Indicator-based and indicator-free magnetic assays connected with disposable electrochemical nucleic acid sensor system

An indicator-based and indicator-free magnetic assays connected with a disposable pencil graphite electrode (PGE) were successfully developed, and also compared for the electrochemical detection of DNA hybridization. The oxidation signals of echinomycin (ECHI) and electroactive DNA bases, guanine and adenine, respectively were monitored in the presence of DNA hybridization by using differential pulse voltammetry (DPV) technique. The biotinylated probe was immobilized onto the magnetic beads (magnetic particles, microspheres) and hybridization with its complementary target at the surface of particles within the medium was exhibited successfully using electrochemical sensor system. For the selectivity studies, the results represent that both indicator-based and indicator-free magnetic assays provide a better discrimination for DNA hybridization compared to duplex with one-base or more mismatches. The detection limits (S/N = 3) of the magnetic assays based on indicator or indicator-free were found in nM concentration level of target using disposable sensor technology with good reproducibility. The characterization and advantages of both proposed magnetic assays connected with a disposable electrochemical sensor are also discussed and compared with those methods previously reported in the literature.     

A label-free electrochemical DNA biosensor based on a Zr(IV)-coordinated DNA duplex immobilised on a carbon nanofibre|chitosan layer

A label-free electrochemical biosensor for detecting DNA hybridisation was developed by monitoring the change in the voltammetric activity of ferrocenecarboxylic acid at the biosensor–solution interface. The biosensor was constructed by initially immobilising on a glassy carbon electrode an anchoring layer consisting of chitosan, carboxyl group functionalised carbon nanofibres and glutaraldehye. Chitosan acted as an adhering agent and carbon nanofibres were strategically used to provide a large surface area with binding points for DNA immobilisation, while glutaraldehye was a linker for DNA probes on the electrode surface. Based on a two-factorial design, cyclic voltammetry of [Fe(CN)₆]^3−/4− was performed to optimise the composition of the anchoring layer. Next, a 17-base pair DNA probe was attached to the anchoring layer, followed by its complementary target. Zr(IV) ion, known to exhibit affinity for oxygen-containing electroactive markers, for example, ferrocenecarboxylic acid, was then coordinated in the DNA duplex. In this way, ferrocenecarboxylic acid was attracted towards the biosensor for oxidation. A change in the voltammetric oxidation current of ferrocenecarboxylic acid pre- and post-hybridisation was used to provide an indication of hybridisation. A linear dynamic range between 0.5 and 40 nM and a detection limit of 88 pM of DNA target were then achieved. In addition, the biosensor exhibited good selectivity, repeatability and stability for the determination of DNA sequences.     

Detection of short oligonucleotide sequences of hepatitis B virus using electrochemical DNA hybridisation biosensor

A novel, sensitive and selective electrochemical hybridisation biosensor was developed for the detection of the hepatitis B virus (HBV) using a manganese(II) complex as electrochemical indicator and a DNA probe-modified carbon paste electrode as the biosensor (DNA/CPE). The results showed that this complex could be accumulated electrochemically the immobilised dsDNA layer rather than in the single-stranded DNA (ssDNA) layer. On the basis of this, the manganese complex was used as an electrochemical hybridisation indicator for the detection of oligonucleotides related to HBV. The hybridisation event was evaluated on the basis of the difference between the reduction signals of the manganese(II) complex with the probe DNA prior to and post hybridisation with a target sequence using a differential pulse mode. Several factors affecting the immobilisation and hybridisation of oligonucleotides as well as the indicator’s accumulation were investigated. Experiments with a non-complementary and mismatch sequences demonstrated the good selectivity of the biosensor. Using this approach, the HBV target oligonucleotide’s sequence could be quantified over arange from 0.22 ng L^?1 to 5.40 ng L^?1, with a linear correlation coefficient of 0.9994 and the limit of detection of 0.07 ng L^?1.     

