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

Improved ligation-mediated PCR method coupled with T7 RNA polymerase for sensitive DNA detection

The ligation-mediated polymerase chain reaction (PCR) method is widely applied for detecting short-length DNA target. The primary principle of this method is based on the linkage of two separated DNA probes as PCR templates via simultaneous hybridization with DNA target by DNA ligase. Even before taking into account low ligation efficiency, a 1:1 stoichiometric ratio between DNA target and the produced PCR template would put an intrinsic limitation on the detection sensitivity. In order to solve this problem, we have developed an improved ligation-mediated PCR method. It is designed such that a transcription reaction by T7 RNA polymerase is integrated into the ligation reaction. In this way, the produced joint DNA strand composed by two DNA probes can be used as a template both in the transcription reaction and the following PCR process. Then a great number of RNA strands containing the same sequence as DNA target are transcribed to act as a target to initiate new cyclic reactions of ligation and transcription. The results indicate that our proposed method can improve the detection sensitivity by ~2 orders of magnitude compared with the conventional ligation-mediated PCR method.

Fabricating a reversible and regenerable electrochemical biosensor for quantitative detection of antibody by using "triplex-stem" DNA molecular switch

A reversible and regenerable electrochemical biosensor is fabricated for quantitative detection of antibody based on "triplex-stem" molecular switches. A hairpin-shaped oligonucleotide (hairpin DNA) labeled with ferrocene (Fc) at the 3'-end is fixed on the gold electrode serving as a signal transduction probe. Its hairpin structure leads Fc close to the surface of gold electrode and produces a strong current signal (on-state). A single-strand oligonucleotide modified with two digoxin molecules on the two arm segments (capture DNA) interact with hairpin DNA with the help of Ag(+) ions. The "triplex-stem" DNA forms, which separates Fc from the electrode and reduces the electrochemical signal (off-state). Binding of digoxin antibody to digoxin releases capture DNA from the hairpin DNA, creating an effective "off-on" current signal switch. The stability of the "triplex-stem" structure of hairpin/capture DNA is critical to the signal switch and the sensitivity of the method, which can be adjusted conveniently and efficiently by changing Ag(+) concentrations. Based on the "off-on" current signal switch, this biosensor is used to detect digoxin antibody sensitively in blood serum. The linear range is 1.0-500 pg with a correlation coefficient of 0.996, and the detection limit is 0.4 pg. Also, this biosensor shows excellent reversibility and reproducibility, which are significant requirements for practical biosensor applications.

Reagentless, ratiometric electrochemical DNA sensors with improved robustness and reproducibility

To make the electrochemical DNA sensors (E-sensor) more robust and reproducible, we have now for the first time adapted the techniques of ratiometric analyses to the field of E-sensors. We did this via the simple expedient way of simultaneously using two redox probes: Methylene blue as the reporter of the conformational change, and ferrocene as an internal control. During the conformational transduction, only the distance between the signal probe and the electrode surface undergoes an appreciable change, while the distance between the control probe and the electrode remains relatively constant. This special design has allowed very reliable target recognition, as illustrated in this report using a human T-lymphotropic virus type I gene fragment. The standard deviation between measurements obtained using different electrodes was an order of magnitude less than that obtained using a classic E-sensor, which we prepared as a control. A limit of detection of 25.1 pM was obtained with our new system, with a single mismatch discrimination factor of 2.33 likewise being observed. Additionally, this concept had general applicability, and preliminary data of a "Signal-On" ratiometric E-sensor are also provided. Taken in concert, these results serve to validate the utility of what we believe will emerge as an easily generalized approach to oligonucleotide recognition and sensing.

Folding-upon-binding and signal-on electrochemical DNA sensor with high affinity and specificity

Here we investigate a novel signal-on electrochemical DNA sensor based on the use of a clamp-like DNA probe that binds a complementary target sequence through two distinct and sequential events, which lead to the formation of a triplex DNA structure. We demonstrate that this target-binding mechanism can improve both the affinity and specificity of recognition as opposed to classic probes solely based on Watson–Crick recognition. By using electrochemical signaling to report the conformational change, we demonstrate a signal-on E-DNA sensor with up to 400% signal gain upon target binding. Moreover, we were able to detect with nanomolar affinity a perfectly matched target as short as 10 bases (K_D = 0.39 nM). Finally, thanks to the molecular “double-check” provided by the concomitant Watson–Crick and Hoogsteen base pairings involved in target recognition, our sensor provides excellent discrimination efficiency toward a single-base mismatched target.

