A signal-on electrochemical DNA biosensor based on exonuclease III-assisted recycling amplification

DNA electrochemical detection technology has attracted tremendous interest in recent years. However, a facile and sensitive method for the detection of the disease indicators or genes is still waiting. Herein, we constructed a signal-on electrochemical platform for detecting the manganese superoxide dismutase (MnSOD) gene by incorporating a redox electrochemical signal probe (methylene blue) and exonuclease III-assisted target recycling signal amplification strategy. The sensor was prepared by self-assembly of a capture DNA probe of thiol-modified on GCE with gold electrodeposition. In the presence of target DNA, the exonuclease III can cleave the duplexes formed by the target DNA and the redox-labeled hairpin probes, release the target DNA and produce a residual sequence. The target DNA can continue to hybridize with the hairpin probe for the next cycle of amplification. The residual sequence hybridized with the surface-immobilized capture probes on AuNPs-modified GCE to generate a significantly amplified redox current. In particular, the redox current value of the resultant sensor showed a linear relationship with MnSOD gene concentration in the range of 1-10⁴ pM with the detection limit as low as 0.3 pM. Furthermore, the sensor has excellent specificity and can distinguish single-base mismatch from perfectly matched target DNA. The sensor is fast in operation, and simple in design for detecting different DNA sequences or DNA identification by selecting the appropriate probe sequence, thus shedding light on a good promising application when encountering disease outbreaks or for the early clinical diagnosis of gene-related diseases.

Ratiometric Electrochemical Biosensing of Methyltransferase Activity

In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).

Application of electrochemical methods for the detection of abiotic stress biomarkers in plants

Abiotic stress is the main cause of low productivity in plants. Therefore, it is important to detect stress and respond to it in a timely manner to avoid irreversible damage to plant productivity and health. The application of traditional methods in agriculture is limited by expensive equipment and cumbersome sample processing. More effective detection methods are urgently needed due to the trace amounts and low stabilities of plant biomarkers. Electrochemical detection methods have the unique advantages of high accuracy, a low detection limit, fast response and easy integration with systems. In this review, the application of three types of electrochemical methods to phytohormone assessment is highlighted including direct electrochemical, immunoelectrochemical, and photoelectrochemical methods. Research on electrochemical methods for detecting abiotic stress biomarkers, including various phytohormones, is also summarized with examples. To date, the detection limit of exogenous plant hormones can reach pg/mL or even lower. Nevertheless, more efforts need to be made to develop a portable instrument for in situ online detection if electrochemical sensors are to be applied to the detection of the endogenous hormones or the physiological state of plants. Additionally, plant-wearable sensors that can be directly attached to or implanted into plants for continuous, noninvasive and real-time monitoring are emphasized. Finally, rational summaries of the considered methods and present challenges and future prospects in the field of abiotic stress detection-based electrochemical biosensors are thoroughly discussed.

A triple-helix molecular switch photoelectrochemical biosensor for ultrasensitive microRNA detection based on position-controllable CdS//CdTe signal enhancement and switching

A triple-helix molecular switch photoelectrochemical biosensor is developed for ultrasensitive microRNA detection based on position-controllable CdS//CdTe signal enhancement and switching.

An electrochemical dual-signaling aptasensor for the ultrasensitive detection of insulin

Insulin plays a central role in physiological glycolmetabolism and is associated with diabetes and related diseases. In this work, a dual-signaling electrochemical aptasensor for insulin detection with high sensitivity and specificity has been reported. Methylene blue (MB)-modified insulin-binding aptamer (IBA) as "signal-off" probe, and (DNA2)/Ferrocene (Fc) co-modified gold nanoparticles (DNA2Fc@GNPs) as the "signal-on" probe were integrated with linker mDNA to fabricate the DNA2Fc@GNPs/mDNA/MB-IBA modified Au electrode as the sensing interface, and the current responses of MB and Fc were used as signal indicators. As expected, the incubation of insulin with DNA2Fc@GNPs/mDNA/MB-IBA/Au electrode resulted in the current responses of MB and Fc decreased and increased, respectively. Based on this strategy, the detection of insulin was successfully achieved, and a linear range from 10 pM to 10 nM with the detectable lowest concentration of 0.1 pM was obtained. By measuring the insulin concentrations in serum samples, this proposed aptasensor has been proven to be of high specificity and accuracy. Moreover, the dual-signaling is useful for the more accurate and reproducible detection through their self-referencing capability. This aptasensor possesses such advantages as simplicity, rapid responses, high sensitivity, specificity and accuracy, which is significant for improving the diagnosis of insulin-related diseases.