QCM DNA biosensor for the diagnosis of a fish pathogenic virus VHSV

Viral haemorrhagic septicaemia (VHS) is one of the most serious viral diseases damaging both fresh and marine fish species. VHS caused by VHSV and diagnosis of VHSV has been dependent on the conventional methods, such as cell culture and RT-PCR, which takes a few days or several hours. This study demonstrates a rapid and sensitive QCM biosensor for diagnosis of VHSV infection in fish. The QCM biosensor was developed to detect a main viral RNA encoding G protein in VHSV using the specific DNA probe. To maximize the sensitivity of the biosensor, we prepared three different DNA probes which modified 3′ end of DNA by thiol, amine, or biotin and compared three different immobilisation methods on quartz surface coated with gold: immobilisation of thiol labelled probe DNA on naked gold surface, immobilisation of amino labelled probe DNA on gold surface prepared as carboxyl chip using MPA followed by EDC/NHS activation, and immobilisation of biotin labelled probe DNA on gold surface after immobilising avidin on carboxyl chip prior to biotin. As a result, immobilisation method using avidin-biotin interaction was most efficient to immobilise probe DNA and to detect target DNA. The QCM biosensor system using biotinylated probe DNA was stable enough to withstand 32 times of repeated regenerations and the detection limit was 0.0016 μM. Diagnosis using the QCM biosensor system was more sensitive and much faster than a conventional RT-PCR analysis in detecting the viral RNA.     

Electrochemical DNA biosensor for human papillomavirus 16 detection in real samples

An electrochemical DNA biosensor for human papillomavirus (HPV) 16 detection has been developed. For this proposed biosensor, l-cysteine was first electrodeposited on the gold electrode surface to form l-cysteine film (CYSFILM). Subsequently, HPV16-specific probe was immobilized on the electrode surface with CYSFILM. Electrochemistry measurement was studied by differential pulse voltammetry method (DPV). The measurement was based on the reduction signals of methylene blue (MB) before and after hybridization either between probe and synthetic target or extracted DNA from clinical samples. The effect of probe concentration was analyzed and the best results were seen at 1000 nM. The hybridization detection presented high sensitivity and broad linear response to the synthetic-target concentration comprised between 18.75 nM and 250 nM as well as to a detection limit of 18.13 nM. The performance of this biosensor was also investigated by checking probe-modified electrode hybridization with extracted DNA from samples. The results showed that the biosensor was successfully developed and exhibited high sensitivity and satisfactory selectivity to HPV16. These results allow for the possibility of developing a new portable detection system for HPVs and for providing help in making an effective diagnosis in the early stages of infection.     

DNA electrochemical biosensors

Disposable electrochemical DNA-based biosensors are reviewed; they have been used for the determination of low-molecular weight compounds with affinity for nucleic acids and for the detection of the hybridisation reaction. The first application is related to the molecular interaction between surface-linked DNA and the target pollutants or drugs, in order to develop a simple device for rapid screening of toxic or similar compounds. The determination of such compounds was measured by their effect on the oxidation signal of the guanine peak of calf thymus DNA immobilised on the electrode surface and investigated by chronopotentiometric analysis. The DNA biosensor is able to detect known intercalating compounds, such as daunomycin, polychlorinated biphenyls (PCBs), aflatoxin B1, and aromatic amines. Applicability to river and waste water samples is also demonstrated. Disposable electrochemical sensors for the detection of a specific sequence of DNA were realised by immobilising synthetic single-stranded oligonucleotides onto a graphite screen-printed electrode. The probes became hybridised with different concentrations of complementary sequences present in the sample. The hybrids formed on the electrode surface were evaluated by chronopotentiometric analysis using daunomycin as indicator of the hybridisation reaction. The hybridisation was also performed using real samples. Application to apolipoprotein E (ApoE) is described, in this case samples have to be amplified by PCR and then analysed by DNA biosensor. The extension of such procedures to samples of environmental interest or to contamination of food is discussed.     

