A simple, fast, and sensitive assay for the detection of DNA, thrombin, and adenosine triphosphate based on Dual-Hairpin DNA structure

A chimeric hairpin DNA aptamer-based biosensor for monitoring the therapeutic drug bevacizumab

The accurate and rapid detection of specific antibodies in blood is very important for efficient diagnosis and precise treatment. Conventional methods often suffer from time-consuming operations and/or a narrow detection range. In this work, for the rapid determination of bevacizumab in plasma, a series of chimeric hairpin DNA aptamer-based probes were designed by the modification, labeling and theoretical computation of an original aptamer. Then, the dissociation constant of the modified hairpin DNA to bevacizumab was measured and screened using microscale thermophoresis. The best chimeric hairpin DNA aptamer-based probe was then selected, and a one-step platform for the rapid determination of bevacizumab was constructed. This strategy has the advantages of being simple, fast and label-free. Because of the design and screening of the hairpin DNA, as well as the optimization of the concentration and electrochemical parameters, a low detection limit of 0.37 pM (0.054 ng mL-1) with a wide linear range (1 pM-1 μM) was obtained. Finally, the rationally constructed biosensor was successfully applied to the determination of bevacizumab in spiked samples, and it showed good accuracy and precision. This method is expected to truly realize accurate and rapid detection of bevacizumab and provides a new idea for the precise treatment of diseases.

A Multiplexable Plasmonic Hairpin-DNA Sensor Based On Target-specific Tether Dynamics

The need for measurements of multiple biomarkers simultaneously at subnanomolar concentrations asks for the development of new sensors with high sensitivity, specificity, precision, and accuracy. Currently, multiplexed sensing in single molecule sensors increases the complexity of the system in terms of reagents and sample read-out. In this letter, we propose a novel approach to multiplex hairpin-based single-DNA molecule sensors, which overcomes the limitations of the present approaches for multiplexing. By target-dependent ssDNA hairpin design, we can create DNA tethers that have distinct tether dynamics upon target binding. Our numerical model shows that by changing the stem length of the ssDNA hairpin, significantly different dynamic tether behavior will be observed. By exploiting the distance-dependent coupling of AuNPs to gold films, we can probe this dynamic behavior along the z-axis using a simple laser equipped microscope.

Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis

Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.

Sub-picomolar label-free detection of thrombin using electrochemical impedance spectroscopy of aptamer-functionalized MoS2

An ultrasensitive aptasensor for the label free non-faradaic detection of thrombin has been demonstrated on molybdenum disulphide (MoS₂) nanosheets. These nanosheets were physiochemically immobilized onto a silicon micro-electrode platform. Thrombin detection was achieved through the charge modulation of the electrical double layer due to the specific and dose dependent binding of thrombin to the surface of thiol terminated ssDNA aptamer functionalized MoS₂ nanosheets. Electrical double layer charge modulation associated with thrombin binding was characterized using electrochemical impedance spectroscopy. Dynamic light scattering was also used to confirm the dose dependent behavior. ATR-FTIR spectroscopy and XPS analysis were independently used to validate the functionalization of the ssDNA aptamer onto MoS₂ nanosheets. ssDNA aptamer functionalized molybdenum disulfide (MoS₂) for selective and specific capture of thrombin was demonstrated both in phosphate buffered saline (PBS) and human serum. The optimized immunoassay enabled the detection of thrombin ranging from 267 fM to 267 pM in phosphate buffer. The limit of detection of 53 pM and the linear dynamic range of detection of thrombin ranged from 53 to 854 pM in human serum. The rapid response time for the electrochemical impedance spectroscopy signal makes it an attractive option for the real-time detection of thrombin based point-of-care diagnostic devices.

