwich assembly signal enhancement. The proposed method avoids any extra chemical labeling steps and offers high selectivity against single-base mismatch sequences and a low detection limit down to 0.36 fM.

Cascadic multienzyme reaction-based electrochemical biosensors

: Since the first glucose biosensor was developed by Clark and Lyons, there have been great efforts to develop effective enzyme biosensors for wide applications. Those efforts are closely related to the enhancement of biosensor performance, including sensitivity improvement, elevation of selectivity, and extension of the range of analytes that may be determined. Introduction of a cascadic multienzyme reaction to the electrochemical biosensor is one of those efforts. By employing more than two enzymes to the biosensor, its sensitivity and accuracy can be enhanced. Also, the narrow application range that is a typical limitation of single enzyme-based biosensor can be overcome. This chapter will discuss the fundamental principles for the development of cascadic multienzyme reaction-based electrochemical biosensors and their applications in clinical and environmental fields.

Aptamer-conjugated gold nanoparticles for bioanalysis

Aptamers are single-stranded oligonucleotides synthesized through an in vitro selection and amplification process that involves systematic evolution of ligands by exponential enrichment. Based on their high binding affinity and specificity towards other molecules, aptamers generated during the final rounds of selection can be utilized in applications ranging from biosensing to diagnostics and therapeutics. Meanwhile, advances in nanotechnology have led to new and improved materials for biomedical applications. Specifically, nanoparticles can readily interact with both intra- and extra-cellular biomolecules to yield improved signal amplification and target recognition. By combining both technologies, aptamer-conjugated nanoparticles, especially gold nanoparticles (Apt–AuNPs), offer great promise for applications in bioanalysis and biomedicine, including early diagnosis and drug delivery. This review summarizes recent methodologies that have increased the application of Apt–AuNPs in biomedicine, and discusses the potential of Apt–AuNPs in bioanalysis.

In situ amplification signaling-based autonomous aptameric machine for the sensitive fluorescence detection of cocaine

The development of autonomous DNA machines and their use for specific sensing purpose have recently attracted considerable research attention. In existing autonomous machines, the target recognition process and signal transduction are separated from each other. This results in misunderstanding of the operation behavior, and the assay capability is compromised when serving as a sensing tool. In this communication, the integrated signal transduction-based autonomous aptameric machine, in which the recognition element and signal reporters are integrated into a DNA strand, is developed. This new machine can execute the in situ amplification of target binding-induced signal. The authentic operation behavior of autonomous DNA machine is discovered: the machine's products directly hybridize to the "track" rather than to the signaling probes. Along this line, the machine is employed to detect the cocaine in a more straightforward fashion, and improved assay characteristics (for example, the dynamic response range is widened by more than 500-fold) are achieved. Our efforts not only clarify the concept described in traditional autonomous DNA machines but also have made technological advancements that are expected to be especially valuable in designing nucleic acid-based machines employed in basic research and medical diagnosis.

A highly sensitive label-free electrochemical aptasensor for interferon-gamma detection based on graphene controlled assembly and nuclease cleavage-assisted target recycling amplification

We report here a highly sensitive and label-free electrochemical aptasensing technology for detection of interferon-gamma (IFN-γ) based on graphene controlled assembly and enzyme cleavage-assisted target recycling amplification strategy. In this work, in the absence of IFN-γ, the graphene could not be assembled onto the 16-mercaptohexadecanoic acid (MHA) modified gold electrode because the IFN-γ binding aptamer was strongly adsorbed on the graphene due to the strong π-π interaction. Thus the electronic transmission was blocked (eT OFF). However, the presence of target IFN-γ and DNase I led to desorption of aptamer from the graphene surface and further cleavage of the aptamer, thereby releasing the IFN-γ. The released IFN-γ could then re-attack other aptamers on the graphene, resulting in the successive release of the aptamers from the graphene. At the same time, the "naked" graphene could be assembled onto the MHA modified gold electrode with hydrophobic interaction and π-conjunction, mediating the electron transfer between the electrode and the electroactive indicator. Then, measurable electrochemical signals were generated (eT ON), which was related to the concentration of the IFN-γ. By taking advantages of graphene and enzyme cleavage-assisted target recycling amplification, the developed label-free electrochemical aptasensing technology showed a linear response to concentration of IFN-γ range from 0.1 to 0.7 pM. The detection limit of IFN-γ was determined to be 0.065 pM. Moreover, this aptasensor shows good selectivity toward the target in the presence of other relevant proteins. Our strategy thus opens new opportunities for label-free and amplified detection of other kinds of proteins.