Fe2O3@Au core/shell nanoparticle-based electrochemical DNA biosensor for Escherichia coli detection

A Fe₂O₃@Au core/shell nanoparticle-based electrochemical DNA biosensor was developed for the amperometric detection of Escherichia coli (E. coli). Magnetic Fe₂O₃@Au nanoparticles were prepared by reducing HAuCl₄ on the surfaces of Fe₂O₃ nanoparticles. This DNA biosensor is based on a sandwich detection strategy, which involves capture probe immobilized on magnetic nanoparticles (MNPs), target and reporter probe labeled with horseradish peroxidase (HRP). Once magnetic field was added, these sandwich complexes were magnetically separated and HRP confined at the surfaces of MNPs could catalyze the enzyme substrate and generate electrochemical signals. The biosensor could detect the concentrations upper than 0.01 pM DNA target and upper than 500 cfu/mL of E. coli without any nucleic acid amplification steps. The detection limit could be lowered to 5 cfu/mL of E. coli after 4.0 h of incubation.     

Synergistic effects of nano-ZnO/multi-walled carbon nanotubes/chitosan nanocomposite membrane for the sensitive detection of sequence-specific of PAT gene and PCR amplification of NOS gene

The remarkable synergistic effects of the zinc oxide (ZnO) nanoparticles and multi-walled carbon nanotubes (MWNTs) were developed for the ssDNA probe immobilization and fabrication of the electrochemical DNA biosensor. The ZnO/MWNTs/chitosan nanocomposite membrane-modified glassy carbon electrode (ZnO/MWNTs/CHIT/GCE) was fabricated and the ssDNA probes were immobilized on the modified electrode surface. The preparation method is quite simple and inexpensive. The hybridization events were monitored by differential pulse voltammetry (DPV) using methylene blue (MB) as an indicator. As compared with previous MWNTs-based DNA biosensors, this composite matrix combined the attractive biocompatibility of ZnO nanoparticles with the excellent electron-transfer ability of MWNTs and fine membrane-forming ability of CHIT increased the DNA attachment quantity and complementary DNA detection sensitivity. The approach described here can effectively discriminate complementary DNA sequence, noncomplementary sequence, single-base mismatched sequence and double-base mismatched sequence related to phosphinothricin acetyltransferase (PAT) gene in transgenic corn. Under optimal conditions, the dynamic detection range of the sensor to PAT gene complementary target sequence was from 1.0 × 10⁻¹¹ to 1.0 × 10⁻⁶ mol/L with the detection limit of 2.8 × 10⁻¹² mol/L. The polymerase chain reaction (PCR) amplification of nopaline synthase (NOS) gene from the real sample of one kind of transgenic soybeans was also satisfactorily detected with this electrochemical DNA biosensor, suggesting that the ZnO/MWNTs/CHIT nanocomposite hold great promises for sensitive electrochemical biosensor applications.     

Electrochemical DNA biosensor for the detection of TT and Hepatitis B virus from PCR amplified real samples by using methylene blue

DNA biosensors based on nucleic acid hybridization processes are rapidly being developed towards the goal of rapid and inexpensive diagnosis of genetic and infectious diseases. Electrochemical transducers are often being used for detecting the DNA hybridization event, due to their high sensitivity, small dimensions, low cost, and compatibility with microfabrication technology. In this study, an electrochemical biosensor for the voltammetric detection of DNA sequences related to the Hepatitis B virus (HBV) and TT virus (TTV) from polymerase chain reaction (PCR) amplified real samples is described for the first time. The biosensor relies on the immobilization of the 21- or 24-mer single stranded oligonucleotides (probe) related to the HBV and TTV sequences and hybridization of these oligonucleotides with their complementary sequences (target) at carbon paste electrode (CPE). The extent of hybridization between the probe and target sequences was determined by using square wave voltammetry (SWV) with moving average baseline correction and methylene blue (MB) as the hybridization indicator. As a result of the interaction between MB and the bound guanine bases of hybrid at CPE surface, the MB signal decreased, when it was compared with the MB signal, which was observed with probe modified CPE. The difference between the MB signals, obtained from the hybrid modified and the probe modified CPE is used to detect the DNA sequences of the infectious diseases from PCR amplified real samples. Numerous factors affecting the target hybridization and indicator binding reactions are optimized to maximize the sensitivity.     

