Impedimetric or Ion-Sensitive Field-Effect Transistor (ISFET) Aptasensors Based on the Self-Assembly of Au Nanoparticle-Functionalized Supramolecular Aptamer Nanostructures

Aptamer based nanobiosensors: Promising healthcare devices

Nanobiosensors based on aptamer are extensively being studied as potent analytical tools in clinical analysis. These biosensors provide high sensitivity, fast response, specificity and desired portability in addition to simplicity and decreased cost compared to conventional methods. The purpose of this manuscript is to provide readers with an overview of current advances about electrochemical, electrochemiluminescent and photoelectrochemical aptasensors from the sea of available literature. These are mainly used for determination of protein-based biomarkers, especially for cancer diagnosis. Here in we have given special emphasis on nanosize-based aptasensors which have been reported to show considerable improvement in the analytical performance.

Integration of a field effect transistor-based aptasensor under a hydrophobic membrane for bioelectronic nose applications

A new bioelectronic nose based on a field effect transistor coupled with an aptamer as the sensing element was developed. The gas-to-liquid extraction interface required for appropriate aptamer function was integrated into standard CMOS technology. It was developed with the use of a sacrificial aluminium etching technique combined with surface modifications by silanes for wettability control. As a proof of concept, aptamer Van74 for vanillin was immobilized on the sensitive surface of the ISFET. The developed microsystem can selectively detect vanillin vapor in a concentration range from 2.7 ppt to 0.3 ppm, with a detection limit of 2.7 ppt. The sensor was able to detect vanillin in a gas sample obtained from roasted coffee beans. This outcome provides a foundation for developing a new generation of bioelectronic noses for the detection and discrimination of volatile compounds.

Selection, Characterization, and Application of ssDNA Aptamer against Furaneol

Furaneol is an aroma compound which occurs naturally in foods and is used as an artificial flavor. Detection of furaneol is required in food science and food processing industry. Capture- Systematic Evolution of Ligands by EXponential enrichment (SELEX) protocol was applied for the isolation of an aptamer binding to furaneol, a small volatile organic substance contributing to the flavor of various products. Thirteen cycles of selection were performed. The resulting DNA pool was cloned, using blunt-end cloning, and ninety-six plasmids were sequenced and analyzed. Eight oligonucleotides were selected as aptamer candidates and screened for the ability to bind to furaneol, using three different methods-magnetic-beads associated elution assay, SYBR Green I assay, and exonuclease protection assay. One of the candidates was further characterized as an aptamer. The apparent equilibrium constant was determined to be (1.1 ± 0.4) µM, by the fluorescent method. The reported aptamer was applied for development of the ion-sensitive field-effect transistor (ISFET)-based biosensor, for the analysis of furaneol, in the concentration range of 0.1⁻10 µM.

Amplified Detection of the Aptamer-Vanillin Complex with the Use of Bsm DNA Polymerase

The electrochemical detection of interactions between aptamers and low-molecular-weight targets often lacks sensitivity. Signal amplification improves the detection of the aptamer-analyte complex; Bsm DNA polymerase was used to amplify the signal from the interaction of vanillin and its aptamer named Van_74 on an ion-sensitive field-effect transistor (ISFET)-based biosensor. The aptamer was immobilized on the ISFET sensitive surface. A short DNA probe was hybridized with the aptamer and dissociated from it upon vanillin addition. A free probe interacted with a special DNA molecular beacon initiated the Bsm DNA polymerase reaction that was detected by ISFET. A buffer solution suitable for both aptamer action and Bsm DNA polymerase activity was determined. The ISFET was shown to detect the Bsm DNA polymerase reaction under the selected conditions. Vanillin at different concentrations (1 × 10-6-1 × 10-8 M) was detected using the biosensor with signal amplification. The developed detection system allowed for the determination of vanillin, starting at a 10-8 M concentration. Application of the Bsm DNA polymerase resulted in a 15.5 times lower LoD when compared to the biosensor without signal amplification (10.1007/s00604-017-2586-4).

Aptamer-modified nanoparticles as biosensors

Aptamers are short oligonucleotides that are capable of selectively binding to their corresponding target. Therefore, they can be thought of as a nucleic acid-based alternative to antibodies and can substitute for their amino acid-based counterparts in analytical applications, including as receptors in biosensors. Here they offer several advantages because their nucleic acid nature and their binding via an induced fit mechanism enable novel sensing strategies. In this article, the utilization of aptamers as novel bio-receptors in combination with nanoparticles as transducer elements is reviewed. In addition to these analytical applications, the medical relevance of aptamer-modified nanoparticles is described.