Nicking endonuclease-assisted recycling of target-aptamer complex for sensitive electrochemical detection of adenosine triphosphate

An electrochemical biosensor was developed for the detection of adenosine triphosphate (ATP) based on target-induced conformation switching and nicking endonuclease (NEase)-assisted signal amplification. The electrochemical biosensor was constructed by base pairing and target recognition. After capture DNA hybridized with the gold electrode, a significant current of Methylene Blue (MB) was obtained by differential pulse voltammetry. In the presence of ATP, the hairpin DNA formed a G-quadruplex structure due to the specific recognition between hairpin DNA and ATP. Then the exposed part of the target-aptamer complex hybridized with the 3'-terminus of capture DNA to form a specific nicking site for Nb.BbvCI, which led to NEase-assisted target-aptamer complex recycling. The released target-aptamer complex hybridized with the remaining capture DNA. Nb.BbvCI-assisted target-aptamer complex recycling caused the continuous cleavage of capture DNA with MB at its 5'-terminus, resulting in release of a certain amount of DNA fragment labeled with MB. Then the current value decreased significantly. The reduced current showed a linear range from 10 nM to 1 μM with a limit of detection as low as 3.4 nM. Furthermore, the proposed strategy can be used for the detection of similar substances.

An ultrasensitive and label-free electrochemical DNA biosensor for detection of DNase I activity

An ultrasensitive and label-free DNA biosensor was developed to detect deoxyribonuclease I activity based on electrochemical method.

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.

Facile construction of a highly sensitive DNA biosensor by in-situ assembly of electro-active tags on hairpin-structured probe fragment

An ultrasensitive DNA biosensor has been developed through in-situ labeling of electroactive melamine-Cu²⁺ complex (Mel-Cu²⁺) on the end of hairpin-like probe using gold nanoparticles (AuNPs) as the signal amplification platform. The 3′-thiolated hairpin-like probe was first immobilized to the gold electrode surface by the Au-S bond. The AuNPs were then tethered on the free 5′-end of the immobilized probe via the special affinity between Au and the modified -NH₂. Followed by, the Mel and Cu²⁺ were assembled on the AuNPs surface through Au-N bond and Cu²⁺-N bond, respectively. Due to the surface area and electrocatalytic effects of the AuNPs, the loading amount and electron transfer kinetic of the Mel-Cu²⁺ were enhanced greatly, resulting in significantly enhanced electrochemical response of the developed biosensor. Compared with the synthesis process of conventional electroactive probe DNA accomplished by homogeneous method, the method presented in this work is more reagent- and time-saving. The proposed biosensor showed high selectivity, wide linear range and low detection limit. This novel strategy could also be extended to the other bioanalysis platforms such as immunosensors and aptasensors.

Utilizing a Key Aptamer Structure-Switching Mechanism for the Ultrahigh Frequency Detection of Cocaine

Aptasensing of small molecules remains a challenge as detection often requires the use of labels or signal amplification methodologies, resulting in both difficult-to-prepare sensor platforms and multistep, complex assays. Furthermore, many aptasensors rely on the binding mechanism or structural changes associated with target capture by the aptameric probe, resulting in a detection scheme customized to each aptamer. It is in this context that we report herein a sensitive cocaine aptasensor that offers both real-time and label-free measurement capabilities. Detection relies on the electromagnetic piezoelectric acoustic sensor (EMPAS) platform. The sensing interface consists of a S-(11-trichlorosilyl-undecanyl)benzenethiosulfonate (BTS) adlayer-coated quartz disc onto which a structure-switching cocaine aptamer (MN6) is immobilized, completing the preparation of the MN6 cocaine aptasensor (M6CA). The EMPAS system has recently been employed as the foundation of a cocaine aptasensor based on a structurally rigid cocaine aptamer variant (MN4), an aptasensor referred to by analogy as M4CA. M6CA represents a significant increase in terms of analytical performance, compared to not only M4CA but also other cocaine aptamer-based sensors that do not rely on signal amplification, producing an apparent K(d) of 27 ± 6 μM and a 0.3 μM detection limit. Remarkably, the latter is in the range of that achieved by cocaine aptasensors relying on signal amplification. Furthermore, M6CA proved to be capable not only of regaining its cocaine-binding ability via simple buffer flow over the sensing interface (i.e., without the necessity to implement an additional regeneration step, such as in the case of M4CA), but also of detecting cocaine in a multicomponent matrix possessing potentially assay-interfering species. Finally, through observation of the distinct shape of its response profiles to cocaine injection, demonstration was made that the EMPAS system in practice offers the possibility to distinguish between the binding mechanisms of structure-switching (MN6) vs rigid (MN4) aptameric probes, an ability that could allow the EMPAS to provide a more universal aptasensing platform than what is ordinarily observed in the literature.