Nano‐Gold Modified Genosensor for Direct Detection of DNA Hybridization

In this paper, nano‐gold modified carbon paste electrode (NGMCPE) was employed to develop an electrochemical DNA hybridization biosensor. The proposed sensor was made up by immobilization of 15‐mer single stranded oligonucleotide probe for detection of target DNA. Hybridization detection relies on the alternation in guanine oxidation signal following hybridization of the probe with complementary genomic DNA. The guanine oxidation was monitored using differential pulse voltammetry (DPV). Different factors such as activation potential, activation time and probe immobilization conditions were optimized. The selectivity of the sensor was investigated by non‐complementary oligonucleotides. Diagnostic performance of the biosensor was described and the detection limit was found 1.9 × 10^?13 M at the NGMCPE surface. All of the investigations were performed in both CPE and NGMCPE and finally their results were compared.     

Electrochemical genosensor array for the simultaneous detection of multiple high-risk human papillomavirus sequences in clinical samples

An electrochemical genosensor array for the simultaneous detection of three high-risk human papillomavirus (HPV) DNA sequences, HPV16, 18 and 45, exhibiting high sensitivity and selectivity is presented. The electrodes of a 4 × 4 array were modified via co-immobilization of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated bipodal thiol. Detection of synthetic and PCR products was carried out in a sandwich type format, with the target hybridized between a surface immobilized probe and a horseradish peroxidase-labelled secondary reporter probe. The detection limits obtained in the detection of each individual target were in the pM range, allowing the application of this sensor for the detection of samples obtained from PCR amplification of cervical scrape samples. The results obtained exhibited an excellent correlation with the HPV genotyping carried out within a hospital laboratory. Multiplexing and cross-reactivity studies demonstrated high selectivity over potential interfering sequences, facilitating application of the developed platform for the high-throughput screening of multiple high-risk DNA sequences.     

Label-free and sequence-specific DNA detection down to a picomolar level with carbon nanotubes as support for probe DNA

This study describes a simple and label-free electrochemical impedance spectroscopic (EIS) method for sequence-specific detection of DNA by using single-walled carbon nanotubes (SWNTs) as the support for probe DNA. SWNTs are confined onto gold electrodes with mixed self-assembly monolayers of thioethanol and cysteamine. Single-stranded DNA (ssDNA) probe is anchored onto the SWNT support through covalent binding between carboxyl groups at the nanotubes and amino groups at 5′ ends of ssDNA. Hybridization of target DNA with the anchored probe DNA greatly increases the interfacial electron-transfer resistance (R_et) at the double-stranded DNA (dsDNA)-modified electrodes for the redox couple of Fe(CN)₆^3−/4−, which could be used for label-free and sequence-specific DNA detection. EIS results demonstrate that the utilization of SWNTs as the support for probe DNA substantially increases the surface loading of probe DNA onto electrode surface and thus remarkably lowers the detection limit for target DNA. Under the conditions employed here, R_et is linear with the concentration of target DNA within a concentration range from 1 to 10 pM with a detection limit down to 0.8 pM (S/N = 3). This study may offer a novel and label-free electrochemical approach to sensitive sequence-specific DNA detection.     

Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification

Using a cascade signal amplification strategy, an ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon (MB) mediated circular strand displacement polymerization (CSDP) and hyperbranched rolling circle amplification (HRCA) was proposed. The hybridization of MB probe to target DNA resulted in a conformational change of the MB and triggered the CSDP in the presence of bio-primer and Klenow fragment (KF exo⁻), leading to multiple biotin-tagged DNA duplex. Furthermore, the HRCA was implemented to product amounts of double-stranded DNA (ds-DNA) fragments using phi29 DNA polymerase via biotin-streptavidin interaction. After the product of HRCA binded numerous biotinylated detection probes, an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor exhibited excellent detection sensitivity and specificity with a log-linear response to target DNA from 0.01 fM to 10 pM as low as 8.9 aM. The proposed method allowed DNA detection with simplicity, rapidness, low cost and high specificity, which might have the potential for application in clinical molecular diagnostics and environmental monitoring.     

