Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures

Determinants of the detection limit and specificity of surface-based biosensors

Here, we employ a model electrochemical DNA sensor to demonstrate that the detection limit and specificity of surface-based sensors often are not dependent on the true affinity of the probe for its target but are simply dependent on the effective probe concentration. Under these circumstances, the observed affinity (and thus the sensor's detection limit and specificity) will depend on the density with which the probes are packed on the surface of the sensor, the surface area, and even the volume of sample employed.

Enzyme-free and ultrasensitive electrochemical detection of nucleic acids by target catalyzed hairpin assembly followed with hybridization chain reaction

An isothermal, enzyme-free and ultrasensitive protocol for electrochemical detection of DNA is proposed based on the ingenious combination of target catalyzed hairpin assembly and hybridization chain reaction (HCR) strategies for two-step signal amplification. The DNA hairpin assembly on the electrode is triggered by target DNA, accompanied by the release of target DNA for the successive hybridization and assembly process. The newly emerging DNA fragment on the electrode after hairpin assembly is further used to propagate the HCR between methylene blue-labeled signal probe and auxiliary probe, inducing a remarkably amplified electrochemical signal. The current dual signal amplification strategy is relatively simple and inexpensive owing to avoid the use of any kind of enzyme or sophisticated equipment. It can achieve a sensitivity of 0.1 fM with a wide linear dynamic range from 1 × 10(-15) to 1 × 10(-10)M and discriminate mismatched DNA from perfect matched target DNA with a high selectivity. The high sensitivity and selectivity make this method a great potential for early diagnosis in gene-related diseases.

Fluorescent sensing ochratoxin A with single fluorophore-labeled aptamer

We explored a fluorescent strategy for sensing ochratoxin A (OTA) by using a single fluorophore-labeled aptamer for detection of OTA. This method relied on the change of the fluorescence intensity of the labeled dye induced by the specific binding of the fluorescent aptamer to OTA. Different fluorescein labeling sites of aptamers were screened, including the internal thymine bases, 3'-end, and 5'-end of the aptamer, and the effect of the labeling on the aptamer affinity was investigated. Some fluorophore-labeled aptamers showed a signal-on or signal-off response. With the fluorescent aptamer switch, simple, rapid, and selective sensing of OTA at nanomolar concentrations was achieved. OTA spiked in diluted red wine could be detected, showing the feasibility of the fluorescent aptamer for a complex matrix. This method shows potential for designing aptamer sensors for other targets.

An electrochemiluminescence aptasensor for thrombin using graphene oxide to immobilize the aptamer and the intercalated [Formula: see text] probe

The immobilization of aptamer and the introduction of signal molecule are two keys for the development of electrochemiluminescence (ECL) aptasensor. Herein, the immobilization strategy with graphene oxide (GO) and a functional oligonucleotide (FO) are used to develop a sensitive aptasensor with the detection of thrombin as a model. After GO is attached on glass carbon or gold electrodes through physical adsorption, the amino-tagged aptamer is immobilized on the electrode surface via an amide linkage between the amino group at the end of aptamer and the carboxyl groups on GO. The FO is designed to contain two parts: the complementary strand and an intermolecular duplex for the intercalation of Ru(phen)₃²⁺ as ECL probe. The hybridization between aptamer and its complementary part at FO achieves the introduction of Ru(phen)₃²⁺ probe onto the electrode surface for high ECL emission. The hybrid between aptamer and thrombin leads to the release of FO containing the intercalated Ru(phen)₃²⁺ probe. Correspondingly, the decreased ECL emission is used to quantify thrombin. The concentration-dependent response of thrombin is observed between 0.90 pM and 226 pM with a detection limit of 0.40 pM. While GO is used to immobilize the aptamer with various electrodes, such as glass carbon electrode and gold electrode in this work, GO can also preconcentrate TPrA on its surface to improve the sensitivity. The well-designed label-free ECL aptasensor strategy can be easily extended to other targets via the selection of their aptamers.