Design of DNA nanostructure-based interfacial probes for the electrochemical detection of nucleic acids directly in whole blood

Here we report a robust and sensitive DNA nanostructure-based electrochemical (E-nanoDNA) sensor that utilizes tetrahedral DNA nanostructures (TDNs) as an interfacial probe to detect biomolecules in a single-step procedure. In this study, we have firstly demonstrated that the use of TDNs can significantly suppress electrochemical background signals compared to traditional linear DNA probes upon introduction of base mismatches in the edges of TDNs. After further optimization of the two functional strands in the TDNs, quantitative, one-step detection of DNA can be achieved in the picomolar range in less than 10 min, and directly in complex media. Moreover, the baseline drift of this biosensor can be greatly decreased even after several hours in flowing whole blood in vitro, which suggests that the sensor holds potential to be employed in live animals. Furthermore, through replacing functional strands with aptamers or other DNA elements, this E-nanoDNA sensor can be easily used to probe various analytes, broadening the application range of the proposed sensor.

Water-soluble mercury ion sensing based on the thymine-Hg2+-thymine base pair using retroreflective Janus particle as an optical signaling probe

Herein, we report an optical sensing platform for mercury ions (Hg²⁺) in water based on the integration of Hg²⁺-mediated thymine-thymine (T-T) stabilization, a biotinylated stem-loop DNA probe, and a streptavidin-modified retroreflective Janus particle (SA-RJP). Two oligonucleotide probes, including a stem-loop DNA probe and an assistant DNA probe, were utilized. In the absence of Hg²⁺, the assistant DNA probe does not hybridize with the stem-loop probe due to their T-T mismatch, so the surface-immobilized stem-loop DNA probe remains a closed hairpin structure. In the presence of Hg²⁺, the DNA forms a double-stranded structure with the loop region via Hg²⁺-mediated T-T stabilization. This DNA hybridization induces stretching of the stem-loop DNA probe, exposing biotin. To translate these Hg²⁺-mediated structural changes in DNA probe into measurable signal, SA-RJP, an optical signaling label, is applied to recognize the exposed biotin. The number of biospecifically bound SA-RJPs is proportional to the concentration of Hg²⁺, so that the concentration of Hg²⁺ can be quantitatively analyzed by counting the number of RJPs. Using the system, a highly selective and sensitive measurement of Hg²⁺ was accomplished with a limit of detection of 0.027nM. Considering the simplified optical instrumentation required for retroreflection-based RJP counting, RJP-assisted Hg²⁺ measurement can be accomplished in a much easier and inexpensive manner. Moreover, the detection of Hg²⁺ in real drinking water samples including tap and commercial bottled water was successfully carried out.

Ratiometric electrochemical assay for sensitive detecting microRNA based on dual-amplification mechanism of duplex-specific nuclease and hybridization chain reaction

We propose a ratiometric electrochemical assay for detecting microRNA (miRNA) on the basis of dual-amplification mechanism by using distinguishable electrochemical signals from thionine (Thi) and ferrocene (Fc). The thiol-modified and ferrocene-labeled hairpin capture probes (CP) are first immobilized on an Au electrode via Au-S reaction. The target miRNA hybridizes with CP and unfolding the hairpin structure of CP to form miRNA-DNA duplexes. Then, kamchatka crab duplex specific nuclease (DSN) specifically cleaves the DNA in miRNA-DNA duplexes, leading to the release of miRNA and another cleaves cycle, meanwhile, numerous Fc leaves away from the electrode surface and leads to the signal-off of Fc. The residual fragment on electrode surface acts as a HCR primer to form dsDNA polymers through in situ HCR with the presence of the primer and two probes (HDNA and HDNA'), resulting in the capture of numerous DNA/Au NPs/Thi and the signal-on of Thi. The dual-amplification mechanism significantly amplifies the decrease of Fc signal and the increase of Thi signal for ratiometric readout (I_Thi/I_Fc), thus providing a sensitive method for the selective detection of miR-141 with a detection limit down to 11aM. The dual-signal ratiometric outputs have an intrinsic self-calibration to the effects from system, which is promising to be applied in biosensing and clinical diagnosis.

