Unlabeled hairpin-DNA probe for the detection of single-nucleotide mismatches by electrochemical impedance spectroscopy

Detection of single-base mutation of DNA oligonucleotides with different lengths by terahertz attenuated total reflection microfluidic cell

Many human genetic diseases are caused by single-base mutation in the gene sequence. Since DNA molecules with single-base mutation are extremely difficult to differentiate, existing detection methods are invariably complex and time-consuming. We propose a new label-free and fast terahertz (THz) spectroscopic technique based on a home-made terahertz attenuated total reflection (ATR) microfluidic cell and a terahertz time-domain spectroscopy (THz-TDS) system to detect single-base-mutated DNA molecules. The detected object DNA molecules are normal hemoglobin gene, sickle cell anemia gene (15 nt), JAK2 gene wild type and JAK2 V617F gene mutation (39 nt) from sickle cell anemia and thrombocytopenia, respectively. Results show that the oligonucleotide fragments with single-base mutation can be identified by THz spectroscopy combined with the ATR microfluidic cell, and the recognition effect of short oligonucleotide fragments with single-base mutation is better than that of long oligonucleotide fragments. The terahertz biosensor is shown to have high sensitivity and can be used to detect DNA molecules directly in the solution environment.

Reagentless Redox Capacitive Assaying of C-Reactive Protein at a Polyaniline Interface

Methods that enable the sensitive and label-free detection of protein biomarkers are well-positioned to make potentially significant contributions to diagnostics and derived personalized healthcare. In support of this goal, a myriad of (electrochemical) methodologies have been developed; recently, electrochemical capacitance spectroscopy emerged as an impedance-derived approach which, in employing surface-confined redox-transducers, circumvents problems associated with the use of solution-phase redox-probes. Herein, we expand this scope by utilizing phytic acid-doped polyaniline as a novel redox-charging polymer support enabling the reagentless assaying of C-reactive protein in serum with good sensitivity. The construction of the sensory interface via electropolymerization allows facile tuning of the surface coverage and redox (capacitive) properties of the polymers, which, in turn, modulate both assay selectivity, fouling, and sensitivity. Significantly, this methodology is readily extendable to a wide range of electrode materials and analytes.

Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors

Despite a large number of publications describing biosensors based on electrochemical impedance spectroscopy (EIS), little attention has been paid to the stability and reproducibility issues of the sensor interfaces. In this work, the stability and reproducibility of faradaic EIS analyses on the aptamer/mercaptohexanol (MCH) self-assembled monolayer (SAM)-functionalized gold surfaces in ferri- and ferrocyanide solution were systematically evaluated prior to and after the aptamer-probe DNA hybridization. It is shown that the EIS data exhibited significant drift, and this significantly affected the reproducibility of the EIS signal of the hybridization. As a result, no significant difference between the charge transfer resistance (R_CT) changes induced by the aptamer-target DNA hybridization and that caused by the drift could be identified. A conditioning of the electrode in the measurement solution for more than 12 h was required to reach a stable R_CT baseline prior to the aptamer-probe DNA hybridization. The monitored drift in R_CT and double layer capacitance during the conditioning suggests that the MCH SAM on the gold surface reorganized to a thinner but more closely packed layer. We also observed that the hot binding buffer used in the following aptamer-probe DNA hybridization process could induce additional MCH and aptamer reorganization, and thus further drift in R_CT. As a result, the R_CT change caused by the aptamer-probe DNA hybridization was less than that caused by the hot binding buffer (blank control experiment). Therefore, it is suggested that the use of high temperature in the EIS measurement should be carefully evaluated or avoided. This work provides practical guidelines for the EIS measurements. Moreover, because SAM-functionalized gold electrodes are widely used in biosensors, for example, DNA sensors, an improved understanding of the origin of the observed drift is very important for the development of well-functioning and reproducible biosensors.