Acoustic detection of DNA conformation in genetic assays combined with PCR

Application of PCR to multiplexing assays is not trivial; it requires multiple fluorescent labels for amplicon detection and sophisticated software for data interpretation. Alternative PCR-free methods exploiting new concepts in nanotechnology exhibit high sensitivities but require multiple labeling and/or amplification steps. Here, we propose to simplify the problem of simultaneous analysis of multiple targets in genetic assays by detecting directly the conformation, rather than mass, of target amplicons produced in the same PCR reaction. The new methodology exploits acoustic wave devices which are shown to be able to characterize in a fully quantitative manner multiple double stranded DNAs of various lengths. The generic nature of the combined acoustic/PCR platform is shown using real samples and, specifically, during the detection of SNP genotyping in Anopheles gambiae and gene expression quantification in treated mice. The method possesses significant advantages to TaqMan assay and real-time PCR regarding multiplexing capability, speed, simplicity and cost.

Functionalized graphene as sensitive electrochemical label in target-dependent linkage of split aptasensor for dual detection

A new type of electrochemical aptasensor was reported here for highly sensitive detection of adenosine triphosphate (ATP) and adenosine deaminase (ADA) activity using functionalized graphene as efficient electrochemical label. The specific binding of ATP and its aptamer could link the split aptamers modified graphene and magnetic beads together. After ADA catalysis and magnetic separation, graphene material anchored on electrode surface would efficiently facilitate electron transfer, thus produce detectable electrochemical signals. The detection limits for ATP and ADA activity were 13.6 nM and 0.01 unit/mL (~1.2 nM), respectively. Our work would supply new horizons for the diagnostic applications of graphene-based materials in biomedicine and biosensors.

A highly sensitive plasmonic DNA assay based on triangular silver nanoprism etching

Specific nucleic acid detection by using simple and low-cost assays is important in clinical diagnostics, mutation detection, and biodefense applications. Most current methods for the quantification of low concentrations of DNA require costly and sophisticated instruments. Here, we have developed a facile DNA detection platform based on a plasmonic triangular silver nanoprism etching process, in which the shape and size of the nanoprisms were altered accompanied by a substantial surface plasmon resonance shift. Through the combination of enzyme-linked hybridization chain reaction amplification and inherent sensitivity of plasmonic silver nanoprims, this assay could detect as low as 6.0 fM target DNA. Considering the high sensitivity and selectivity of this plasmonic DNA assay, it is expected to be of great interest in clinical diagnostics.

Exonuclease III-aided autocatalytic DNA biosensing platform for immobilization-free and ultrasensitive electrochemical detection of nucleic acid and protein

Homogenous electrochemical biosensor has attracted substantial attention owing to its simplicity, rapid response, and improved recognition efficiency compared with heterogeneous biosensor, but the relatively low detection sensitivity and the limited detection analytes prohibit its potential applications. To address these issues, herein, a simple, rapid, isothermal, and ultrasensitive homogeneous electrochemical DNA biosensing platform for target DNA and protein detection has been developed on the basis of an exonuclease III (Exo III)-aided autocatalytic target recycling strategy. A ferrocene-labeled hairpin probe (HP1) is ingeniously designed, which contains a protruding DNA fragment at 3'-termini as the recognition unit for target DNA. Also, the DNA fragment that could be used as secondary target analogue was introduced, but it was caged in the stem region of HP1. In the presence of target DNA, its recognition with the protruding fragment of HP1 triggered the Exo III cleavage process, accompanied with the target recycling and autonomous generation of secondary target analogues. This accordingly resulted into the autonomous accumulation of ferrocene-labeled mononucleotide, inducing a distinct increase in the electrochemical signal owing to its elevated diffusivity toward indium tin oxide (ITO) electrode surface. The autocatalytic biosensing system was further extended for protein detection by advising an aptamer hairpin switch with the use of thrombin as a model analyte. The current developed autocatalytic and homogeneous strategy provided an ultrasensitive electrochemical detection of DNA and thrombin down to the 0.1 and 5 pM level, respectively, with a high selectivity. It should be further used as a general autocatalytic and homogeneous strategy toward the detection of a wide spectrum of analytes and may be associated with more analytical techniques. Thus, it holds great potential for the development of ultrasensitive biosensing platform for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.