Folding- and Dynamics-Based Electrochemical DNA Sensors

A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. Since electrochemically active contaminants are less common, these sensors are resistant to false-positive signals arising from the nonspecific adsorption of contaminants and perform well even when employed directly in serum, whole blood, and other realistically complex sample matrices. Moreover, because all of the sensor components are chemisorbed to the electrode, the E-DNA sensors are essentially label-free and readily reusable. To date, these sensors have achieved state-of-the-art sensitivity, while offering the unprecedented selectivity, reusability, and the operational convenience of direct electrochemical detection. This chapter reviews the recent advances in the development of both "signal-off" and "signal-on" E-DNA sensors. Critical aspects that dictate the stability and performance of these sensors are also addressed so as to provide a realistic overview of this oligonucleotide detection platform.

Bioinspired Assemblies and Plasmonic Interfaces for Electrochemical Biosensing

Electrochemical biosensing represents a collection of techniques that may be utilized for capture and detection of biomolecules in both simple and complex media. While the instrumentation and technological aspects play important roles in detection capabilities, the interfacial design aspects are of equal importance, and often, those inspired by nature produce the best results. This review highlights recent material designs, recognition schemes, and method developments as they relate to targeted electrochemical analysis for biological systems. This includes the design of electrodes functionalized with peptides, proteins, nucleic acids, and lipid membranes, along with nanoparticle mediated signal amplification mechanisms. The topic of hyphenated surface plasmon resonance assays is also discussed, as this technique may be performed concurrently with complementary and/or confirmatory measurements. Together, smart materials and experimental designs will continue to pave the way for complete biomolecular analyses of complex and technically challenging systems.

Conformational Changes of Enzymes and Aptamers Immobilized on Electrodes

Conformation constitutes a vital property of biomolecules, especially in the cases of enzymes and aptamers, and is essential in defining their molecular recognition ability. When biomolecules are immobilized on electrode surfaces, it is very important to have a control on all the possible conformational changes that may occur, either upon the recognition of their targets or by undesired alterations. Both enzymes and aptamers immobilized on electrodes are susceptible to conformational changes as a response to the nature of the charge of the surface and of the surrounding environment (pH, temperature, ionic strength, etc.). The main goal of this review is to analyze how the conformational changes of enzymes and aptamers immobilized on electrode surfaces have been treated in reports on biosensors and biofuel cells. This topic was selected due to insufficient information found on the actual conformational changes involved in the function of these bioelectrochemical devices despite its importance.

A "signal on" protection-displacement-hybridization-based electrochemical hepatitis B virus gene sequence sensor with high sensitivity and peculiar adjustable specificity

One "signal on" electrochemical sensing strategy was constructed for the detection of a specific hepatitis B virus (HBV) gene sequence based on the protection-displacement-hybridization-based (PDHB) signaling mechanism. This sensing system is composed of three probes, one capturing probe (CP) and one assistant probe (AP) which are co-immobilized on the Au electrode surface, and one 3-methylene blue (MB) modified signaling probe (SP) free in the detection solution. One duplex are formed between AP and SP with the target, a specific HBV gene sequence, hybridizing with CP. This structure can drive the MB labels close to the electrode surface, thereby producing a large detection current. Two electrochemical testing techniques, alternating current voltammetry (ACV) and cyclic voltammetry (CV), were used for characterizing the sensor. Under the optimized conditions, the proposed sensor exhibits a high sensitivity with the detection limit of ∼5fM for the target. When used for the discrimination of point mutation, the sensor also features an outstanding ability and its peculiar high adjustability.