An electrochemical aptasensor for thrombin detection based on the recycling of exonuclease III and double-stranded DNA-templated copper nanoparticles assisted signal amplification

In this paper, we report an improved electrochemical aptasensor based on exonuclease III and double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) assisted signal amplification. In this sensor, duplex DNA from the hybridization of ligated thrombin-binding aptamer (TBA) subunits and probe DNA can act as an effective template for the formation of CuNPs on the electrode surface, so copper ions released from acid-dissolution of CuNPs may catalyze the oxidation of ο-phenylenediamine to produce an amplified electrochemical response. In the presence of thrombin, a short duplex domain with four complementary base pairs can be stabilized by the binding of TBA subunits with thrombin, in which TBA subunit 2 can be partially digested from 3′ terminal with the cycle of exonuclease III, so the ligation of TBA subunits and the subsequent formation of CuNPs can be inhibited. By electrochemical characterization of dsDNA-templated CuNPs on the electrode surface, our aptasensor can display excellent performances for the detection of thrombin in a broad linear range from 100 fM to 1 nM with a low detection limit of 20.3 fM, which can also specially distinguish thrombin in both PBS and serum samples. Therefore, our aptasensor might have great potential for clinical diagnosis of biomarkers in the future.     

Electrochemical impedance probing of DNA hybridisation on oligonucleotide-functionalised polypyrrole

We report a new approach for detecting DNA hybridisation using non faradaic electrochemical impedance spectroscopy. The technique was applied to a system of DNA probes bearing amine groups that are immobilized by covalent grafting on a supporting polypyrrole matrix functionalised with activated ester groups.The kinetics of the attachment of the ss-DNA probe was monitored using the temporal evolution of the open circuit potential (OCP). This measurement allows the determination of the time necessary for the chemical reaction of ss-DNA probe into the polypyrrole backbone.The hybridisation reactions with the DNA complementary target and non complementary target were investigated by non faradaic electrochemical impedance spectroscopy. Results show a significant modification in the Nyquist plot upon addition of the complementary target whereas, in presence of the non complementary target, the Nyquist plot is not modified. The spectra, in the form of Nyquist plot, were analysed with the Randles circuit. The transfer charge resistance R₂ shows a linear variation versus the complementary target concentration. Sensitivity and detection limit (0.2 nM) were determined and detection limit was lower of one order of magnitude than that obtained with the same system and measuring variation of the oxidation current at constant potential.     

A DNA biosensor based on the electrocatalytic oxidation of amine by a threading intercalator

An electrochemical biosensor for the detection of DNA based a peptide nucleic acid (PNA) capture probe (CP) modified indium tin oxide electrode (ITO) is described in this report. After hybridization, a threading intercalator, N,N′-bis[(3-propyl)-imidazole]-1,4,5,8-naphthalene diimide (PIND) imidazole complexed with Ru(bpy)₂Cl (PIND-Ru, bpy = 2,2′-bipyridine), was introduced to the biosensor. PIND-Ru selectively intercalated to double-stranded DNA (ds-DNA) and became immobilized on the biosensor surface. Voltammetric tests showed highly stable and reversible electrochemical oxidation/reduction processes and the peak currents can directly be utilized for DNA quantification. When the tests were conducted in an amine-containing medium, Tris-HCl buffer for example, a remarkable improvement in the voltammetric response and noticeable enhancements of voltammetric and amperometric sensitivities were observed due to the electrocatalytic activity of the [Ru(bpy)₂Cl] redox moieties. Electrocatalytic current was observed when as little as 3.0 attomoles of DNA was present in the sample solution.     

Surface plasmon resonance biosensor for genetically modified organisms detection

The development of a surface plasmon resonance (SPR) affinity biosensor based on DNA hybridisation is described. This biosensor has been applied to genetically modified organisms (GMOs) detection. Single stranded DNA (ssDNA) probes were immobilised on the sensor chip of an SPR device and the hybridisation between the immobilised probe and the complementary sequence (target) was monitored. The probe sequences were internal to the sequence of 35S promoter and NOS terminator which are inserted sequences in the genome of GMO regulating the transgene expression. The system has been optimised using synthetic oligonucleotides, then applied to real samples analysis. Samples, containing the transgenic target sequences, were amplified by polymerase chain reaction (PCR) and then detected with the SPR biosensor.     