Optical aptasensors for the analysis of the vascular endothelial growth factor (VEGF)

The vascular endothelial growth factor, VEGF, is an important biomarker for different diseases and clinical disorders. We present a series of optical aptasensor-based sensing platforms for VEGF that include the following: (i) A FRET-based sensor that involves the VEGF-induced separation of aptamer-functionalized quantum dots blocked by a quencher nucleic acid (detection limit 1 nM). (ii) A FRET-based sensor based on the VEGF-induced assembly of the aptamer subunits functionalized with QDs and a dye acceptor (Cy5), respectively (detection limit 12 nM). (iii) A chemiluminescence aptasensor based on VEGF-induced assembly of a hemin/G-quadruplex catalyst (detection limit 18 nM). (iv) A chemiluminescence aptasensor based on the VEGF-stimulated assembly of two aptamer subunits into the hemin/G-quadruplex catalyst (detection limit 2.6 nM). (v) A chemiluminescence resonance energy transfer (CRET) aptasensor based on the VEGF-induced assembly of a semiconductor QDs-hemin/G-quadruplex supramolecular structure (detection limit 875 pM). Furthermore, an amplified optical aptasensor system based on the Exonuclease III (Exo III) recycling of the VEGF analyte was developed. In this system, one aptamer subunit is modified at its 5' and 3' ends with QDs and a black hole quencher, respectively. The VEGF-induced self-assembly of the aptamer subunits result in the digestion of the quencher units and the autonomous recycling of the analyte, while triggering-on the luminescence of the QDs (detection limit 5 pM). The system was implemented to analyze VEGF in human sera samples.

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.

Aptamer sensor for cocaine using minor groove binder based energy transfer

We report on an optical aptamer sensor for cocaine detection. The cocaine sensitive fluorescein isothiocyanate (FITC)-labeled aptamer underwent a conformational change from a partial single-stranded DNA with a short hairpin to a double-stranded T-junction in the presence of the target. The DNA minor groove binder Hoechst 33342 selectively bound to the double-stranded T-junction, bringing the dye within the Förster radius of FITC, and therefore initiating minor groove binder based energy transfer (MBET), and reporting on the presence of cocaine. The sensor showed a detection limit of 0.2 μM. The sensor was also implemented on a carboxy-functionalized polydimethylsiloxane (PDMS) surface by covalently immobilizing DNA aptamers. The ability of surface-bound cocaine detection is crucial for the development of microfluidic sensors.

Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects

In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.

An electrochemical aptasensor based on enzyme linked aptamer assay

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

Chemiluminescence and chemiluminescence resonance energy transfer (CRET) aptamer sensors using catalytic hemin/G-quadruplexes

The incorporation of hemin into the thrombin/G-quadruplex aptamer assembly or into the ATP/G-quadruplex nanostructure yields active DNAzymes that catalyze the generation of chemiluminescence. These catalytic processes enable the detection of thrombin and ATP with detection limits corresponding to 200 pM and 10 μM, respectively. The conjugation of the antithrombin or anti-ATP aptamers to CdSe/ZnS semiconductor quantum dots (QDs) allowed the detection of thrombin or ATP through the luminescence of the QDs that is powered by a chemiluminescence resonance energy-transfer (CRET) process stimulated by the hemin/G-quadruplex/thrombin complex or the hemin/G-quadruplex/ATP nanostructure, in the presence of luminol/H(2)O(2). The advantages of applying the CRET process for the detection of thrombin or ATP, by the resulting hemin/G-quadruplex DNAzyme structures, are reflected by low background signals and the possibility to develop multiplexed aptasensor assays using different sized QDs.

Amplified surface plasmon resonance based DNA biosensors, aptasensors, and Hg2+ sensors using hemin/G-quadruplexes and Au nanoparticles

Thiolated nucleic acid hairpin nanostructures that include in their stem region a "caged" G-quadruplex sequence, and in their single-stranded loop region oligonucleotide recognition sequences for DNA, adenosine monophosphate (AMP), or Hg(2+) ions were linked to bare Au surfaces or to Au nanoparticles (NPs) linked to Au surfaces. The opening of the hairpin nanostructures associated with the bare Au surface by the complementary target DNA, AMP substrate, or Hg(2+) ions, in the presence of hemin, led to the self-assembly of hemin/G-quadruplexes on the surface. The resulting dielectric changes on the surface exhibited shifts in the surface plasmon resonance (SPR) spectra, thus providing a readout signal for the recognition events. A similar opening of the hairpin nanostructures, immobilized on the Au NPs associated with the Au surface, by the DNA, AMP, or Hg(2+) led to an ultrasensitive SPR-amplified detection of the respective analytes. The amplification originated from the coupling between the localized surface plasmon associated with the NPs and the surface plasmon wave, an effect that cooperatively amplifies the SPR shifts that result from the formation of the hemin/G-quadruplexes. The different sensing platforms reveal impressive sensitivities and selectivities toward the target analytes.

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.

DNA aptamer folding on magnetic beads for sequential detection of adenosine and cocaine by substrate-resolved chemiluminescence technology

We have developed a new aptamer-based chemiluminescence (CL) biosensing platform for the sequential detection of two small molecules as exemplified by adenosine and cocaine. Each biosensing platform comprises NH(2)-functionalized capture DNA immobilized on magnetic beads; this can hybridize with one end of the aptamer. A corresponding reporter DNA probe labeled with either digoxigenin or biotin on its 5'-terminus recognizes the other end of the aptamer. The target compounds adenosine or cocaine act as specific competitors to aptamer-reporter DNA binding, and the corresponding aptamers preferentially form target-aptamer complexes. This results in detachment of the reporter DNA probe from the magnetic beads, with more target molecules resulting in less reporter DNA probe remaining on the beads. Those left are sequentially detected by using substrate-resolved anti-digoxigenin-alkaline phosphatase and streptavidin-horseradish peroxidase. Experimental results confirm that this CL immunosensing platform has good sensitivity with detection limits of 5.2 x 10(-9) M and 3.2 x 10(-9) M for adenosine and cocaine, respectively. Because it is straightforward to adapt this strategy to detect a spectrum of small molecules by using different aptamers, this method may offer a new direction in designing high-performance CL aptasensors for sensitive and sequential determination of a limited number of small molecules.