A reagentless DNA-based electrochemical silver(I) sensor for real time detection of Ag(I) - the effect of probe sequence and orientation on sensor response

Ag(I) is known to interact with cytosine (C) via the formation C-Ag(I)-C complexes. The authors have utilized this concept to design six electrochemical Ag(I) sensors using C-rich DNA probes. Alternating current voltammetry and cyclic voltammetry were used to analyze the sensors. The results show that the dual-probe sensors that require the use of both 5'- and 3'-thiolated DNA probes are not suitable for this application, the differences in probe orientation impedes formation of C-Ag(I)-C complexes. Sensors fabricated with DNA probes containing both thymine (T) and C, independent of the location of the alkanethiol linker, do not response to Ag(I) either; T-T mismatches destabilize the duplex even in the presence of Ag(I). However, sensors fabricated with DNA probes containing both adenine (A) and C are ideal for this application, owing to the formation of C-Ag(I)-C complexes, as well as other lesser known interactions between A and Ag(I). Both sensors are sensitive, specific and selective enough to be used in 50% human saliva. They can also be used to detect silver sulfadiazine, a commonly prescribed antimicrobial drug. With further optimization, this sensing strategy may offer a promising approach for detection of Ag(I) in environmental and clinical samples.

Methylene blue phosphoramidite for DNA labelling

We report the first synthesis of a methylene blue (MB) phosphoramidite derivative suitable for DNA solid-phase synthesis. The electrochemical and optical properties of the resulting MB modified oligonucleotides were confirmed. This new molecule is an important breakthrough in the design of new probes labelled with MB.

Smart protein biogate as a mediator to regulate competitive host-guest interaction for sensitive ratiometric electrochemical assay of prion

A novel competitive host-guest strategy regulated by protein biogate was developed for sensitive and selective analysis of prion protein. The methylene blue (MB)-tagged prion aptamer (MB-Apt) was introduced to the multiwalled carbon nanotubes-β-cyclodextrins (MWCNTs-β-CD) composites-modified glassy carbon (GC) electrode through the host-guest interaction between β-CD and MB. In the absence of prion, MB-Apt could be displaced by ferrocenecarboxylic acid (FCA) due to its stronger binding affinity to β-CD, resulting in a large oxidation peak of FCA. However, in the presence of prion, the specific prion-aptamer interaction drove the formation of protein biogate to seal the cavity of β-CD, which hindered the guest displacement of MB by FCA and resulted in the oxidation peak current of MB (I_MB) increased and that of FCA (I_FCA) decreased. The developed aptasensor showed good response towards the target (prion protein) with a low detection limit of 160 fM. By changing the specific aptamers, this strategy could be easily extended to detect other proteins, showing promising potential for extensive applications in bioanalysis.

Electrochemical Detection of Platinum(IV) Prodrug Satraplatin in Serum

We report the design and fabrication of a reagentless and reusable electrochemical sensor for detection of satraplatin (SAT), a platinum(IV) prodrug. The detection strategy is based on the electrocatalytic reaction between the Pt(IV) center of SAT and surface-immobilized methylene blue. We systematically evaluated the effect of passivating diluent chain length on the overall sensor performance. Our results show that the use of a shorter diluent like 2-mercaptoethanol is more advantageous than using a longer and more passivating diluent such as 6-mercapto-1-hexanol. Independent of the use of cyclic voltammetry or chronoamperometry as the sensor interrogation technique, all three sensors, each passivated with a different alkanethiol diluent, have been demonstrated to be sensitive; the limit of detection is in the range of 1-10 μM. They are also highly specific and do not respond to Pt(II) drugs such as cisplatin and carboplatin. More importantly, they are selective enough to be employed directly in 50% serum. This sensing strategy has potential applications in clinical pharmacokinetics studies.

Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors

Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors.

Incorporation of extra amino acids in peptide recognition probe to improve specificity and selectivity of an electrochemical peptide-based sensor