Development of fluorescent nanoparticle-labeled lateral flow assay for the detection of nucleic acids

The rapid, specific and sensitive detection of nucleic acids is of utmost importance for the identification of infectious agents, diagnosis and treatment of genetic diseases, and the detection of pathogens related to human health and safety. Here we report the development of a simple and sensitive nucleic acid sequence-based and Ru(bpy)3 (2+)-doped silica nanoparticle-labeled lateral flow assay which achieves low limit of detection by using fluorescencent nanoparticles. The detection of the synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, was utilized to demonstrate this assay. The 30 nm spherical Ru(bpy)3 (2+)-doped silica nanoparticles were prepared in aqueous medium by a novel method recently reported. The nanoparticles were modified by 3-glycidoxypropyl trimethoxysilane in order to conjugate to amine-capped oligonucleotide reporter probes. The fluorescent intensities of the fluorescent assays were quantified on a mictrotiter plate reader using a custom holder. The experimental results showed that the lateral flow fluorescent assay developed was more sensitive compared with the traditional colloidal gold test strips. The limit of detection for the fluorescent lateral flow assay developed is approximately 0.066 fmols as compared to approximately 15 fmols for the colloidal gold. The limit of detection can further be reduced about one order of magnitude when "dipstick" format was used.

Accurate zygote-specific discrimination of single-nucleotide polymorphisms using microfluidic electrochemical DNA melting curves

We report the first electrochemical system for the detection of single-nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real-time melting-curve analysis of surface-immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late-onset Alzheimer's disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe-target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP-based diseases and personalized medicine.

Graphene platform used for electrochemically discriminating DNA triplex

Triplex DNA has received great attention as new molecular biology tools and therapeutic agents due to their possible novel functions in biology systems. Therefore, it is important to distinguish triplex from among different forms of DNA, such as single-stranded and double-stranded DNA. In this report, several electrochemical techniques, cyclic voltammetry, electrochemical impedance spectroscopy, different pulse voltammetry, and electrochemiluminescence were used for distinguishing this unique structure among different DNA formations by using functionalized graphene/Nafion-Ru(bpy)3(2+) (bpy = 2, 2'-bipyridine) modified glass carbon electrode. The different interactions between nucleotides and graphene surface and Ru(bpy)3(2+) mediated guanine oxidation produced quite different electrochemical responses. Guanine bases are hidden inside the folded triplex DNAs, which are much less susceptible to be oxidized by Ru(bpy)3(3+) produced on electrodes. Furthermore, the effect of guanine bases stacking in triplex also influences the electrochemical behaviors. By changing the different position and distance of guanine bases in DNA sequences, we found that the conjoint way of several guanines strongly influenced the catalytic electrochemical responses on graphene surface. Our results provide new insight into determination of less stable protonated triplex formation by using graphene-based rapid, low-cost and sensitive electrochemical techniques.

A mathematical method for extracting cell secretion rate from affinity biosensors continuously monitoring cell activity

Our laboratory has previously developed miniature aptasensors that may be integrated at the site of a small group of cells for continuous detection of cell secreted molecules such as inflammatory cytokine interferon gamma (IFN-γ). In a system such as this, the signal measured at the sensor surfaces is a complex function of transport, reaction, as well as of cellular activity. Herein, we report on the development of a mathematical framework for extracting cell production rates from binding curves generated with affinity biosensors. This framework consisted of a diffusion-reaction model coupled to a root finding algorithm for determining cell production rates values causing convergence of a predetermined criterion. To experimentally validate model predictions, we deployed a microfluidic device with an integrated biosensor for measuring the IFN-γ release from CD4 T cells. We found close agreement between secretion rate observed theoretically and those observed experimentally. After taking into account the differences in sensor geometry and reaction kinetics, the method for cell secretion rate determination described in this paper may be broadly applied to any biosensor continuously measuring cellular activity.