Ultrasensitive electrochemical DNA detection based on dual amplification of circular strand-displacement polymerase reaction and hybridization chain reaction

We developed a novel electrochemical strategy for ultrasensitive DNA detection using a dual amplification strategy based on the circular strand-displacement polymerase reaction (CSDPR) and the hybridization chain reaction (HCR). In this assay, hybridization of hairpin-shaped capture DNA to target DNA resulted in a conformational change of the capture DNA with a concomitant exposure of its stem. The primer was then hybridized with the exposed stem and triggered a polymerization reaction, allowing a cyclic reaction comprising release of target DNA, hybridization of target with remaining capture DNA, polymerization initiated by the primer. Furthermore, the free part of the primer propagated a chain reaction of hybridization events between two DNA hairpin probes with biotin labels, enabling an electrochemical reading using the streptavidin-alkaline phosphatase. The proposed biosensor showed to have very high sensitivity and selectivity with a dynamic response range through 10fM to 1nM, and the detect limit was as low as 8fM. The proposed strategy could have the potential for molecular diagnostics in complex biological systems.

Fluorescence quenching of gold nanoparticles integrating with a conformation-switched hairpin oligonucleotide probe for microRNA detection

We report a new strategy for microRNA analysis based on the fluorescence quenching of gold nanoparticles (AuNPs) integrating with a conformation-switched hairpin-structured oligonucleotide probe for improving selectivity.

Effect of signaling probe conformation on sensor performance of a displacement-based electrochemical DNA sensor

Here we report the effect of the signaling probe conformation on sensor performance of a "signal-on" folding-based electrochemical DNA sensor. The sensor is comprised of a methylene blue (MB)-modified signaling probe and an unlabeled capture probe that partially hybridize to each other at the distal end. In presence of the full-complement target which binds to the unlabeled capture probe, the labeled signaling probe is released. Two different signaling probes were used in this study, in which one is capable of assuming a stem-loop conformation (SLP-MB), whereas the other probe adopts a flexible linear conformation (LP-MB). In the presence of the full complement target DNA, both sensors showed a large increase in MB current when interrogated using alternating current (ac) voltammetry, verifying the release of the signaling probe. Overall, the SLP-MB sensor showed higher % signal enhancement; the LP-MB sensor, however, showed distinctly faster binding kinetics when interrogated under the same experimental conditions. The SLP-MB sensor displayed a wider usable ac frequency range when compared to the LP-MB sensor. Despite these differences, the detection limit and dynamic range were found to be similar among the two sensors. In addition to 6-mercapto-1-hexanol, longer chain hydroxyl-terminated alkanethiols were used to construct these sensors. Our results showed that sensors fabricated with longer chain diluents, independent of the sensor architecture, were not only functional, the signaling capability was significantly enhanced.

"Fitting" makes "sensing" simple: label-free detection strategies based on nucleic acid aptamers