We investigated the effect of incorporating extra amino acids (AA) at the n-terminus of the thiolated and methylene blue-modified peptide probe on both specificity and selectivity of an electrochemical peptide-based (E-PB) HIV sensor. The addition of a flexible (SG)3 hexapeptide is, in particular, useful in improving sensor selectivity, whereas the addition of a highly hydrophilic (EK)3 hexapeptide has shown to be effective in enhancing sensor specificity. Overall, both E-PB sensors fabricated using peptide probes with the added AA (SG-EAA and EK-EAA) showed better specificity and selectivity, especially when compared to the sensor fabricated using a peptide probe without the extra AA (EAA). For example, the selectivity factor recorded in the 50% saliva was ∼2.5 for the EAA sensor, whereas the selectivity factor was 7.8 for both the SG-EAA and EK-EAA sensors. Other sensor properties such as the limit of detection and dynamic range were minimally affected by the addition of the six AA sequence. The limit of detection was 0.5 nM for the EAA sensor and 1 nM for both SG-EAA and EK-EAA sensors. The saturation target concentration was ∼200 nM for all three sensors. Unlike previously reported E-PB HIV sensors, the peptide probe functions as both the recognition element and antifouling passivating agent; this modification eliminates the need to include an additional antifouling diluent, which simplifies the sensor design and fabrication protocol.

Use of thiolated oligonucleotides as anti-fouling diluents in electrochemical peptide-based sensors

We incorporated short thiolated oligonucleotides as passivating diluents in the fabrication of electrochemical peptide-based (E-PB) sensors, with the goal of creating a negatively charged layer capable of resisting non-specific adsorption of matrix contaminants. The E-PB HIV sensors fabricated using these diluents were found to be more specific and selective, while retaining attributes similar to the sensor fabricated without these diluents. Overall, these results highlight the advantages of using oligonucleotides as anti-fouling diluents in self-assembled monolayer-based sensors.

Target catalyzed hairpin assembly for constructing a ratiometric electrochemical aptasensor

In this paper, we develop a novel dual-signaling amplified aptasensor for protein detection via target-catalyzed hairpin assembly. Thrombin was chosen as a model target. This aptasensor contains two DNA hairpins termed as H1 and H2. H1, which is modified at its 3' ends with a methylene blue (MB), consists of the aptamer sequence of human thrombin. Meanwhile, H2 which is modified at its 3' ends with a ferrocene (Fc), is partially complementary to H1. Upon the addition of target protein, it can facilitate the opening of the hairpin structure of H1 and thus accelerate the hybridization between H1 and H2, the target protein can be displaced from hairpin H1 by hairpin H2 through a process similar to DNA branch migration. The released target found another H1 to trigger the cycle, resulting in the multiplication of the Fc confined near the GE surface and MB away from the GE surface. When IFc/IMB is used as the response signal for quantitative determination of thrombin, the detection limit (41 fM) is much lower than that by using either MB or Fc alone. This new dual-signaling aptasensor is readily regenerated and shows good response toward the target. Furthermore, this amplified aptasensor shows high selectivity toward its target protein. The clever combination of the functional DNA hairpin and the novel device achieved a ratiometric electrochemical aptasensor, which could be used as a simple, sensitive high repeatability and selective platform for target protein detection.

Multilayer graphene-gold nanocomposite modified stem-loop DNA biosensor for peanut allergen-Ara h1 detection

In this study, we developed an electrochemically-amplified, stem-loop DNA biosensor to detect the peanut allergen Ara h1. Specifically, we electrodeposited a multilayer graphene-gold nanocomposite onto a glassy carbon electrode and then immobilised a thiolated hairpin DNA-biotin probe onto the modified electrode surface. The multilayer graphene-gold composite has good dispersion ability, and can amplify the electrochemical signal due to its high electron-transfer efficiency. The probe was switched to an "off" state in the presence of target DNA. The prepared biosensor demonstrated a linear response ranging from 10(-16) to 10(-13)M, with an ultrasensitive detection limit of 0.041 fM. Moreover, the biosensor showed excellent selectivity, as well as the ability to discriminate between a complementary target and a one-base mismatch or non-complementary sequence. Results show that this prepared DNA biosensor can be successfully used to detect the peanut allergen Ara h1 in a peanut milk beverage. Findings can be applied to the prevention of allergic reactions, thus improving human health and safety.