Label-free and amplified aptasensor for thrombin detection based on background reduction and direct electron transfer of hemin

In this work, we describe the development of a sensitive and label-free aptasensor for thrombin detection based on background noise reduction by exonuclease I (Exo I) and signal amplification by direct electron transfer (DET) of hemin. The thrombin binding aptamers (TBAs) are self-assembled on a sensing electrode. In the absence of the target thrombin, the TBAs are digested by Exo I, which avoids the association of hemin and significantly minimizes the background current noise. The presence of thrombin stabilizes the folded TBA G-quadruplex and prevents it from degrading by Exo I. The G-quadruplex bound hemin thus generates amplified signal output. In our sensing approach, the introduction of Exo I significantly enhances the signal to noise ratio of the sensor response and achieves sensitive detection of thrombin. Our new method is also coupled with good selectivity against other non-target proteins and thus holds great potential for the development of robust aptasensors for the detection of different types of targets.

An electronic channel switching-based aptasensor for ultrasensitive protein detection

Due to the ubiquity and essential of the proteins in all living organisms, the identification and quantification of disease-specific proteins are particularly important. Because the conformational change of aptamer upon its target or probe/target/probe sandwich often is the primary prerequisite for the design of an electrochemical aptameric assay system, it is extremely difficult to construct the electrochemical aptasensor for protein assay because the corresponding aptamers cannot often meet the requirement. To circumvent the obstacles mentioned, an electronic channel switching-based (ECS) aptasensor for ultrasensitive protein detection is developed. The essential achievement made is that an innovative sensing concept is proposed: the hairpin structure of aptamer is designed to pull electroactive species toward electrode surface and makes the surface-immobilized IgE serve as a barrier that separates enzyme from its substrate. It seemingly ensures that the ECS aptasensor exhibits most excellent assay features, such as, a detection limit of 4.44×10(-6)μg mL(-1) (22.7fM, 220zmol in 10-μL sample) (demonstrating a 5 orders of magnitude improvement in detection sensitivity compared with classical electronic aptasensors) and dynamic response range from 4.44×10(-6) to 4.44×10(-1)μg mL(-1). We believe that the described sensing concept here might open a new avenue for the detection of proteins and other biomacromolecules.

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.

Fractal gold modified electrode for ultrasensitive thrombin detection

We report a label-free and ultrasensitive aptasensor based on a fractal gold modified (FracAu) electrode for thrombin detection with a femtomolar detection limit. The FracAu electrode was prepared by electrodeposition of hydrogen tetrachloroaurate (HAuCl(4)) onto a bare indium tin oxide (ITO) electrode surface. After this process the electrode was characterized by SEM. A thiol-modified aptamer against thrombin was immobilized on the FracAu electrode through a self-assembling process. Upon thrombin binding, the interfacial electron transfer of the FracAu electrode was perturbed by the formation of an aptamer-thrombin complex. The concentration of thrombin in the sample solution was determined by measuring the change in the oxidation peak current of hydroxymethyl ferrocene (C(11)H(12)FeO) with differential pulse voltammetry (DPV). The current response (reduced peak current) had a linear relationship with the logarithm of thrombin concentrations in the range of 10(-15) to 10(-10) M with a detection limit of 5.7 fM. Furthermore, the as-prepared FracAu electrode exhibited high selectivity. The application of FracAu electrodes may be extended to prepare other types of biosensors, such as immunosensors, enzyme biosensors and DNA biosensors. These results show that FracAu electrodes have great promise for clinical diagnosis of disease-related biomarkers.

Sensitive and homogeneous protein detection based on target-triggered aptamer hairpin switch and nicking enzyme assisted fluorescence signal amplification

Specific and sensitive detection of proteins in biotechnological applications and medical diagnostics is one of the most important goals for the scientific community. In this study, a new protein assay is developed on the basis of hairpin probe and nicking enzyme assisted signal amplification strategy. The metastable state hairpin probe with short loop and long stem is designed to contain a protein aptamer for target recognition. A short Black Hole Quencher (BHQ)-quenching fluorescence DNA probe (BQF probe) carrying the recognition sequence and cleavage site for the nicking enzyme is employed for fluorescence detection. Introduction of target protein into the assay leads to the formation change of hairpin probe from hairpin shape to open form, thus faciliating the hybridization between the hairpin probe and BQF probe. The fluorescence signal is amplified through continuous enzyme cleavage. Thrombin is used as model analyte in the current proof-of-concept experiments. This method can detect thrombin specifically with a detection limit as low as 100 pM. Additionally, the proposed protein detection strategy can achieve separation-free measurement, thus eliminating the washing steps. Moreover, it is potentially universal because hairpin probe can be easily designed for other proteins by changing the corresponding aptamer sequence.