Nucleic acid aptamers are small sequences of DNA made via in vitro selection techniques to bind targets with high affinity and specificity. The term aptamer derives from the Latin, aptus, meaning "to fit", emphasizing the lock-and-key relationship between aptamers and their binding targets. In 2004, aptamers began to attract researchers' attention as new binding elements for biosensors (i.e. aptasensors). Their advantages over other sensors include a diverse range of possible target molecules, high target affinity, simple synthesis, and ability to form Watson-Crick base pairs. These attributes create an enormous array of possible sensing applications and target molecules, spanning nearly all detection methods and readout techniques. In particular, aptamers provide an opportunity for designing "label-free" sensors, meaning sensors that do not require covalently labeling a signal probe to either the analyte or the recognition element (here, the aptamer). "Label-free" systems previously could only analyze large molecules using a few readout techniques, such as when employing the other recognition elements like antibodies. "Label-free" methods are one of the most effective and promising strategies for faster, simpler, and more convenient detection, since they avoid the expensive and tedious labeling process and challenging labeling reactions, while retaining the highest degree of activity and affinity for the recognition element. "Label-free" sensors are one of the most promising future biosensors. In this Account, we describe our efforts exploring and constructing such label-free sensing strategies based on aptamers. Our methods have included using various readout techniques, employing novel nanomaterials, importing lab-on-a-chip platforms, and improving logical recognition. The resulting sensors demonstrate that aptamers are ideal tools for "label-free" sensors. We divide this Account into three main parts describing three strategies for designing "label-free" sensors: (1) Label-free, separation-free strategies. These include colorimetric sensors based on G-quadruplex-hemin complex, and fluorescent sensors based on fluorescent small molecules, novel conjugated polymers, and metal ion clusters. (2) Label-free, separation-required strategies. In this part, electrochemical sensors are introduced, including sensors with different subtechniques using an electrode array. (3) Logic sensors. Some logic recognition systems are introduced. We emphasize that label-free aptasensors are not merely simple. We hope our introduction illustrates the powerful, flexible, and smart functions of aptamers in carrying out various detection tasks or playing various recognition games. Our work is only a start. We believe this field will bring additional knowledge on general designs, anti-interference, multianalysis, minimization, and auto-operation of aptamer biosensors.

Electrochemical detection of individual DNA hybridization events

We report on real-time electrochemical detection of individual DNA hybridization events at an electrode surface. The experiment is carried out in a microelectrochemical device configured with a working electrode modified with single-stranded DNA probe molecules. When a complementary DNA strand labelled with a catalyst hybridizes to the probe, an easily detectable electrocatalytic current is observed. In the experiments reported here, the catalyst is a platinum nanoparticle and the current arises from electrocatalytic oxidation of hydrazine. Two types of current transients are observed: short bursts and longer-lived steps. At low concentrations of hydrazine, the average size of the current transients is proportional to the amount of hydrazine present, but at higher concentrations the hydrazine oxidation reaction interferes with hybridization.

Electrochemiluminescent biosensor of ATP using tetrahedron structured DNA and a functional oligonucleotide for Ru(phen)3(2+) intercalation and target identification

Restricted target accessibility and surface-induced perturbation of the aptamer structure are the main limitations in single-stranded DNA aptamer-based electrochemical sensors. Chemical labeling of the aptamer with a probe at the end of aptamer is inefficient and time-consuming. In this work, tetrahedron-structured DNA (ts-DNA) and a functionalized oligonucleotide (FO) were used to develop an electrochemiluminescence (ECL) aptasensor with adenosine triphosphate (ATP) as a model target. The ts-DNA was formed with three thiolated oligonucleotides and one oligonucleotide containing anti-ATP aptamer. The FO contained a complementary strand to the anti-ATP aptamer and an intermolecular duplex for Ru(phen)3(2+) intercalation. After the ts-DNA was immobilized on the electrode surface through gold-thiol interactions, hybridization between the anti-ATP aptamer and its complementary strand introduced the intercalated Ru(phen)3(2+) to the electrode. ECL emission from Ru(phen)3(2+) was observed with tripropylamine as a co-reactant. Once ATP reacted with its aptamer, the aptamer-complimentary strand duplex dissociated and the intermolecular duplex containing Ru(phen)3(2+) was released. The difference in emission before and after reaction with ATP was used to quantify ATP with a detection limit of 0.2nM. The ts-DNA increased the sensitivity compared to conventional methods, and the intercalation strategy avoided a complex chemical labeling procedure.

Electrochemical direct detection of DNA deamination catalyzed by APOBEC3G

APOBEC3G catalyzes deamination of cytosines in HIV-1 genome, and restricts the HIV-1 infection. Here, we propose a picomole-scale assay for the detection of DNA deamination catalyzed by APOBEC3G. Our results show the suitability of the developed method for a time course analysis of enzyme-catalyzed DNA modifications.