A Novel Electrochemical Biosensor Based on a Double-Signal Technique for d(CAG)n Trinucleotide Repeats

Electrochemical sensors now play an important role in analysis and detection of nucleic acids. In this work, we present a novel double-signal technique for electrochemically measuring the sequence and length of the d(CAG)_n repeat. The double-signal technique used an electrochemical molecular beacon (a hairpin DNA labeled with ferrocene), which was directly modified on the surface of a gold electrode, while a reporter probe (a DNA sequence labeled with horseradish peroxidase) was hybridized to the target DNA. First a simple single-signal sensor was characterized in which d(CAG)_n repeats were detected using a short reporter DNA strand labeled with horseradish peroxidase. To obtain a reliable signal that was dependent on repeat number, a double-signal biosensor was created in which the single strand capture DNA in single-signal sensor was replaced by an electrochemical molecular beacon labeled with ferrocene. When the hairpin DNA hybridized to the target-reporter DNA complex, it opened, resulting in a decreased ferrocene current. Both electrochemical biosensors exhibited high selectivity and sensitivity with low detection limits of 0.21 and 0.15 pM, respectively, for the detection of d(CAG)_n repeats. The double-signal sensor was more accurate for the determination of repeat length, which was measured from the ratio of signals for HRP and ferrocene (H/F). A linear relationship was found between H/F and the number of repeats (n), H/F = 0.1398n + 9.89788, with a correlation coefficient of 0.974. Only 10 nM of target DNA was required for measurements based on the value of H/F in the double-signal technique. These results indicated that this new double-signal electrochemical sensor provided a reliable method for the analysis of CAG trinucleotide repeats.

Synergistic effect of magnetite and gold nanoparticles onto the response of a label-free impedimetric hepatitis B virus DNA biosensor

A magnetite and gold nanoparticle modified carbon paste electrode (CPE) was prepared for the immobilization of a thiol modified Hepatitis B virus (HBV) probe DNA and determination trace amount of target HBV DNA. Indeed, the sensing platform integrated two nanoparticles that had previously been employed individually in the DNA biosensors. The proposed DNA biosensor could measure target HBV DNA virus concentration with a low detection limit of 3.1 (±0.1)×10-(13)M, which was greatly lower than the detection limit reported with gold or magnetite nanoparticles alone. The change of interfacial charge transfer resistance (RCT) was confirmed the hybrid formation between probe and target HBV DNA. The RCT difference (before and after hybridization with the target HBV DNA) was in a linear relationship with the logarithm of complementary oligonucleotide concentrations in the range of 8.3 (±0.1)×10(-13) to 6.4 (±0.2)×10(-7)M. In addition, the novel methodology for specific DNA sequence detection was highly selective, repeatable, and reproducible. Finally, this work was successfully utilized for the sensitive and label free impedimetric determination of HBV target DNA in the urine and blood plasma samples.

Sensitive impedimetric biosensor based on duplex-like DNA scaffolds and ordered mesoporous carbon nitride for silver(I) ion detection

This study demonstrates a new, unlabeled immobilized DNA-based biosensor with ordered mesoporous carbon nitride material (MCN) for the detection of Ag(+) by electrochemical impedance spectroscopy (EIS) with [Fe(CN)6](4-/3-) as the redox couple. The unlabeled immobilized DNA initially formed the hairpin-like structure through hybridization with the probe, and then changed to duplex-like structure upon interaction with Ag(+) in solution to form a C-Ag(+)-C complex at electrode surface. As a result, the interfacial charge-transfer resistance of the electrode towards the [Fe(CN)6](4-/3-) redox couple was changed. Thus, a declined charge transfer resistance (Rct) was obtained, corresponding to Ag(+) concentration. MCN provide an excellent platform for DNA immobilization and faster electron transfer. Impedance data were analyzed with the help of Randles equivalent circuit. The lower detection limit of the biosensor for Ag(+) is 5 × 10(-11) M with good specificity. All results showed that this novel approach provides a reliable method for Ag(+) detection with sensitivity and specificity, potentially useful for practical applications. Moreover, other DNA detection methods for more heavy metals may be obtained from this idea and applied in the environmental field.