Sensitive bifunctional aptamer-based electrochemical biosensor for small molecules and protein

In this paper, a bifunctional electrochemical biosensor for highly sensitive detection of small molecule (adenosine) or protein (lysozyme) was developed. Two aptamer units for adenosine and lysozyme were immobilized on the gold electrode by the formation of DNA/DNA duplex. The detection of adenosine or lysozyme could be carried out by virtue of switching structures of aptamers from DNA/DNA duplex to DNA/target complex. The change of the interfacial feature of the electrode was characterized by cyclic voltammertic (CV) response of surface-bound [Ru(NH(3))(6)](3+). On the other hand, DNA functionalized Au nanoparticles (DNA-AuNPs) were used to enhance the sensitivity of the aptasensor because DNA-AuNPs modified interface could load more [Ru(NH(3))(6)](3+) cations. Thus, the assembly of two aptamer-contained DNA strands integrated with the DNA-AuNPs amplification not only improves the sensitivity of the electrochemical aptasensor but also presents a simple and general model for bifunctional aptasensor. The proposed aptasensor has low detection limit (0.02 nM for adenosine and 0.01 microg mL(-1) for lysozyme) and exhibits several advantages such as high sensitivity and bifunctional recognition.

Electrochemical, photoelectrochemical, and surface plasmon resonance detection of cocaine using supramolecular aptamer complexes and metallic or semiconductor nanoparticles

Metallic or semiconductor nanoparticles (NPs) are used as labels for the electrochemical, photoelectrochemical, or surface plasmon resonance (SPR) detection of cocaine using a common aptasensor configuration. The aptasensors are based on the use of two anticocaine aptamer subunits, where one subunit is assembled on a Au support, acting as an electrode or a SPR-active surface, and the second aptamer subunit is labeled with Pt-NPs, CdS-NPs, or Au-NPs. In the different aptasensor configurations, the addition of cocaine results in the formation of supramolecular complexes between the NPs-labeled aptamer subunits and cocaine on the metallic surface, allowing the quantitative analysis of cocaine. The supramolecular Pt-NPs-aptamer subunits-cocaine complex allows the detection of cocaine by the electrocatalyzed reduction of H(2)O(2). The photocurrents generated by the CdS-NPs-labeled aptamer subunits-cocaine complex, in the presence of triethanol amine as a hole scavenger, allows the photoelectrochemical detection of cocaine. The supramolecular Au-NPs-aptamer subunits-cocaine complex generated on the Au support allows the SPR detection of cocaine through the reflectance changes stimulated by the electronic coupling between the localized plasmon of the Au-NPs and the surface plasmon wave. All aptasensor configurations enable the analysis of cocaine with a detection limit in the range of 10(-6) to 10(-5) M. The major advantage of the sensing platform is the lack of background interfering signals.

DNAzyme self-assembled gold nanoparticles for determination of metal ions using fluorescence anisotropy assay

Gold nanoparticles can be exploited to facilitate a highly sensitive and selective metal ion detection based on fluorescence anisotropy assay with metal ion-dependent DNA-cleaving DNAzyme. This assay allows rapid and accurate determination of metal ions in aqueous medium at room temperature. The method has been demonstrated for determination of Cu(2+) and Pb(2+) ions. The detection sensitivity can be significantly improved to 1 nM by using a "nanoparticle enhancement" approach. Moreover, the assay was also tested in 384-well plates for high-throughput routine determination of toxic metal ions in environmental samples. The method showed distinct advantages over conventional methods in terms of its potential sensitivity, specificity, and ability for rapid response.

Aptamer-DNAzyme hairpins for amplified biosensing

Engineered nucleic acid hairpin structures are used for the amplified analysis of low-molecular-weight substrates (adenosine monophosphate, AMP) or proteins (lysozyme). The hairpin structures consist of the anti-AMP or antilysozyme aptamer units linked to the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The HRP-mimicking DNAzyme sequence is protected in a "caged", inactive structure in the stem regions of the respective hairpins, whereas the loop regions include a part of the respective aptamer sequence. The opening of the hairpins by the analytes, AMP or lysozyme, through the formation of the respective analyte-aptamer complexes, results in the self-assembly of the active HRP-mimicking DNAzyme. The DNAzyme catalyzes the H(2)O(2)-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the colored ABTS(*-), thus providing the amplified optical detection of the respective analytes. The engineered aptamer-DNAzyme hairpin structures reveal significantly improved analytical performance, as compared to analogous fluorophore-quencher-labeled hairpins.