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.

An electrochemical sensor based on label-free functional allosteric molecular beacons for detection target DNA/miRNA

We report two novel electrochemical sensors (E-sensors) for the detection of target DNA and miRNA. The E-sensors were fabricated using label-free functional allosteric molecular beacons (aMBs), which can form streptavidin aptamers to bind to streptavidin peroxidase polymer and so generate catalytic currents in the presence of the targets. These E-sensors eliminate the antigen antibody interactions which require sophisticated DNA modification. During the experiment, we found a pair of CV peaks located at around 0.17 V. These peaks contributed to the redox reaction between TMB and TMB(+), and the adsorption-desorption process of TMB(+) to the negative aMB backbone. When the E-sensor was hybridized with the complement of the aMB sequence, a pair of CV peaks were found at around 0.47 V which were related to the redox reaction between TMB(+) and TMB(2+), and the process of intercalation of the planar structure of TMB(2+) to dsDNA. The RSV-aMB E-sensor could detect 44 amol RSV DNA in the 4 μL sample and performed well in complicated biological environments. The let-7a-aMB E-sensor reached a detection limit of 13.6 amol let-7a miRNA in the 4 μL sample and showed good selectivity for one base mismatched miRNA.

Rational design of allosteric inhibitors and activators using the population-shift model: in vitro validation and application to an artificial biosensor

The population-shift mechanism can be used for rational re-engineering of structure-switching biosensors to enable their allosteric inhibition and activation. As a proof-of-principle example of this, we have introduced distal allosteric sites into molecular beacons, which are optical sensors for the detection of specific nucleic acid sequences. The binding of inhibitors and activators to these sites enabled the rational modulation of the sensor's target affinity-and thus its useful dynamic range-over 3 orders of magnitude. The convenience with which this was done suggests that the population-shift mechanism may prove to be a useful method by which allosteric regulation can be introduced into biosensors, "smart" biomaterials, and other artificial biotechnologies.

Bioelectrochemical switches for the quantitative detection of antibodies directly in whole blood

The development of rapid, low-cost point-of-care approaches for the quantitative detection of antibodies would drastically impact global health by shortening the delay between sample collection and diagnosis and by improving the penetration of modern diagnostics into the developing world. Unfortunately, however, current methods for the quantitative detection of antibodies, including ELISAs, Western blots, and fluorescence polarization assays, are complex, multiple-step processes that rely on well-trained technicians working in well-equipped laboratories. In response, we describe here a versatile, DNA-based electrochemical "switch" for the rapid, single-step measurement of specific antibodies directly in undiluted whole blood at clinically relevant low-nanomolar concentrations.

Quantitation of affinity, avidity, and binding kinetics of protein analytes with a dynamically switchable biosurface

A label-free method for the analysis of interactions of proteins with surface-tethered ligands is introduced. Short DNA levers are electrically actuated on microelectrodes by ac potentials, and their switching dynamics are measured in real-time by fluorescence energy transfer. Binding of proteins to ligands attached to the top of the DNA levers is detected by time-resolved measurements of the levers' dynamic motion. We demonstrate the quantitation of binding kinetics (k(on), k(off) rate constants), dissociation constants (K(D) in the pM regime), and the influence of competitive binders (EC(50) values). Moreover, the "switchSENSE" method reveals avidity effects and allows discriminating between analytes with one or more binding sites. In a comparative study, interactions of six hexa-histidine-tagged proteins with tris-nitrilotriacetic acid (NTA(3)) ligands are quantitated. Their binding kinetics and affinities are found to vary over up to 2 orders of magnitude, evidencing that the proteins' individual chemical environments significantly influence the His(6)-NTA(3) interaction.

Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits

Catalyzed hairpin assembly (CHA) is a robust enzyme-free signal-amplification reaction that has a wide range of potential applications, especially in biosensing. Although most studies of the analytical applications of CHA have focused on the measurement of concentrations of biomolecules, we show here that CHA can also be used to probe the spatial organization of biomolecules such as single-stranded DNA. The basis of such detection is the fact that a DNA structure that brings a toehold and a branch-migration domain into close proximity can catalyze the CHA reaction. We quantitatively studied this phenomenon and applied it to the detection of domain reorganization that occurs during DNA self-assembly processes such as the hybridization chain reaction (HCR). We also show that CHA circuits can be designed to detect certain types of hybridization defects. This principle allowed us to develop a "signal on" assay that can simultaneously respond to multiple types of mutations in a DNA strand in one simple reaction, which is of great interest in genotyping and molecular diagnostics. These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields.

Analyte-driven switching of DNA charge transport: de novo creation of electronic sensors for an early lung cancer biomarker

A general approach is described for the de novo design and construction of aptamer-based electrochemical biosensors, for potentially any analyte of interest (ranging from small ligands to biological macromolecules). As a demonstration of the approach, we report the rapid development of a made-to-order electronic sensor for a newly reported early biomarker for lung cancer (CTAP III/NAP2). The steps include the in vitro selection and characterization of DNA aptamer sequences, design and biochemical testing of wholly DNA sensor constructs, and translation to a functional electrode-bound sensor format. The working principle of this distinct class of electronic biosensors is the enhancement of DNA-mediated charge transport in response to analyte binding. We first verify such analyte-responsive charge transport switching in solution, using biochemical methods; successful sensor variants were then immobilized on gold electrodes. We show that using these sensor-modified electrodes, CTAP III/NAP2 can be detected with both high specificity and sensitivity (K(d) ~1 nM) through a direct electrochemical reading. To investigate the underlying basis of analyte binding-induced conductivity switching, we carried out Förster Resonance Energy Transfer (FRET) experiments. The FRET data establish that analyte binding-induced conductivity switching in these sensors results from very subtle structural/conformational changes, rather than large scale, global folding events. The implications of this finding are discussed with respect to possible charge transport switching mechanisms in electrode-bound sensors. Overall, the approach we describe here represents a unique design principle for aptamer-based electrochemical sensors; its application should enable rapid, on-demand access to a class of portable biosensors that offer robust, inexpensive, and operationally simplified alternatives to conventional antibody-based immunoassays.

Re-engineering electrochemical biosensors to narrow or extend their useful dynamic range

Here we demonstrate two convenient methods to extend and narrow the useful dynamic range of a model electrochemical DNA sensor. We did so by combining DNA probes of different target affinities but with similar specificity on the same electrode. We were able to achieve an extended dynamic response spanning 3 orders of magnitude in target concentration. Using a different strategy we have also narrowed the useful dynamic range of an E-DNA sensor to only an 8-fold range of target concentrations.

Affinity and enzyme-based biosensors: recent advances and emerging applications in cell analysis and point-of-care testing

The applications of biosensors range from environmental testing and biowarfare agent detection to clinical testing and cell analysis. In recent years, biosensors have become increasingly prevalent in clinical testing and point-of-care testing. This is driven in part by the desire to decrease the cost of health care, to shift some of the analytical tests from centralized facilities to "frontline" physicians and nurses, and to obtain more precise information more quickly about the health status of a patient. This article gives an overview of recent advances in the field of biosensors, focusing on biosensors based on enzymes, aptamers, antibodies, and phages. In addition, this article attempts to describe efforts to apply these biosensors to clinical testing and cell analysis.

Aptamer-based origami paper analytical device for electrochemical detection of adenosine

Paper biosensors: an origami sensor is printed on a single piece of paper, folded into a three-dimensional fluidic device, and encapsulated by thermal lamination. Aptamer is trapped in the fluidic channel, where it binds to the target and releases an enzyme to generate a signal. The device is read out using a digital multimeter.