Electrochemistry, biosensors and microfluidics: a convergence of fields

Electrochemistry, biosensors and microfluidics are popular research topics that have attracted widespread attention from chemists, biologists, physicists, and engineers. Here, we introduce the basic concepts and recent histories of electrochemistry, biosensors, and microfluidics, and describe how they are combining to form new application-areas, including so-called "point-of-care" systems in which measurements traditionally performed in a laboratory are moved into the field. We propose that this review can serve both as a useful starting-point for researchers who are new to these topics, as well as being a compendium of the current state-of-the art for experts in these evolving areas.

DNA biosensor based on hybridization refractory mutation system approach for single mismatch detection

We report on a simple approach to enhance solid-phase hybridization-based single base mismatch discrimination at high ionic strength based on the deliberate insertion of a natural DNA base mismatch in the surface-tethered probe. A large drop in hybridization signal of single base mismatched alleles using the designed probe as compared with the conventional probe, from 80% to less than 25% of the signal obtained with the fully complementary, non-mutation-containing sequence, when using colorimetric detection was further improved to 20% when using electrochemical detection, attributable to a difference of spacing of immobilized probes. Finally, the designed probe was used for the electrochemical detection of the DQA1*05:05 allele amplified from real human blood samples.

A universal lateral flow biosensor for proteins and DNAs based on the conformational change of hairpin oligonucleotide and its use for logic gate operations

A universal lateral flow biosensor for proteins and DNAs was designed on the base of target-induced conformational changes of hairpin oligonucleotide (HO). CEA (carcinoembryonic antigen) protein and c-DNA were detected both with the naked eye and a strip reader. The scheme of detecting proteins and DNAs were based on the unique molecular recognition properties of HO to the targets to form different quantities of "active" biotin groups on the surface of gold nanoparticles (AuNPs). The output of the strip is the color of the test line, which inspired us to combine strip biosensor with logic gate. Two strip logic gates ("OR" and "INH") were designed in our paper and the combinatorial logic gates in our paper could be used to make high-throughput judgment about what targets were present in the input samples according to the output results. The biosensor facilitates a portable analysis at ambient temperature as it is simple to be conducted and no requirement of training is needed. The strip logic system is proved an excellent selection and can operate effectively as well as in human serum samples. Therefore, we indicate that such logic strips a foreseeable promise in application of intelligent point-of-care and in-field diagnostics.

Detection of haplotype mutations of the MD-2 gene promoter associated with Der p2-induced allergy using a nanostructured biosensor

Group 2 allergens (Der p2) have been reported to be a major cause of the human immune response to dust mite allergens. In this study, we have demonstrated for the first time the effective differentiation between haplotype mutation and normal genes in the MD-2 gene promoter using a nanostructured biosensor. A 70-mer gene fragment containing the haplotype of two single nucleotide polymorphisms in the MD-2 gene promoter region was used as a probe to detect haplotype mutations associated with Der p2-induced allergy. Discrimination was achieved using electrochemical impedance spectroscopy. The discrimination experiments employed 30 haplotype mutation samples and 30 normal target samples. The haplotype mutation samples and normal target samples could be clearly discriminated, even using samples produced by a five-cycle polymerase chain reaction process. The time and cost of sample preparation for the polymerase chain reaction process in the clinical setting can thus be reduced.

Perylene derivative-bridged Au–graphene nanohybrid for label-free HpDNA biosensor

A novel PDI-bridged Au–graphene nanohybrid was synthesized and used to fabricate a label-free hpDNA biosensor.

An electrochemical impedance sensor based on a small molecule modified Au electrode for the recognition of a trinucleotide repeat

A small molecule modified sensor was developed for the detection of XGG trinucleotide repeats (X = C, T) by electrochemical impedance spectroscopy.