Homogeneously ultrasensitive electrochemical detection of adenosine triphosphate based on multiple signal amplification strategy

An ultrasensitive electrochemical aptasensor was successfully fabricated for the detection of adenosine triphosphate (ATP). For the first time, one detection system combined several elements: magnetic aptamer sequences for target recognition and separation, a DNAzyme assisted cyclic signal amplification strategy, layer-by-layer (LBL) quantum dots (QDs) composites for promoting square wave anodic stripping voltammetric (SWASV) analysis and Bi, Nafion (Nf) and three-dimensional ordered macroporous polyaniline-ionic liquid (Bi/Nf/3DOM PANI-IL) film modified glassy carbon electrode (GCE) for monitoring enhanced SWASV signal. The modification of Nf/3DOM PANI-IL on GCE showed that the preconcentration efficiency was improved by the electrostatic absorption of Cd(2+) with negative Nf layer with the enhanced analytical sensitivity due to a large active surface area of 3DOM structure. The increased SWASV peak current values of the label (CdS)4@SiO2 composites were found to be proportional to the logarithmic value of ATP concentrations in the range of 1pM-10nM and 10nM-1µM, with the detection limit as low as 0.5pM. The proposed aptasensor has shown an excellent performance such as high sensitivity, good selectivity and analytical application in real samples. The results demonstrated that the multiple signal amplified strategy we developed was feasible for clinical ATP assay and would provide a promising model for the detection of other small molecules.

Fabrication of magneto-controlled moveable architecture to develop reusable electrochemical biosensors

Electrochemical biosensors have been studied intensively for several decades. Numerous sensing concepts and related interface architectures have been developed. However, all such architectures suffer a trade-off: simple architectures favour usability, whereas complex architectures favour better performance. To overcome this problem, we propose a novel concept by introducing a magneto-controlled moveable architecture (MCMA) instead of the conventional surface-fixed architecture. As a model, human breast cancer cells were used in this study. The results showed that a detection range from 100 to 1 × 10⁶ cells could be achieved. Moreover, the whole detection cycle, including the measurement and the regeneration, could be completed in only 2 min. Thus, usability and excellent performance can be achieved in a single biosensor.

Rational design of a redox-labeled chiral target for an enantioselective aptamer-based electrochemical binding assay

A series of redox-labeled L-tyrosinamide (L-Tym) derivatives was prepared and the nature of the functional group and the chain length of the spacer were systematically varied in a step-by-step affinity optimization process of the tracer for the L-Tym aptamer. The choice of the labeling position on L-Tym proved to be crucial for the molecular recognition event, which could be monitored by cyclic voltammetry and is based on the different diffusion rates of free and bound targets in solution. From this screening approach an efficient electroactive tracer emerged. Comparable dissociation constants Kd were obtained for the unlabeled and labeled targets in direct or competitive binding assays. The enantiomeric tracer was prepared and its enantioselective recognition by the corresponding anti-D-Tym aptamer was demonstrated. The access to both enantiomeric tracer molecules opens the door for the development of one-pot determination of the enantiomeric excess when using different labels with well-separated redox potentials for each enantiomer.

An ultrasensitive biosensor for DNA detection based on hybridization chain reaction coupled with the efficient quenching of a ruthenium complex to CdTe quantum dots

A highly sensitive and selective DNA biosensor based on hybridization chain reaction is described, which combines CdTe quantum dots (QDs) and a ruthenium complex. Based on the variation of fluorescence signals of the CdTe QDs, the target DNA is determined.