A nano-porous CeO(2)/Chitosan composite film as the immobilization matrix for colorectal cancer DNA sequence-selective electrochemical biosensor

CeO₂/Chitosan (CHIT) composite matrix was firstly developed for the single-stranded DNA (ssDNA) probe immobilization and the fabrication of DNA biosensor related to the colorectal cancer gene. Such matrix combined the advantages of CeO₂ and chitosan, with good biocompatibility, nontoxicity and excellent electronic conductivity, showing the enhanced loading of ssDNA probe on the surface of electrode. The preparation method is quite simple and inexpensive. The hybridization detection was accomplished by using methylene blue (MB), an electroactive lable, as the indicator. The differential pulse voltammetry (DPV) was employed to record the signal response of MB and determine the amount of colorectal cancer target DNA sequence. The experimental conditions were optimized. The established biosensor has high detection sensitivity, a relatively wide linear range from 1.59 × 10⁻¹¹ to 1.16 × 10⁻⁷ mol L⁻¹ and the ability to discriminate completely complementary target sequence and four-base-mismatched sequence.     

A sensitive DNA electrochemical biosensor based on magnetite with a glassy carbon electrode modified by muti-walled carbon nanotubes in polypyrrole

A novel sensitive electrochemical biosensor based on magnetite nanoparticle for monitoring DNA hybridization by using MWNT-COOH/ppy-modified glassy carbon electrode is described. In this new detection system, mercapatoacetic acid (RSH)-coated magnetite nanoparticles, capped with 5′-(NH₂) oligonucleotide, is used as DNA probe to complex 29-base polynucleotide target (a piece of human porphobilinogen deaminase PBGD promoter from 170 to 142). Target sequence hybridized with the probe results in the decrease of the reduction peak current of daunomycin connected with probe. The response of non-complementary sequence was almost the same as the blank, and the response of three-base mismatched sequence within 29-base polynucleotide was obviously distinguished from complementary sequence, which can easily identify point mutation of DNA. The equation of calibration plot is i_p (μA) = 0.8255 − 0.0847c_{target oligonucleotide} × 10¹³ in the range of 6.9 × 10⁻¹⁴ to 8.6 × 10⁻¹³ mol/L, and correlation coefficient is 0.9974. The detective limit is 2.3 × 10⁻¹⁴ mol/L of target oligonucleotide. This device can be optimized for the detection of complex sequence.     

Enzyme inhibition-based biosensor for the electrochemical detection of microcystins in natural blooms of cyanobacteria

An electrochemical biosensor for the detection of microcystin has been developed based on the inhibition of the protein phosphatase 2A (PP2A) by this cyanobacterial toxin. The enzyme has been immobilised by entrapment using a poly(vinyl alcohol) azide-unit pendant water-soluble photopolymer (PVA-AWP). Electrode supports and immobilisation conditions have been optimised by colorimetric assays, the highest immobilisation yields being obtained with screen-printed graphite electrodes and the 1:2 PP2A:PVA ratio. Catechyl monophosphate (CMP), α-naphthyl phosphate (α-NP) and 4-methylumbelliferyl phosphate (4-MUP) have been used as phosphorylated substrates to monitor the protein phosphatase activity by electrochemical methods, the former providing the highest chronoamperometric currents at appropriate working potentials (+450 mV versus Ag/AgCl). Incubation with standard microcystin solutions has demonstrated the inhibition of the immobilised enzyme, proportional to the toxin concentration. The standard inhibition curve has provided a 50% inhibition coefficient (IC₅₀) of 83 μg L⁻¹, a limit of detection (LOD; 35% inhibition) of 37 μg L⁻¹, and 100% inhibition at about 1000 μg L⁻¹. Real samples of cyanobacterial blooms from the Tarn River (Midi-Pyrénées, France) have been analysed using the developed amperometric biosensor and the toxin contents have been compared to those obtained by a conventional colorimetric protein phosphatase inhibition (PPI) assay and high-performance liquid chromatography (HPLC). The results clearly justify the use of the developed amperometric biosensor as screening method for microcystin detection.