Graphene and other nanomaterial-based electrochemical aptasensors

Electrochemical aptasensors, which are based on the specificity of aptamer-target recognition, with electrochemical transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. Aptamers are functional nucleic acids with specific and high affinity to their targets, similar to antibodies. However, they are completely selected in vitro in contrast to antibodies. Due to their stability, easy chemical modifications and proneness to nanostructured device construction, aptamer-based sensors have been incorporated in a variety of applications including electrochemical sensing devices. In recent years, the performance of aptasensors has been augmented by incorporating novel nanomaterials in the preparation of better electrochemical sensors. In this review, we summarize the recent trends in the use of nanomaterials for developing electrochemical aptasensors.

Aptameric molecular switch for cascade signal amplification

BACKGROUND

High sensitivity of analysis is constantly in demand in biomedical research and clinical diagnosis. In recent years aptamer-based analytical methods have been developed for protein detection. We developed a cascade signal amplification strategy based on molecular switches and aptamers to improve protein detection.

METHODS

Our cascade signal amplification strategy based on molecular switches and aptamers consisted of 2 steps, including the recognition and the triggering of a polymerase reaction. The procedure was designed to simplify the analysis by detecting trace amounts of target isothermally, in real time, and in a homogeneous solution. We applied this method to measure thrombin in human serum samples.

RESULTS

This cascade signal amplification strategy exhibited a linear response in thrombin concentration from 0.3 to 10 nmol/L, with a detection limit of 1.7 × 10(-10) mol/L within 60 min. Results of the analysis of thrombin in human serum diluted 1:1 appeared to be linear, as was observed in buffer, in the tested concentration range of 0.3-10 nmol/L.

CONCLUSIONS

The aptameric sensor provides promising potential for detecting and screening trace concentrations of biomarkers in complex matrices for clinical applications.

Aptamer-functionalized microgel particles for protein detection

Highly sensitive and multiplexed detection of clinically relevant proteins in biologically complex samples is crucial for the advancement of clinical proteomics. In recent years, aptamers have emerged as useful tools for protein analysis due to their specificity and affinity for protein targets as well as their compatibility with particle-based detection systems. In this study, we demonstrate the highly sensitive detection of human α-thrombin on encoded hydrogel microparticles functionalized with an aptamer capture sequence. We use static imaging and microfluidic flow-through analysis techniques to evaluate the detection capabilities of the microgels in sandwich-assay formats that utilize both aptamers and antibodies for the reporting of target-binding events. Buffers and reagent concentrations were optimized to provide maximum reaction efficiency while still maintaining an assay with a simple workflow that can be easily adapted to the multiplexed detection of other clinically relevant proteins. The three-dimensional, nonfouling hydrogel immobilization scaffold used in this work provides three logs of dynamic range, with a limit of detection of 4 pM using a single aptamer capture species and without the need for spacers or signal amplification.

Fabrication of a highly sensitive aptasensor for potassium with a nicking endonuclease-assisted signal amplification strategy

A novel strategy to fabricate an aptasensor for potassium with high sensitivity and selectivity by using nicking endonuclease is proposed in this work. A nicking endonuclease (Nt.CviPII), which may recognize specific nucleotide sequences in double-stranded DNA formed by a potassium-binding aptamer and a linker DNA but cleave only the linker strand, may transfer and amplify the quantitative information of the potassium detection to that of the linker DNA through elaborate strand-scission cycles. Since the technique for gene assay is much more mature, the linker DNA can thereby be detected by a number of available methods. Here, taking advantage of a simple and fast gold nanoparticles-based sensing technique, we are able to assay the linker and consequently potassium ion simply by UV-vis spectroanalysis and even with the naked eye. Results show that a 2 μL sample containing 0.1 mM of potassium is enough to induce distinct color appearance of the nanoparticles, and the potassium ion can be easily distinguished from many other ions. The strategy proposed in this work shows some unique advantages over some traditional methods and may be further developed for the detection of some other chemicals in the future.

Electrochemical Aptamer-Based Biosensors: Recent Advances and Perspectives

This paper reviews the advancements of a wide range of electrochemical aptamer-based biosensors, electrochemical aptasensors, for target analytes monitoring. Methods for immobilizing aptamers onto an electrode surface are discussed. Aptasensors are presented according to their detection strategies. Many of these are simply electrochemical, aptamer-based equivalents of traditional immunochemical approaches, sandwich and competition assays employing electroactive signaling moieties. Others, exploiting the unusual physical properties of aptamers, are signal-on (positive readout signal) and signal-off (negative readout signal) aptasensors based on target binding-induced conformational change of aptamers. Aptamer label-free devices are also discussed.