"Signal off" aptasensor based on enzyme inhibition induced by conformational switch

A novel sensing strategy for electrochemical aptamer-based sensors is presented. Nucleic acid aptamers are considered alternatives to antibodies. However, some of their intrinsic properties, such as that they can undergo conformational changes during the binding of the target, can be used to design novel sensing strategies. Unlike other electrochemical "signal off" aptamer-based sensors, we report a strategy based on enzymatic inhibition. Our approach shows the feasibility to detect small molecules based on the aptamer conformational change induced by the target that leads to the inhibition of the enzyme used as a label. Additionally, we prove the ability to regenerate the function of the aptasensor by simply applying a short potential pulse. As a proof-of-concept, the widely used aptamer for ochratoxin A (OTA) has been selected as a model. After self-assembling short oligonucleotides onto a gold electrode, complementary to the 3' end of the aptamer, hybridization of the aptamer takes place. To investigate the mechanism induced by the OTA-binding, surface plasmon resonance assays were performed, which confirmed the conformational switch of the aptamer rather than the aptamer displacement by dehybridization from the DNA-modified sensor surface. The electrochemical sensor can successfully detect OTA in wine at the limits stipulated by the European Commission. Given its sensitivity, rapid and easy detection, and regeneration, it can be envisaged as screening tool for OTA detection. Moreover, this sensing strategy has the potential to be applied to other aptamer-based biochemical assays for the detection of small molecules in the fields of food safety, environmental monitoring, and medical diagnostics.

Enzyme-free and label-free ultrasensitive electrochemical detection of DNA and adenosine triphosphate by dendritic DNA concatamer-based signal amplification

Hybridization chain reaction (HCR) strategy has been well developed for the fabrication of various biosensing platforms for signal amplification. Herein, a novel enzyme-free and label-free ultrasensitive electrochemical DNA biosensing platform for the detection of target DNA and adenosine triphosphate (ATP) was firstly proposed, in which three auxiliary DNA probes were ingeniously designed to construct the dendritic DNA concatamer via HCR strategy and used as hexaammineruthenium(III) chloride (RuHex) carrier for signal amplification. With the developed dendritic DNA concatamer-based signal amplification strategy, the DNA biosensor could achieve an ultrasensitive electrochemical detection of DNA and ATP with a superior detection limit as low as 5 aM and 20 fM, respectively, and also demonstrate a high selectivity for DNA and ATP detection. The currently proposed dendritic DNA concatamer opens a promising direction to construct ultrasensitive DNA biosensing platform for biomolecular detection in bioanalysis and clinical biomedicine, which offers the distinct advantages of simplicity and cost efficiency owing to no need of any kind of enzyme, chemical modification or labeling.

Conformational change and biocatalysis-triggered spectral shift of single Au nanoparticles

The conformational change of guanine-rich DNA and the biocatalytic process of DNAzyme are observed directly on single gold nanoparticles through NPPR spectra.

Signal amplified two-dimensional photonic crystal biosensor immobilized with glyco-nanoparticles

A two-dimensional, glycopolymer-immobilized, photonic crystal (PhC) biosensor was developed for the detection of proteins.

Identification of allosteric nucleotide sites of tetramethylrhodamine-labeled aptamer for noncompetitive aptamer-based fluorescence anisotropy detection of a small molecule, ochratoxin A

Aptamer-based fluorescence anisotropy (FA) assay combines the advantages of affinity aptamers in good stability, easy generation, and facile labeling and the benefits of FA in homogeneous analysis, such as robustness, simplicity, and high reproducibility. By using a fluorophore-labeled aptamer, FA detection of a small molecule is not as easy as detection of protein because the binding of a small molecule cannot cause significant increase of molecular weight of the dye-labeled aptamer. The intramolecular interaction between labeled tetramethylrhodamine (TMR) and DNA aptamer bases dramatically affects the local rotation and FA of TMR. This intramolecular interaction can be altered by aptamer conformation change upon target binding, leading to a significant change of FA of TMR. Taking this unique feature of a TMR-labeled aptamer, we described a noncompetitive aptamer-based fluorescence anisotropy assay for detection of small molecules by using ochratoxin A (OTA) as a model. We successfully identified the specific TMR-labeling sites of aptamers with sensitive FA response to OTA from the 5'-end, 3'-end and the internal thymine (T) bases. The aptamer with a TMR labeled on the 10th T base exhibited a remarkable FA reduction response to OTA (Δr = 0.078), without requiring any proteins or nanomaterials as FA signal enhancers. This FA approach for OTA showed high sensitivity with a detection limit of 3 nM, a dynamic range from 3 nM to 3 μM, and good selectivity over the tested compounds with similar structures to OTA. The new strategy allowed the detection of OTA in diluted red wine and urine samples.