Detection of adenosine triphosphate in HeLa cell using capillary electrophoresis-laser induced fluorescence detection based on aptamer and graphene oxide

A method for ATP quantification based on dye-labeled aptamer/graphene oxide (aptamer/GO) using capillary electrophoresis-laser induced fluorescence (CE-LIF) detecting technique has been established. In this method, the carboxyfluorescein (FAM)-labelled ATP aptamers were adsorbed onto the surface of GO, leading to the fluorescence quenching of FAM; after the incubation with a limited amount of ATP, stronger affinity between ATP aptamer and ATP resulted in the desorption of aptamers and the fluorescence restoration of FAM. Then, aptamer-ATP complex and excess of aptamer/GO and GO were separated and quantified by CE-LIF detection. It was shown that a linear relation was existing in the CE-LIF peak intensity of aptamer-ATP and ATP concentration in range of 10-700 μM, the regression equation was F=1.50+0.0470C(ATP) (R(2)=0.990), and the limit of detection was 1.28 μM (3S/N, n=5), which was one order magnitude lower than that of detection in solution by fluorescence method. The approach with excellent specificity and reproducibility has been successfully applied to detecting concentration of ATP in HeLa cell.

A regenerative electrochemical biosensor for mercury(II) by using the insertion approach and dual-hairpin-based amplification

A simple and effective biosensor for Hg(2+) determination was investigated. The novel biosensor was prepared by the insertion approach that the moiety-labeled DNA inserted into a loosely packed cyclic-dithiothreitol (DTT) monolayer, improving the hybridization efficiency. Electrochemical impedance spectroscopy studies of two biosensors (single-hairpin and dual-hairpin structure DNA modified electrodes) used for Hg(2+) detection indicated that the dual-hairpin modified electrode had a larger electron transfer resistance change (ΔRct). Consequently, the dual-hairpin structure was used as a signal amplifier for the preparation of a selective Hg(2+) biosensor. This biosensor exhibited an excellent selectivity toward Hg(2+) over Cd(2+), Pd(2+), Co(2+) etc. Also, a linear relation was observed between the ΔRct and Hg(2+) concentrations in a range from 0.1 nM to 5 μM with a detection limit of 28 pM under optimum conditions. Moreover, the biosensor can be reused by using L-cysteine and successfully applied for detecting Hg(2+) in real samples.

Resonance light scattering spectroscopy of procyanidin-CPB-DNA ternary system and its potential application

A new method for the determination of calf thymus DNA at nanogram level was proposed based on the enhanced resonance light scattering (RLS) signals of DNA in the presence of procyanidin and cetylpyridinium bromide dihydrate (CPB). Under the experimental conditions, the RLS intensity of DNA at 291.0 nm was greatly enhanced by procyanidin-CPB at pH 7.0. There was a good linear relationship (r=0.9993) between the enhanced RLS intensity (ΔI(RLS)) and DNA concentration of 0.0084-3.36 μg mL(-1). The limit of detection (LOD) was 2.27 ng mL(-1) (3S0/S). Three synthetic DNA samples were measured with satisfactory, and the recovery was 102.3-107.2%.

