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.     

Impedimetic biosensor for the DNA of the human papilloma virus based on the use of gold nanosheets

The authors describe an impedimetric method for the quantitation of the DNA of the human papilloma virus (HPV) type 16. A glassy carbon electrode (GCE) was modified with gold nanosheets and is shown to be superior to a common gold disk electrode. A single-stranded 25mer oligonucleotide (ssDNA) acting as the probe DNA was immobilized via its thiolated 5′ end on both electrodes. After hybridization with target (analyte) DNA, electrochemical impedance spectra were acquired in the presence of hexacyanoferrate as a redox marker. The sensor can distinguish between complementary, non-complementary and single base pair mismatches of HPV ssDNA. At a 1 mM hexacyanoferrate concentration, the biosensors respond to target DNA in the 1 μM to 1 pM concentration range, and the detection limit is 0.15 pM. The results illustrate that the use of gold nanosheets on a GCE distinctly improves the detection and differentiation of HPV compared to using bare gold.

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Graphical abstract Schematic of exploiting gold nanosheets as a platform for HPV detection. The method works in the 1 μM to 1 pM HPV concentration range and has a 0.15 pM detection limit..

     

Application of graphene oxide nanosheets as probe oligonucleotide immobilization platform for DNA sensing

In this work, a simple and novel electrochemical biosensor based on a glassy carbon electrode (GCE) modified with graphene oxide nanosheets (GO) was developed for detection of DNA sequences. The morphology of prepared nanoplatform was investigated by scanning electron microscopy, infrared (FTIR) and UV/Vis absorption spectra. The fabrication processes of electrochemical biosensor were characterized with cyclic voltammetry and electrochemical impedance spectroscopy (EIS) in an aqueous solution. The optimization of experimental conditions such as immobilization of the probe BRCA1 and its hybridization with the complementary DNA was performed. Due to unique properties of graphene oxide nanosheets such as large surface area and high conductivity, a wide liner range of 1.0 × 10^?17–1.0 × 10^?9 M and detection limit of 3.3 × 10^?18 M were obtained for detection of BRCA1 5382 mutation by EIS technique. Under the optimum conditions, the proposed biosensor (ssDNA/GO/GCE) revealed suitable selectivity for discriminating the complementary sequences from non-complementary sequences, so it can be applicable for detection of breast cancer.     

Liquid crystal-based detection of DNA hybridization using surface immobilized single-stranded DNA

The authors have investigated (a) the self-assembly of single-stranded DNA (ssDNA) on glass surfaces, and (b) the interaction of DNA with liquid crystals (LCs) on solid surfaces. The results suggest that ssDNA (compared to dsDNA) on the solid interface causes particularly different orientations in LCs. The LC molecules assume a uniform homeotropic orientation on the surface with a typical surface ssDNA coverage of ~2.4 × 10¹² molecules per square cm. Once complementary DNA is hybridized on the surface, the homotropic orientation of the LCs becomes disrupted. This orientation transition can be visually observed by using a crossed polarizer. The findings were exploiting to design an assay for target DNA (= analyte DNA) that has an ~0.1 nM detection limit. The assay is highly selective and can easily differentiate target DNA from single-base mismatch and non-complementary DNA. In our perception, it represents a powerful, label-free and portable DNA detection scheme.

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Graphical abstract Schematic illustration of the mechanism for orientation behavior of a liquid crystal film supported on different surfaces. The homeotropic orientation of LC molecules was induced by ssDNA with appropriate surface coverage and was disrupted by ssDNA with lower or higher surface coverage or P1/T1 complex. 5CB: 4-Cyano-4′-pentylbiphenyl. TEA: Triethoxysilylbutyraldehyde.

     

<Emphasis Type="Italic">Escherichia coli</Emphasis> single-strand binding protein–DNA interactions on carbon nanotube-modified electrodes from a label-free electrochemical hybridization sensor

An electrochemical hybridization biosensor based on the intrinsic oxidation signals of nucleic acids and proteins has been designed, that makes use of the unique binding event between Escherichia coli single-strand binding protein (SSB) and single-stranded DNA (ssDNA). The voltammetric signal from guanine oxidation significantly decreased upon binding of SSB to single-stranded oligonucleotides (probe), anchored on a single-walled carbon nanotube (SWCNT) -modified screen-printed carbon electrode (SPE). Simultaneously, oxidation of the tyrosine (Tyr) and tryptophan (Trp) residues of the SSB protein increased upon binding of the SSB protein to ssDNA and ss-oligonucleotides. After the hybridization, SSB did not bind to the double helix form, and the guanine signal could be observed along with the disappearance of the oxidation signal of the protein. The amplification of intrinsic guanine and protein oxidation signals by SWCNT, and a washing step with sodium dodecylsulfate, enabled the specific detection of a point mutation. Monitoring the changes in the guanine and protein signals upon hybridization greatly simplified the detection procedure. The detection limit of 0.15 g/ml target DNA can be applied to genetic assays. To the best of our knowledge, this is the first work that utilizes the monitoring of SSB–DNA interactions on a solid transducer for the electrochemical detection of DNA hybridization by using intrinsic oxidation signals.     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