Rationally designed nucleobase and nucleotide coordinated nanoparticles for selective DNA adsorption and detection

Nanomaterials for DNA adsorption are useful for sequence-specific DNA detection. Current materials for DNA adsorption employ electrostatic attraction, hydrophobic interaction, or π-π stacking, none of which can achieve sequence specificity. Specificity might be improved by involving hydrogen bonding and metal coordination. In this work, a diverse range of nucleobase/nucleotide (adenine, adenosine, adenosine 5'-triphosphate (ATP), adenosine 5'-monophosphate (AMP), and guanosine 5'-triphosphate (GTP)) coordinated materials containing various metal ions (Au(III), Ag(I), Ce(III), Gd(III), and Tb(III)) are prepared. In most cases, nanoparticles are formed. These materials have different surface charges, and positively charged particles only show nonspecific DNA adsorption. Negatively charged materials give different adsorption kinetics for different DNA sequences, where complementary DNA homopolymers are adsorbed faster than other sequences. Therefore, the bases in the coordinated materials can still form base pairs with the DNA. The adsorption strength is mainly controlled by the metal ions, where Au shows the strongest adsorption while lanthanides are weaker. These materials can be used as sensors for DNA detection and can also deliver DNA into cells with no detectable toxicity. By tuning the nanoparticle formulation, enhanced detection can be achieved. This study is an important step toward rational design of materials to achieve specific interactions between biomolecules and synthetic nanoparticle surfaces.

A label-free electrochemical biosensor for highly sensitive and selective detection of DNA via a dual-amplified strategy

In this work, by combining the enzymatic recycling reaction with the DNA functionalized gold nanoparticles (AuNPs)-based signal amplification, we have developed an electrochemical biosensor for label-free detection of DNA with high sensitivity and selectivity. In the new designed biosensor, a hairpin-structured probe HP was designed to hybridize with target DNA first, and an exonuclease ExoIII was chosen for the homogeneous enzymatic cleaving amplification. The hybridization of target DNA with the probe HP induced the partial cleavage of the probe HP by ExoIII to release the enzymatic products. The enzymatic products could then hybridize with the hairpin-structured capture probe CP modified on the electrode surface. Finally, DNA functionalized AuNPs was further employed to amplify the detection signal. Due to the capture of abundant methylene blue (MB) molecules by both the multiple DNAs modified on AuNPs surface and the hybridization product of capture DNA and enzymatic products, the designed biosensor achieved a high sensitivity for target DNA, and a detection limit of 0.6 pM was obtained. Due to the employment of two hairpin-structured probes, HP and CP, the proposed biosensor also exhibited high selectivity to target DNA. Moreover, since ExoIII does not require specific recognition sequences, the proposed biosensor might provide a universal design strategy to construct DNA biosensor which can be applied in various biological and medical samples.

A highly oriented hybrid microarray modified electrode fabricated by a template-free method for ultrasensitive electrochemical DNA recognition

Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors.

Point-of-care nucleic acid detection using nanotechnology

Recent developments in nanotechnology have led to significant advancements in point-of-care (POC) nucleic acid detection. The ability to sense DNA and RNA in a portable format leads to important applications for a range of settings, from on-site detection in the field to bedside diagnostics, in both developing and developed countries. We review recent innovations in three key process components for nucleic acid detection: sample preparation, target amplification, and read-out modalities. We discuss how the advancements realized by nanotechnology are making POC nucleic acid detection increasingly applicable for decentralized and accessible testing, in particular for the developing world.