Amperometric carbohydrate antigen 19-9 immunosensor based on three dimensional ordered macroporous magnetic Au film coupling direct electrochemistry of horseradish peroxidase

A sandwich-type electrochemical immunosensor for the detection of carbohydrate antigen 19-9 (CA 19-9) antigen based on the immobilization of primary antibody (Ab1) on three dimensional ordered macroporous magnetic (3DOMM) electrode, and the direct electrochemistry of horseradish peroxidase (HRP) that was used as both the label of secondary antibody (Ab2) and the blocking reagent. The 3DOMM electrode was fabricated by introducing core-shell Au-SiO2@Fe3O4 nanospheres onto the surface of three dimensional ordered macroporous (3DOM) Au electrode via the application of an external magnet. Au nanoparticles functionalized SBA-15 (Au@SBA-15) was conjugated to the HRP labeled secondary antibody (HRP-Ab2) through the Au-SH or Au-NH3(+) interaction, and HRP was also used as the block reagent. The formation of antigen-antibody complex made the combination of Au@SBA-15 and 3DOMM exhibit remarkable synergistic effects for accelerating direct electron transfer (DET) between HRP and the electrode. Under the optimal conditions, the DET current signal increased proportionally to CA 19-9 concentration in the range of 0.05 to 15.65 U mL(-1) with a detection limit of 0.01 U mL(-1). Moreover, the immunosensor showed high selectivity, good stability, satisfactory reproducibility and regeneration. Importantly, the developed method was used to assay clinical serum specimens, achieving a good relation with those obtained from the commercialized electrochemiluminescent method.

Development of a "signal-on" electrochemical DNA sensor with an oligo-thymine spacer for point mutation detection

We report a reagentless and reusable "signal-on" electrochemical DNA sensor that utilizes oligo-thymine as a flexible spacer. This sensor design is sensitive, specific, and selective; it is potentially generalizable for detection of a wide range of biomedical-relevant nucleic acid sequences.

Sensitive electrochemical aptasensor by coupling "signal-on'' and "signal-off'' strategies

A simple electrochemical aptasensor for sensitive and selective determination of adenosine triphosphate (ATP) has been developed on the basis of a new dual-signaling amplification strategy. This aptasensor features both ''signal-on'' and ''signal-off'' elements. The ferrocene (Fc)-labeled aptamer probe (Fc-P) is designed to hybridize with the thiolated methylene blue (MB)-modified DNA probe (MB-P) on gold electrode to form rigid duplex DNA. In the presence of ATP, the interaction between ATP and the aptamer leads to the dissociation of the duplex DNA structure and thereby the release of the Fc-P from the sensing interface. The single-stranded MB-P could thus tend to form a hairpin structure through the hybridization of the complementary sequences at both its ends. Such conformational changes result in the oxidation peak current of Fc decreases and that of MB increases, and the changes of dual signals are linear with the concentration of ATP. When "ΔI = ΔI(MB) + |ΔI(Fc)|" (ΔI(MB) and ΔI(Fc) are the change values of the oxidation peak currents of MB and Fc, respectively.) is used as the response signal for quantitative determination of ATP, the detection limit (1.9 nM) is much lower than that by using either MB-P or Fc-P alone. This new dual-signaling aptasensor is readily regenerated and shows good response toward the target. It will have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

Electrochemical techniques for characterization of stem-loop probe and linear probe-based DNA sensors

Here we present a summary of the sensor performance of the stem-loop probe (SLP) and linear probe (LP) electrochemical DNA sensors when interrogated using alternating current voltammetry (ACV), cyclic voltammetry (CV), and differential pulse voltammetry (DPV). Specifically, we identified one critical parameter for each voltammetric technique that can be adjusted for optimal sensor performance. Overall, the SLP sensor displayed good sensor performance (i.e., 60+% signal attenuation in the presence of the target) over a wider range of experimental conditions when compared to the LP sensor. When used with ACV, the optimal frequency range was found to be between 5 and 5000 Hz, larger than the 5-100 Hz range observed with the LP sensor. A similar trend was observed for the two sensors in CV; the LP sensor was operational only at scan rates between 30 and 100 V/s, whereas the SLP sensor performed well at scan rates between 1 and 1000 V/s. Unlike ACV and CV, DPV has demonstrated to be a more versatile sensor interrogation technique for this class of sensors. Despite the minor differences in total signal attenuation upon hybridization to the target DNA, both SLP and LP sensors performed optimally under most pulse widths used in this study. More importantly, when used with longer pulse widths, both sensors showed "signal-on" behavior, which is generally more desirable for sensor applications.

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.

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.