Prussian blue nanoparticles as peroxidase mimetics for sensitive colorimetric detection of hydrogen peroxide and glucose

Prussian blue nanoparticles (PB NPs) exhibits an intrinsic peroxidase-like catalytic activity towards the hydrogen peroxide (H2O2)-mediated oxidation of classical peroxidase substrate 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt to produce a colored product. The catalysis follows Michaelis-Menen kinetics and shows strong affinity for H2O2. Using PB NPs as a peroxidase mimetics, a colorimetric method was developed for the detection of 0.05-50.0 μM H2O2, with a detection limit of 0.031 μM. When the catalytic reaction of PB NPs was coupled with the reaction of glucose oxidation catalyzed by glucose oxidase, a sensitive and selective colorimetric method for the detection of glucose was realized. The limit of detection for glucose was determined to be as low as 0.03 μM and the linear range was from 0.1 μM to 50.0 μM. The method was successfully applied to the determination of glucose in human serum. Compared with other nanomaterials-based peroxidase mimetics, PB NPs provides 10-100 times higher sensitivity toward the detection of H2O2 and glucose. The detection platform developed showed great potential applications in varieties of physiological importance substances when merged with appropriate H2O2-producing oxidases.

Sensitive, simultaneous quantitation of two unlabeled DNA targets using a magnetic nanoparticle-enzyme sandwich assay

We report herein the development of a simple, sensitive colorimetric magnetic nanoparticle (MNP)-enzyme-based DNA sandwich assay that is suitable for simultaneous, label-free quantitation of two DNA targets down to 50 fM level. It can also effectively discriminate single-nucleotide polymorphisms (SNPs) in genes associated with human cancers (KRAS codon 12/13 SNPs). This assay uses a pair of specific DNA probes, one being covalently conjugated to an MNP for target capture and the other being linked to an enzyme for signal amplification, to sandwich a DNA target, allowing for convenient magnetic separation and subsequent efficient enzymatic signal amplification for high sensitivity. Careful optimization of the MNP surfaces and assay conditions greatly reduced the background, allowing for sensitive, specific detection of as little as 5 amol (50 fM in 100 μL) of target DNA. Moreover, this sensor is robust, it can effectively discriminate cancer-specific SNPs against the wild-type noncancer target, and it works efficiently in 10% human serum. Furthermore, this sensor can simultaneously quantitate two different DNA targets by using two pairs of unique capture- and signal-DNA probes specific for each target. This general, simple, and sensitive DNA sensor appears to be well-suited for a wide range of genetics-based biosensing and diagnostic applications.

Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification

We report herein the development of a highly sensitive and selective approach for label-free DNA detection by combining target-recycled ligation (TRL), magnetic nanoparticle assisted target capture/separation, and efficient enzymatic amplification. We show that our approach can detect as little as 30 amol (600 fM in 50 μL) of unlabelled single-stranded DNA targets and offer an exquisitely high discrimination ratio (up to >380 fold with background correction) between a perfect-match cancer mutant and its single-base mismatch (wild-type) DNA target. Furthermore, it can quantitate the rare cancer mutant (KRAS codon 12) in a large excess of coexisting wild-type DNAs down to 0.75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications.

Electrochemical detection of the amino-substituted naphthalene compounds based on intercalative interaction with hairpin DNA by electrochemical impedance spectroscopy

The amino-substituted naphthalene compounds, such as 1,8-diaminonaphthalene (1,8-DANAP), 2,3-diaminonaphthalene (2,3-DANAP), 1,5-diaminonaphthalene (1,5-DANAP), 1-naphthylamine (1-NAP) and 2-naphthylamine (2-NAP), were investigated by electrochemical impedance spectroscopy (EIS), which was based on the interaction with hairpin DNA immobilized on the gold electrodes. Upon hairpin DNA interacting with the target chemicals, the charge transfer resistance (RCT) of the hairpin DNA films was significantly decreased and the charge transfer resistance change (ΔR(CT)) decreased in a sequence of ΔR(CT) (1,8-DANAP)>ΔR(CT) (2,3-DANAP)>ΔR(CT) (1,5-DANAP)>ΔR(CT) (1-NAP)>ΔR(CT) (2-NAP). The ΔR(CT) changes were due to the difference in the binding constant (K(SV)) of the target chemicals to DNA. In addition, the interaction mechanism was further explored using 1,8-DANAP as a model analyte by fluorescence spectra, Raman spectroscopy, differential pulse voltammetry (DPV) and EIS, correspondingly. The results demonstrated that the amino-substituted naphthalene compounds intercalated into "stem" appearing in the hairpin DNA. Moreover, the hairpin DNA sensor exhibited high sensitivity to the amino-substituted naphthalene compounds with the detection limit of nano-mole, and maintained high selectivity over other selected environmental pollutants. Finally, the DNA sensor was challenged in natural water sample with a recovery of 96-102%, which offered a platform for prospective future development of a simple, rapid, sensitive and low-cost assay for the detection of target aromatic amine pollutants.

Highly sensitive detection of α-naphthol based on G-DNA modified gold electrode by electrochemical impedance spectroscopy

A highly sensitive, reusable G-rich DNA sensor was reported for the detection of α-naphthol by electrochemical impedance spectroscopy (EIS). Specifically, a single-stranded G-rich DNA was self-assembled on the electrode and transformed into K(+)-stabilized G-quadruplex, which could catalyze H2O2-mediated oxidation of α-naphthol (with hemin as a cofactor) to 1, 4-naphthoquinone precipitated on the DNA films. Due to the insolubility of 1, 4-naphthoquinone, the charge transfer resistance (RCT) was increased to maximum within 15 min. Depending on the difference in charge transfer resistance change (ΔRCT), the α-naphthol could be detected with the detection limit of 0.1 nM in Tris-ClO4 buffer solution (20mM, pH=7.4). Moreover, the sensor demonstrated a high selectivity over other selected phenolic compounds. The performance of the sensor in the real lake water was also explored with the detection limit of 0.8 nM. Finally, the regeneration of the sensor was investigated, which allowed for reuse more than 4 cycles with a mean recovery of 94% of the original signal.

Electroanalysis of single-nucleotide polymorphism by hairpin DNA architectures

Genetic analysis of infectious and genetic diseases and cancer diagnostics require the development of efficient tools for fast and reliable analysis of single-nucleotide polymorphism (SNP) in targeted DNA and RNA sequences often responsible for signalling disease onset. Here, we highlight the main trends in the development of electrochemical genosensors for sensitive and selective detection of SNP that are based on hairpin DNA architectures exhibiting better SNP recognition properties compared with linear DNA probes. SNP detection by electrochemical hairpin DNA beacons is discussed, and comparative analysis of the existing SNP sensing strategies based on enzymatic and nanoparticle signal amplification schemes is presented.

Electrochemical detection of peanut allergen Ara h 1 using a sensitive DNA biosensor based on stem-loop probe

A novel electrochemical DNA sensor was developed by using a stem-loop probe for peanut allergen Ara h 1 detection. The probe was modified with a thiol at its 5' end and a biotin at its 3' end. The biotin-tagged "molecular beacon"-like probe was attached to the surface of a gold electrode to form a stem-loop structure by self-assembly through facile gold-thiol affinity. 6-Mercaptohexanol (MCH) was used to cover the remnant bare region. The stem--loop probe was "closed" when the target was absent, and then the hybridization of the target induced the conformational change to "open", along with the biotin at its 3' end moved away from the electrode surface. The probe conformational change process was verified by circular dichroism (CD); meanwhile, electron-transfer efficiency changes between probe and electrode were proved by electrochemical impedance spectroscopy (EIS). The detection limit of this method was 0.35 fM with the linear response ranging from 10(-15) to 10(-10) M. Moreover, a complementary target could be discriminated from one-base mismatch and noncomplementarity. The proposed strategy has been successfully applied to detect Ara h 1 in the peanut DNA extracts of peanut milk beverage, and the concentration of it was 3.2 × 10(-13) mol/L.

Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor

The application of a nanoporous gold electrode (NPGE) in the fabrication of an electrochemical sensing system for the detection of single base mismatches (SBMs) using ferrocene-modified DNA probe has been investigated in the present manuscript. Ferrocene carboxylic acid is covalently attached to the amino-modified probe using EDC/NHS chemistry. By covalent attachment of the redox reporter molecules on the top of DNA, the direct oxidation of the ferrocene on the electrode surface is avoided. On the other hand, the electrochemical signals are amplified by anodizing the electrode surface and converting it to nanoporous form. By improving the sensitivity of the biosensor, the different SBMs including the thermodynamically stable G-A and G-T mismatches, can be easily distinguished. In this research, NPGE was prepared by anodization and chemical reduction of Au surface and used for signal amplification. Nanoporous electrode enhances the sensitivity of DNA biosensor and makes it capable to detect complementary target DNA in sub-nanomole scales.