Recent advances and achievements in nanomaterial-based, and structure switchable aptasensing platforms for ochratoxin A detection

Aptamer-based bioreceptors that can easily adopt their surroundings have captured the attention of scientists from a wide spectrum of domains in designing highly sensitive, selective and structure switchable sensing assays. Through elaborate design and chemical functionalization, numerous aptamer-based assays have been developed that can switch their conformation upon incubation with target analyte, resulting in an enhanced output signal. To further lower the detection limits to picomolar levels, nanomaterials have attracted great interest in the design of aptamer-based sensing platforms. Associated to their unique properties, nanomaterials offer great promise for numerous aptasensing applications. This review will discuss current research activities in the aptasensing with typical example of detection of ochratoxin A (OTA). OTA, a secondary fungal metabolite, contaminates a variety of food commodities, and has several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic activities. The review will introduce advances made in the methods of integrating nanomaterials in aptasensing, and will discuss current conformational switchable design strategies in aptasensor fabrication methodologies.

Spectrophotometric and ultrasensitive DNA bioassay by circular-strand displacement polymerization reaction

We demonstrated a new spectrophotometric DNA detection approach based on a circular strand-displacement polymerization reaction for the quantitative detection of sequence specific DNA. In this assay, the hybridization of an immobilized hairpin probe on the microtiter plate, to target DNA, results in a conformational change and leads to a stem separation. A short primer thus anneals with the open stem and triggers a polymerization reaction, allowing a cyclic reaction comprising the release of target DNA and hybridization of the target with the remaining immobilized hairpin probe. Through this cyclical process, a large number of duplex DNA complexes are produced. Finally, the biotin modified duplex DNA products can be detected via the HRP catalyzed substrate 3,3',5,5'-tetramethylbenzidine using a spectrophotometer. As a proof of concept, a short DNA sequence (20-nt) related to the South East Asia (SEA) type deletion of α-thalassemia was chosen as the model target. This proposed assay has a very high sensitivity and selectivity with a dynamic response ranging from 0.1 fM to 10 nM and the detection limit was 8 aM. It can be performed within 2 hours, and it can differentiate target SEA DNA from wild-type DNA. By substituting the hairpin probes used in the present work, this assay can be used to detect other subtypes of genetic disorders.

A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism

Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF(T1799A) oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF(T1799A) DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF(T1799A) DNA in complex human serum with excellent recovery (94-103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.

Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor

Aptamers are selected DNA ligands that target biomolecules such as proteins. In recent years, they are showing an increasing interest as potential therapeutic agents or recognition elements in biosensor applications. In both cases, the need for characterizing the mating between the target and the aptamer either in solution or immobilized on a surface, is pressing. In this context, we have developed a kinetic biosensor made of micro-arrayed anti-thrombin aptamers to assess the kinetic parameters of this interaction. The binding of label-free thrombin on the biosensor was monitored in real-time by Surface Plasmon Resonance imaging. Remarkable performances were obtained for the quantification of thrombin without amplification (sub-nanomolar limit of detection and linear range of quantification to two orders of magnitude). The independent determinations of both the solution- and surface-phase affinities, respectively K_D^Sol and K_D^Surf, revealed distinct values illustrating the importance of probes, targets or surface interactions in biosensors. Interestingly, K_D^Surf values depend on the aptamer grafting density and linearly extrapolate towards K_D^Sol for highly diluted probes. This suggests a lesser impact of the surface compared to the probe or target cooperativity interactions since the latter decrease with a reduced grafting density.

Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification

A novel, high sensitive, and specific DNA assay based on gold nanoparticle (AuNP) colorimetric detection and hybridization chain reaction (HCR) amplification has been demonstrated in this article. Two hairpin auxiliary probes were designed with single-stranded DNA (ssDNA) sticky ends which stabilize AuNPs and effectively prevent them from salt-induced aggregation. The target DNA hybridized with the hairpin auxiliary probes and triggered the formation of extended double-stranded DNA (dsDNA) polymers through HCR. As a result, the formed dsDNA polymers provide less stabilization without ssDNA sticky ends, and AuNPs undergo aggregation when salt concentration is increased. Subsequently, a pale purple-to-blue color variation is observed in the colloid solution. The system is simple in design and convenient in operation. The novel strategy eliminates the need for enzymatic reactions, separation processes, chemical modifications, and sophisticated instrumentation. The detection and discrimination process can be seen with the naked eye. The detection limit of this method is lower than or at least comparable to previous AuNP-based methods. Importantly, the protocol offers high selectivity for the determination between perfectly matched target oligonucleotides and targets with single base-pair mismatches.