Quantitation of femtomolar protein levels via direct readout with the electrochemical proximity assay

We have developed a separation-free, electrochemical assay format with direct readout that is amenable to highly sensitive and selective quantitation of a wide variety of target proteins. Our first generation of the electrochemical proximity assay (ECPA) is composed of two thrombin aptamers which form a cooperative complex only in the presence of target molecules, moving a methylene blue (MB)-conjugated oligonucleotide close to a gold electrode. Without washing steps, electrical current is increased in proportion to the concentration of a specific target protein. By employing a DNA-based experimental model with the aptamer system, we show that addition of a short DNA competitor can reduce background current of the MB peak to baseline levels. As such, the detection limit of aptamer-based ECPA for human thrombin was 50 pM via direct readout. The dual-probe nature of ECPA gave high selectivity and 93% recovery of signal from 2.5 nM thrombin in 2% bovine serum albumin (BSA). To greatly improve the flexibility of ECPA, we then proved the system functional with antibody-oligonucleotide conjugates as probes; the insulin detection limit was 128 fM with a dynamic range of over 4 orders of magnitude in concentration, again with high assay selectivity. ECPA thus allows separation-free, highly sensitive, and highly selective protein detection with a direct electrochemical readout. This method is extremely flexible, capable of detecting a wide variety of protein targets, and is amenable to point-of-care protein measurement, since any target with two aptamers or antibodies could be assayed via direct electrochemical readout.

Supramolecular complexation for environmental control

Supramolecular complexes offer a new and efficient way for the monitoring and removal of many substances emanating from technical processes, fertilization, plant and animal protection, or e.g. chemotherapy. Such pollutants range from toxic or radioactive metal ions and anions to chemical side products, herbicides, pesticides to drugs including steroids, and include degradation products from natural sources. The applications involve usually fast and reversible complex formation, due to prevailing non-covalent interactions. This is of importance for sensing as well as for separation techniques, where the often expensive host compounds can then be reused almost indefinitely. Immobilization of host compounds, e.g. on exchange resins or on membranes, and their implementation in smart new materials hold particular promise. The review illustrates how the design of suitable host compounds in combination with modern sensing and separation methods can contribute to solve some of the biggest problems facing chemistry, which arise from the everyday increasing pollution of the environment.

Biomimetic sensing based on chemically induced assembly of a signaling DNA aptamer on a fluid bilayer membrane

The adenosine aptamer was split into two halves and linked to a fluid liposome surface; addition of adenosine resulted in aptamer assembly, which did not occur if the split aptamer was attached to silica nanoparticles, demonstrating the feasibility of using aptamer probes to study diffusion within lipid membranes.

Quantification of transcription factor binding in cell extracts using an electrochemical, structure-switching biosensor

Transcription factor expression levels, which sensitively reflect cellular development and disease state, are typically monitored via cumbersome, reagent-intensive assays that require relatively large quantities of cells. Here, we demonstrate a simple, quantitative approach to their detection based on a simple, electrochemical sensing platform. This sensor sensitively and quantitatively detects its target transcription factor in complex media (e.g., 250 μg/mL crude nuclear extracts) in a convenient, low-reagent process requiring only 10 μL of sample. Our approach thus appears a promising means of monitoring transcription factor levels.

Au(III)-assisted core-shell iron oxide@poly(o-phenylenediamine) nanostructures for ultrasensitive electrochemical aptasensors based on DNase I-catalyzed target recycling

A redox-active Au(III)-assisted core-shell iron oxide@poly(o-phenylenediamine) nanostructure was designed as a sensing platform for ultrasensitive electrochemical detection of small molecules (ATP, used as a model here) by coupling with DNase I-catalyzed target recycling.

Entropic and electrostatic effects on the folding free energy of a surface-attached biomolecule: an experimental and theoretical study

Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged-but otherwise apparently inert-surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxylalkane-coated gold surface. We find that whereas surface attachment is destabilizing at low ionic strength, it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis, we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate.