Detection of mismatched caspase-3 DNA oligonucleotides with an SPR biosensor following amplification by Taq polymerase

We demonstrate that base mismatches of caspase-3 DNA sequences can be detected by surface plasmon resonance (SPR) following signal amplification by polymerase from Thermus aquaticus (Taq). The concentration of magnesium ions and the respective dNTPs for polymerase binding to the oligonucleotides on the sensing surface were optimized. Taq polymerase binds to double-stranded DNA that is self-assembled on the gold surface of the biosensor to induce an SPR signal. Experiments are presented on the effect of Mg(II) and dNTP concentrations on the activity of the polymerase on the sensing surface. The detection limits are 50 pM, 0.1 nM, 0.7 nM, 7 nM, and 20 nM for correctly matched, single-base mismatched, two-base mismatched, three-base mismatched and four-base mismatched DNA of caspase-3, respectively. This is attributed to the optimized experimental conditions, with samples containing 2 μM of Mg(II) and 0.3 mM of dNTP.

Aptamer-based molecular recognition for biosensor development

Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.

Direct surface plasmon resonance immunosensing of pyraclostrobin residues in untreated fruit juices

A surface plasmon resonance (SPR) immunoassay for on-line detection of the strobilurin fungicide pyraclostrobin in untreated fruit juices is presented. The analysis of pyraclostrobin residues is accomplished in apple, grape, and cranberry samples by monitoring the recognition events occurring separately in a two-channel home-made SPR biosensor. Covalent coupling of the analyte derivative results in a reversible method, enabling more than 80 measurements on the same sensor surface. Optimization of the immunoassay conditions provides limits of detection as low as 0.16?μg?L^?1. The selectivity and reproducibility of the analysis is ensured by studying both non-specific interactions with unrelated compounds and inter-assay coefficients of variation. Excellent recovery ranging from 98 to 103?% was achieved by a simple 1:5 dilution of fruit juice with assay buffer before the analysis. The lack of previous cleaning and homogenization procedures reduces the analysis time of a single food sample to only 25?min, including the regeneration cycle.

Biosensor for bisphenol A leaching from baby bottles using a glassy carbon electrode modified with DNA and single walled carbon nanotubes

We have developed a biosensor for highly sensitive and selective determination of the endocrinic disruptor bisphenol A (BPA). It is based on glassy carbon electrode modified with calf thymus DNA and a composited prepared from single walled carbon nanotubes (SWNT) and Nafion. The interaction between BPA and DNA was studied by voltammetry. The binding constant was determined to be 3.55?×?10³ M^?1, and the binding site has a length of 4.3 base pairs. These electrochemical studies provide further information for a better understanding of the toxicity and carcinogenicity of BPA. Under optimal conditions, the biosensor displays a linear electrochemical response to BPA in the 10 nM to 20 μM concentration range, with a detection limit as low as 5.0 nM (at an S/N of 3). The method was successfully applied to the quantification of BPA in leachates from plastic baby bottles. Recoveries range from 94.0 % to 106.0 % which underpins the excellent performance of this SWNT-based DNA sensor.

Electrochemical genosensor for detection of human mammaglobin in polymerase chain reaction amplification products of breast cancer patients

Human mammaglobin (MG) has been found to be the most specific molecular marker for the hematogenous spread of breast cancer cells. In our study, an electrochemical impedance spectroscopic DNA biosensor was established for the detection of MG in breast cancer patients. The working conditions for the biosensor, such as immobilization time, rinse process, and hybridization process, were optimized. Under the optimal conditions, the charge transfer resistance of the proposed DNA biosensor shows excellent correlation with the amount of the complementary oligonucleotides in the range from 1.0?×?10^?9 to 2.0?×?10^?8?M. The detection limit is 5.0?×?10^?10?M. The proposed biosensor was used to detect the polymerase chain reaction amplification products of actual clinical breast cancer samples. The results were compared with that obtained by conventional gel electrophoresis. The results indicate that the electrochemical impedance spectroscopic assay is significantly sensitive and time-saving. The simple strategy described here is expected to be used in clinical application for early diagnosis of breast cancer.

Selection and identification of ssDNA aptamers recognizing zearalenone

Zearalenone (ZEN) is a nonsteroidal estrogenic mycotoxin produced by Fusarium graminearum on maize and barley. Because most current methods of ZEN detection rely on the use of low-stability antibodies or expensive equipment, we sought to develop a rapid, low-cost determination method using aptamers instead of antibodies as the specific recognition ligands. This work describes the isolation and identification of single-stranded DNA (ssDNA) aptamers recognizing ZEN using the modified systematic evolution of ligands by exponential enrichment methodology based on magnetic beads. After 14 rounds of repeated selection, a highly enriched ssDNA library was sequenced and 12 representative sequences were assayed for their affinity and specificity. The best aptamer, 8Z₃₁, with a dissociation constant (K _d) of 41?±?5 nM, was successfully applied in the specific detection of ZEN in binding buffer and in real samples based on a magnetic separation/preconcentration procedure. This analytical method provided a linear range from 3.14?×?10^?9 to 3.14?×?10^?5 M for ZEN, and the detection limit was 7.85?×?10^?10 M. The selected aptamers are expected to be used in the potential development of affinity columns, biosensors, or other analytical systems for the determination of ZEN in food and agricultural products.

Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

We report on a highly sensitive chemiluminescent (CL) biosensor for the sequenc-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H₂O₂ and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L^-1 of target DNA.

Ultra-sensitive electrochemical DNA biosensor based on signal amplification using gold nanoparticles modified with molybdenum disulfide,graphene and horseradish peroxidase

We have developed an ultra-sensitive electrochemical DNA biosensor by assembling probe ssDNA on a glassy carbon electrode modified with a composite made from molybdenum disulfide, graphene, chitosan and gold nanoparticles. A thiol-tagged DNA strand coupled to horseradish peroxidase conjugated to AuNP served as a tracer. The nanocomposite on the surface acts as relatively good electrical conductor for accelerating the electron transfer, while the enzyme tagged gold nanoparticles provide signal amplification. Hybridization with the target DNA was studied by measuring the electrochemical signal response of horseradish peroxidase using differential pulse voltammetry. The calibration plot is linear in the 5.0?×?10^?14 and 5.0?×?10^?9 M concentration range, and the limit of detection is 2.2?×?10^?15 M. The biosensor displays high selectivity and can differentiate between single-base mismatched and three-base mismatched sequences of DNA. The approach is deemed to provide a sensitive and reliable tool for highly specific detection of DNA.

Streptavidin-enhanced surface plasmon resonance biosensor for highly sensitive and specific detection of microRNA

We are presenting a method for sensitive and specific detection of microRNA (miRNA) using surface plasmon resonance. A thiolated capture DNA probe with a short complete complementary sequence was immobilized on the gold surface of the sensor to recognize the part sequence of target miRNA, and then an oligonucleotide probe linked to streptavidin was employed to bind the another section of the target. The use of the streptavidin-oligonucleotide complex caused a ~5-fold increase in signal, improved the detection sensitivity by a factor of ~24, and lowered the detection limit to 1.7 fmol of miR-122. This specificity allowed a single mismatch in the target miRNA to be discriminated. The whole assay takes 30 min, and the surface of the sensor can be regenerated at least 30 times without loss in performance. The method was successfully applied to the determination of miRNA spiked into human total RNA samples.

Electrochemical detection of in situ DNA damage induced by enzyme-catalyzed Fenton reaction. Part I: in phosphate buffer solution

We report on a biosensor for the electrochemical detection of the damage of DNA and of antioxidant protecting DNA. The biosensor was constructed by co-immobilization of DNA and glucose oxidase (GOx) on a glassy carbon electrode. Under aerobic conditions, GOx catalyzes the oxidation of glucose, and the hydrogen peroxide produced reacts with ferrous ions in a Fenton-type reaction to generate hydroxy radical. This was validated by UV–vis spectroscopy. The hydroxy radical can cause serious oxidative damage to DNA, and this can be detected by square wave voltammetry of the electroactive indicator Co(bpy) ₃ ³⁺ . The effects of pH value, incubation time, and the concentration of glucose and ferrous ion were optimized. The effects of the antioxidants ascorbic acid and aloe emodin on DNA damage were also investigated within the concentration range from 0.05 to 200?μM. This work provides an in-vitro model system to mimic the processes in oxidative DNA damage by a simple electrochemical approach.

Interaction of mercury(II) ions with immobilized apo-metallothioneins studied by scanning electrochemical microscopy combined with surface plasmon resonance

Scanning electrochemical microscopy (SECM) was combined with surface plasmon resonance (SPR) and applied for in-situ monitoring of the incorporation of Hg²⁺ by apo-metallothionein (apo-MT) immobilized on the SPR substrate. Hg²⁺ was anodically stripped from the Hg-coated SECM Pt tip and sequestered by apo-MT upon its diffusion to the SPR substrate. The high sensitivity of the SPR instrument enabled the detection of the change in the composition and structure of apo-MT molecules that was induced by the metal sequestration of Hg²⁺. The SPR response revealed that the saturation co-ordination number of Hg²⁺ binding to apo-MT was 18. Moreover, an unexpected collapse of the structure of MT was observed when the stoichiometric ratio of Hg²⁺/MT was ~70, and the structure cannot be further altered even by adding a large excess of Hg²⁺. This collapse was also confirmed by Raman spectroscopy. The results are potentially useful for a deeper understanding of the detoxification mechanism of MT to mercury ion.

Highly selective DNA biosensor based on the long-range electron transfer of indigo carmine through DNA duplex

We have developed a highly selective DNA biosensor. It was based on the long-range electron transfer (LRET) from the electroactive dye indigo carmine (IC) through the DNA duplex on a glassy carbon electrode. Voltammetric experiments showed that IC interacts with dsDNA through a typical intercalative mode with a relatively strong affinity of 2.3(±0.6)?×?10⁶?M^-1. If incubated with DNA in IC solution, no response was observed with the ssDNA-modified probe electrode. However, a pair of well-defined redox peak was observed with a DNA-hybridized electrode, proving the presence of LRET on the biosensor. The biosensor also can differentiate complementary sequences, non-complementary sequences, and even the mutated sequences with single-base mismatches at different sites.

A hydrogen peroxide biosensor based on direct electron transfer from hemoglobin to an electrode modified with Nafion and activated nanocarbon

A biosensor for hydrogen peroxide (HP) was developed by immobilizing hemoglobin on a glassy carbon electrode modified with activated carbon nanoparticles/Nafion. The characteristics of the sensor were studied by UV?Cvis spectroscopy and electrochemical methods. The immobilized Hb retained its native secondary structure, undergoes direct electron transfer (with a heterogeneous rate constant of 3.37?±?0.5?s^?1), and displays excellent bioelectrocatalytic activity to the reduction of HP. Under the optimal conditions, its amperometric response varies linearly with the concentration of HP in the range from 0.9???M to 17???M. The detection limit is 0.4???M (at S/N?=?3). Due to the commercial availability and low cost of activated carbon nanoparticles, it can be considered as a useful supporting material for construction of other third-generation biosensors.

Reagentless d-sorbitol biosensor based on d-sorbitol dehydrogenase immobilized in a sol–gel carbon nanotubes–poly(methylene green) composite

A reagentless d-sorbitol biosensor based on NAD-dependent d-sorbitol dehydrogenase (DSDH) immobilized in a sol–gel carbon nanotubes–poly(methylene green) composite has been developed. It was prepared by durably immobilizing the NAD⁺ cofactor with DSDH in a sol–gel thin film on the surface of carbon nanotubes functionalized with poly(methylene green). This device enables selective determination of d-sorbitol at 0.2 V with a sensitivity of 8.7?μA?mmol^?1?L?cm^?2 and a detection limit of 0.11 mmol?L^?1. Moreover, this biosensor has excellent operational stability upon continuous use in hydrodynamic conditions.

A lipase-based electrochemical biosensor for target DNA

A lipase-based electrochemical biosensor has been fabricated for the quantitative determination of target DNA. It is based on a stem-loop nucleic acid probe labeled with ferrocene containing a butanoate ester that is hydrolyzed by lipase. The other end of the probe DNA is linked, via carboxy groups, to magnetic nanoparticles. The binding of target DNA transforms the hairpin structure of the probe DNA and causes the exposure of ester bonds. This results in the release of electro-active ferrocene after hydrolysis of the ester bonds, and in an observable electrochemical response. The quantity of target DNA in the concentration range between 1?×?10^?12 mol·L^?1 and 1?×?10^?8 mol·L^?1 can be determined by measuring the electrochemical current. The method can detect target DNA with rapid response (30 min) and low interference.

Screening interaction between ochratoxin A and aptamers by fluorescence anisotropy approach

By taking advantage of the intrinsic fluorescence of ochratoxin A (OTA), we present a fluorescence anisotropy approach for rapid analysis of the interactions between OTA and aptamers. The specific binding of OTA with a 36-mer aptamer can induce increased fluorescence anisotropy (FA) of OTA as the result of the freedom restriction of OTA and the increase of molecular volume, and the maximum FA change is about 0.160. This FA approach enables an easy way to investigate the effects of buffer compositions like metal ions on the affinity binding. FA analysis shows the interaction between OTA and aptamer is greatly enhanced by the simultaneous presence of Ca²⁺ and Na⁺, while the binding affinity of aptamer decreases more than 18-fold when only Ca²⁺ exists, and the binding is completely lost when Ca²⁺ is absent. Crucial region of the aptamer for binding can be mapped through FA analysis and aptamer mutation. The demonstrated FA approach maintains the advantages of FA in simplicity, rapidity, and robustness. This investigation will help the development of aptamer-based assays for OTA detection in optimizing the binding conditions, modification of aptamers, and rational design.

Synthesis of multi-branched gold nanoparticles by reduction of tetrachloroauric acid with Tris base, and their application to SERS and cellular imaging

A biosensor for hydrogen peroxide was constructed by immobilizing horseradish peroxidase on chitosan-wrapped NiFe₂O₄ nanoparticles on a glassy carbon electrode (GCE). The electron mediator carboxyferrocene was also immobilized on the surface of the GCE. UV?Cvis spectra, Fourier transform IR spectra, scanning electron microscopy, and electrochemical impedance spectra were acquired to characterize the biosensor. The experimental conditions were studied and optimized. The biosensor responds linearly to H₂O₂ in the range from 1.0?×?10^?5 to 2.0?×?10^?3?M and with a detection limit of 2.0?×?10^?6?M (at S/N?=?3).

Label-free and ultrasensitive electrochemiluminescence detection of microRNA based on long-range self-assembled DNA nanostructures

Electrochemiluminescence (ECL) integrates the advantages of electrochemical detection and chemiluminescent techniques. The method has received particular attention because it is highly sensitive and selective, has a wide linear range but low reagent costs. The use of nanomaterials with their unique physical and chemical properties has led to new kinds of biosensors that exhibit high sensitivity and stability. Compared to other nanomaterials, DNA nanostructures are more biocompatible, more hydrophilic, and thus less prone to nonspecific adsorption onto the electrode surface. We describe here a label-free and ultrasensitive ECL biosensor for detecting a cancer-associated microRNA at a femtomolar level. We have designed two auxiliary probes that cause the formation of a long-range self-assembly in the form of a μm-long 1-dimensional DNA concatamer. These can be used as carriers for signal amplification. The intercalation of the ECL probe Ru(phen)₃ ²⁺ into the grooves of the concatamers leads to a substantial increase in ECL intensity. This amplified sensor shows high selectivity for discriminating complementary target and other mismatched RNAs. The biosensor enables the quantification of the expression of microRNA-21 in MCF-7 cells. It also displays very low limits of detection and provides an alternative approach for the detection of RNA or DNA detection in diagnostics and gene analysis.

Electrochemical DNA biosensor for the detection of Trichoderma harzianum based on a gold electrode modified with a composite membrane made from an ionic liquid, ZnO nanoparticles and chitosan, and by using acridine orange as a redox indicator

An electrochemical DNA biosensor was developed that is based on a gold electrode modified with a nanocomposite membrane made from an ionic liquid, ZnO nanoparticles and chitosan. A single-stranded DNA probe was immobilized on this electrode. Acridine orange was used as the hybridization probe for monitoring the hybridization of the target DNA. The biosensor was capable of detecting target DNA in the concentration range from 1.0?×?10?C14 to 1.8?×?10?C4?mol?L-1, with a detection limit of 1.0?×?10?C15?mol?L-1. The approach towards constructing a DNA biosensor allows studies on the hybridization even with crude DNA fragments and also to analyze sample obtained from real samples. The results show that the DNA biosensor has the potential for sensitive detection of a specific sequence of the Trichoderma harzianum gene and provides a quick, sensitive and convenient method for the study of microorganisms.

Fluorogenic assays for activated protein C using aptamer modified magnetic beads

We describe a fluorogenic assay for activated protein C (APC) by using magnetic beads modified with DNA aptamers, taking advantage of strong binding affinity of aptamer, facile magnetic separation, and signal amplification via an enzymatic reaction. APC is specifically captured from a sample by the DNA aptamers on magnetic beads, and the concentrated APC then catalyzes the conversion of a fluorogenic substrate of APC to a fluorescent product. Detection of APC is achieved by measuring the generated product. This method is simple, sensitive, and specific. APC can be detected at 0.4 pM concentration level in a sample volume of 250 μL, corresponding to 0.1 femtomole of APC, when 2-h enzymatic reaction is employed. The proteins thrombin, trypsin, proteinase K, chymotrypsin, and elastase do not interfere.