A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine

A label-free G-quadruplex-based luminescent switch-on assay has been developed for the selective detection of micromolar histidine in aqueous solution. In this study, an iridium(III) complex was employed as a G-quadruplex-specific luminescent probe while a guanine-rich oligonucleotide (Pu27, 5'-TG4AG3TG4AG3TG4A2G2-3')/cupric ion (Cu(2+)) ensemble was employed as a recognition unit for histidine. The initial luminescence of the iridium(III) complex in the presence of G-quadruplex DNA is effectively quenched by Cu(2+) ions due to the Cu(2+)-mediated unfolding of the G-quadruplex motif. The addition of histidine sequesters Cu(2+) ions from the ensemble, thereby restoring the luminescence of the system. The assay could detect down to 1 μM of histidine in aqueous media, and also exhibited good selectivity for histidine over other amino acids with the use of the cysteine, masking agent N-ethylmaleimide. Furthermore, the application of the assay for the detection of histidine in diluted urine samples was demonstrated.

Sensitive ECL immunosensor for detection of retinol-binding protein based on double-assisted signal amplification strategy of multiwalled carbon nanotubes and Ru(bpy)3(2+) doped mesoporous silica nanospheres

A novel electrochemiluminescence (ECL) strategy based on the sandwich-type immunosensor for sensitive detection of retinol-binding protein (RBP) was developed. The primary antibody anti-RBP was immobilized onto multiwalled carbon nanotubes (MWCNTs), which have large surface area and high electrical conductivity. The RBP antigen and Ru-Nafion@SiO2-labeled secondary antibody were then successively conjugated to form sandwich-type immunocomplexes through the specific interaction between antigen and antibody. The ECL signal amplification was significantly improved due to the synergistic effect of MWCNTs and mesoporous silica nanospheres (mSiO2). The developed ECL immunosensor exhibited high sensitivity and specificity for the detection of RBP and responded linearly to the clinically-relevant concentration of RBP from 78 to 5000 ng mL(-1). Moreover, the MWCNT-based ECL immunosensor displayed excellent stability and reproducibility, as well as successfully achieved the detection of RBP in patient urine samples with desirable results. The present work provided a promising technique for the clinical screening of RBP and point-of-care diagnostics.

rhEPO/EPO discrimination with ultrasensitive electrochemical biosensor based on sandwich-type nano-Au/ZnO sol-gel/nano-Au signal amplification

This research established a non-labeled electrochemical biosensor for discrimination of recombinant human erythropoietin (rhEPO) and endogenous erythropoietin (EPO). We prepared a glassy carbon electrode (GCE) modified by a unique sandwich-like nano-Au/ZnO sol-gel/nano-Au compound membrane for signal amplification. The porous sol-gel structure facilitates protein activity maintenance and thermostability. Nano-Au is characterized by a large specific surface area, high surface activity, high absorbability, and good electro-conductivity and biocompatibility. By combining the advantages of both ZnO sol-gel and nano-Au, the amount of erythropoietin receptor (EPOR) increased substantially, and electron transfer of EPOR protein and electrode surface increased accordingly. In the present study, the effects of experimental conditions such as nano-Au electrodeposition time and nano-Au concentration were investigated by cyclic voltammetry, and the process of GCE modification was characterized electrochemically. We successfully developed a new method for electrochemical detection of trace rhEPO/EPO. More importantly, the response current change (ΔI) of the nano-Au/ZnO sol-gel/nano-Au modified GCE increases 3-fold when compared with that of the unmodified electrode and the sensor detection sensitivity increases significantly. In conclusion, this electrochemical biosensor is simple to prepare and allows fast, accurate, and specific detection of trace rhEPO in clinical monitoring and stimulant discrimination.