DNA-wrapped carbon nanotubes as sensitive electrochemical labels in controlled-assembly-mediated signal transduction for the detection of sequence-specific DNA

A novel electrochemical strategy that uses DNA-wrapped carbon nanotubes (CNTs) as electrochemical labels is developed for sensitive and selective detection of sequence-specific DNA. The presence of target DNA mediates the formation of a sandwiched complex between the DNA-wrapped CNT and a hairpin DNA capture probe immobilized on magnetic beads. This allows target-selective collection of the CNT labels by magnetic separation and transfer on the electrode surface modified with an insulating self-assembled monolayer (SAM). After treatment with N,N-dimethylformamide, the collected sandwiched complex releases the bare CNTs and facilitates the removal of magnetic beads from the electrode surface. The bare CNTs can then assemble on the SAM-modified electrode surface and mediate efficient electron transfer between the electrode and the electroactive species in the solution with a strong current signal generated. The results indicate that the developed strategy shows a sensitive response to target DNA with a desirable signal gain and a low detection limit of 0.9 pM. This strategy is also demonstrated to provide excellent differentiation of single-base mismatch in target DNA. It is expected that this electrochemical strategy may hold great potential as a novel platform for clinical diagnostics and genetic analysis.

Plasmonic-based electrochemical impedance spectroscopy: application to molecular binding

Plasmonic-based electrochemical impedance spectroscopy (P-EIS) is developed to investigate molecular binding on surfaces. Its basic principle relies on the sensitive dependence of surface plasmon resonance (SPR) signal on surface charge density, which is modulated by applying an ac potential to a SPR chip surface. The ac component of the SPR response gives the electrochemical impedance, and the dc component provides the conventional SPR detection. The plasmonic-based impedance measured over a range of frequency is in quantitative agreement with the conventional electrochemical impedance. Compared to the conventional SPR detection, P-EIS is sensitive to molecular binding taking place on the chip surface and less sensitive to bulk refractive index changes or nonspecific binding. Moreover, this new approach allows for simultaneous SPR and surface impedance analysis of molecular binding processes.

Impedimetric immunosensor doped with reduced graphene sheets fabricated by controllable electrodeposition for the non-labelled detection of bacteria

A facile, sensitive and reliable impedimetric immunosensor doped with reduced graphene sheets (RGSs) and combined with a controllable electrodeposition technique was developed for the selective detection of marine pathogenic sulphate-reducing bacteria (SRB). The morphology of RGSs and the electrochemical properties of RGSs-doped chitosan (CS) nanocomposite film were investigated by atomic force microscopy, Fourier transform infrared spectroscopy, and cyclic voltammetry (CV). Electrochemical impedance spectroscopy and CV were used to verify the stepwise assembly of the sensor system. Faradic impedance spectroscopy for charge transfer for the redox probe Fe(CN)(6)(3-/4-) was done to determine SRB concentrations. The diameter of the Nyquist diagram that is equal to the charge-transfer resistance (R(ct)) increased with increasing SRB concentration. A linear relationship between R(ct) and SRB concentration was obtained in the SRB concentration range of 1.8×10(1) to 1.8×10(7) cfu/ml. The impedimetric biosensor gave a distinct response to SRB, but had no obvious response to Vibrio angillarum. It showed a high selectivity for the detection of the pathogen. Based on a combination of the biocompatibility of CS and good electrical conductivity of RGSs, a nanocomposite film with novel architecture was used to immobilize biological and chemical targets and to develop a new type of biosensor.

Electrochemical impedance study of the interaction of metal ions with unlabeled PNA

The interactions of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with thin films of peptide nucleic acids (PNAs) were studied by electrochemical impedance spectroscopy (EIS), and the results show that Zn(2+), Ni(2+) and Co(2+) interacted favorably with the PNA film involving the backbone and the nucleobases with the exception of Mg(2+) for which the interaction with the backbone appears to be dominant.