Ultra-high frequency piezoelectric aptasensor for the label-free detection of cocaine

This paper describes a label-free and real-time piezoelectric aptasensor for the detection of cocaine. The acoustic wave sensing platform is a quartz substrate functionalized with an adlayer of S-(11-trichlorosilyl-undecanyl)-benzenethiosulfonate (BTS) cross-linker onto which the anti-cocaine MN4 DNA aptamer is next immobilized. Preparation of the sensor surface was monitored using X-ray photoelectron spectroscopy (XPS), while the binding of cocaine to surface-attached MN4 was evaluated using the electromagnetic piezoelectric acoustic sensor (EMPAS). The MN4 aptamer, unlike other cocaine aptamer variants, has its secondary structure preformed in the unbound state with only tertiary structure changes occurring during target binding. It is postulated that the highly sensitive EMPAS detected the binding of cocaine through target mass loading coupled to aptamer tertiary structure folding. The sensor achieved an apparent Kd of 45 ± 12 µM, and a limit of detection of 0.9 µM. Repeated regenerability of the sensor platform was also demonstrated. This work constitutes the first application of EMPAS technology in the field of aptasensors. Furthermore, it is so far one of the very few examples of a bulk acoustic wave aptasensor that is able to directly detect the binding interaction between an aptamer and a small molecule in a facile one-step protocol without the use of a complex assay or signal amplification step.

Facile fabrication of a three-dimensional gold nanowire array for high-performance electrochemical sensing

A three-dimensional gold nanowire array (3D GNA) was successfully prepared with a facile template-assisted approach, in order to construct an ultrasensitive electrochemical biosensor.

Versatile biosensing platform for DNA detection based on a DNAzyme and restriction-endonuclease-assisted recycling

On the basis of a DNAzyme and a restriction-endonuclease-assisted target recycling strategy using Pd-Au alloy nanocrystals to immobilize probe DNA on an electrode and catalyze the reduction of H2O2 which amplified signal and promoted the detection sensitivity, a versatile biosensing platform for DNA detection was proposed. Using p53 and oral cancer genes as models, hemin/G-quadruplex simultaneously acted as a reduced nicotinamide adenine dinucleotide (NADH) oxidase and a horseradish peroxidase (HRP)-mimicking DNAzyme, and a versatile DNA biosensor was designed for the first time based on the good electrocatalytic activity of Pd-Au alloy nanocrystals. Hemin/G-quadruplex catalyzed the reduction of H2O2, which was generated from NADH in the presence of O2, to produce an electrochemical signal when thionine functioned as the electron mediator. Moreover, the nicking endonuclease N.BstNB I caused the target DNA to cycle for multiple rounds and further amplified the electrochemical response. This versatile DNA biosensor exhibited linear ranges for the detection of p53 and oral cancer genes from 0.1 fmol L(-1) to 0.1 nmol L(-1) and 0.1 fmol L(-1) to 1 nmol L(-1), respectively. The detection limits, established as 3σ, were estimated to be 0.03 and 0.06 fmol L(-1) for the p53 and oral cancer genes, respectively. The as-prepared biosensor could discriminate mismatched sequences, indicating a satisfactory selectivity and validating the feasibility of the proposed strategy. More importantly, simply by changing the helper DNA, this versatile DNA biosensor could detect different target DNA species, which could create a new avenue for the potential diagnosis of cancer.

A sensitive and versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch

In the present study, a versatile "signal-on" electrochemical aptasensor based on a triple-helix molecular switch has been developed. An aptamer probe is designed to hybridize with the methylene blue (MB)-modified DNA capture probe immobilized on the gold electrode to form rigid triple-helix DNA, impeding the efficient electron transfer of MB to the electrode and resulting in the decreased oxidation peak current of MB. However, upon introduction of the perfectly matched target, for example, human α-thrombin (Tmb), the interaction between Tmb and the aptamer probe leads to the dissociation of the triple-helix DNA structure and thereby liberates the MB-modified end of the capture probe, allowing the MB to collide with the electrode surface and resulting in an increase of the oxidation peak currents of MB. Therefore, the sensitive signal-on detection of Tmb is realized, and the detection limit of Tmb is 0.12 nM. The proposed approach also demonstrates excellent regenerability, reproducibility and stability. Additionally, it also has the advantages of simplicity in design and easy operation. The success in the present biosensor provides a promising alternative to the electrochemical detection of a variety of analytes and may have potential applications in point-of-care testing and clinical diagnosis.