Lable‐Free Electrochemical DNA Sensor Based on Gold Nanoparticles/Poly(neutral red) Modified Electrode

We present a new strategy for the label‐free electrochemical detection of DNA hybridization based on gold nanoparticles (AuNPs)/poly(neutral red) (PNR) modified electrode. Probe oligonucledotides with thiol groups at the 5‐end were covalently linked onto the surface of AuNPs/PNR modified electrode via S‐Au binding. The hybridization event was monitored by using differential pulse voltammetry (DPV) upon hybridization generates electrochemical changes at the PNR‐solution interface. A significant decrease in the peak current was observed upon hybridization of probe with complementary target ssDNA, whereas no obvious change was observed with noncomplementary target ssDNA. And the DNA sensor also showed a high selectivity for detecting one‐mismatched and three‐mismatched target ssDNA and a high sensitivity for detecting complementary target ssDNA, the detection limit is 4.2×10^?12 M for complementary target ssDNA. In addition, the DNA biosensor showed an excellent reproducibility and stability under the DNA‐hybridization conditions.     

CtrA gene based electrochemical DNA sensor for detection of meningitis

Electrochemical DNA sensor has been fabricated by immobilizing thiolated single stranded oligonucleotide (ssDNA) probe onto gold (Au) coated glass electrode for meningitis detection using hybridization with complementary DNA (CtrA) in presence of methylene blue (MB). These electrodes (ssDNA/Au and dsDNA/Au) have been characterized using atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FT-IR), electrochemical impedance spectroscopy (EIS) and cyclic voltammetric (CV) technique. The DNA/Au electrode can detect the complementary DNA in the range of 7–42 ng/μl in 5 min (hybridization) with response time 60 s and electrode is stable for about 4 months when stored at 4 °C. The sensitivity of dsDNA/Au electrode is 115.8 μA/ng with 0.917 regression coefficient (R).     

Electrochemical detection of a Vibrio parahaemolyticus sequence-specific gene based on a gold electrode modified with a single stranded probe

An electrochemical DNA biosensor for specific-sequences detection of Vibrio parahaemolyticus (VP) was fabricated. A single-stranded 20-mer oligonucleotide (ssDNA) and 6-mercapto-1-hexanol (MCH) were immobilized via a thiol linker on gold disk electrodes by self-assembling. The ssDNA underwent hybridization in a hybridization solution containing complementary or non-complementary or single base pair mismatched DNA sequences of VP. Examination of changes in response to these three target DNAs showed that the developed biosensor had a high selectivity and sensitivity.     

CdS quantum dots as a fluorescent sensing platform for nucleic acid detection

We demonstrate that CdS quantum dots (QDs) can be applied to fluorescence-enhanced detection of nucleic acids in a two-step protocol. In step one, a fluorescently labeled single-stranded DNA probe is adsorbed on the QDs to quench its luminescence. In step two, the hybridization of the probe with its target ssDNA produces a double-stranded DNA which detaches from the QD. This, in turn, leads to the recovery of the fluorescence of the label. The lower detection limit of the assay is as low as 1?nM. The scheme (that was applied to detect a target DNA related to the HIV) is simple and can differentiate between perfectly complementary targets and mismatches.

An Electrochemical Sol–Gel Sensor for Determining Iron by Stripping Voltammetry

Electrochemical sensors were developed based on thick-film carbon-containing electrodes coated with thin xerogel films fabricated by the sol–gel technology. The effect of the composition of a hydrolyzed mixture and the types of carbon-containing inks and a support on the properties of sol–gel electrodes was studied. Conditions for preparing sol–gel film sensors modified with 1,10-phenanthroline, 2,2-dipyridyl, Chrome Azurol S, and Eriochrome Cyanine were chosen, and the electrochemical properties of these sensors were studied. Optimum conditions are found for determining total iron by stripping voltammetry (SVA) using sol–gel sensors modified with 1,10-phenanthroline and 2,2-dipyridyl. The detection limit for iron(II, III) was found to be 0.02 mg/L at an accumulation time of 60 s. The sol–gel sensors were used in the analysis of natural waters.     

Cholinesterase sensors based on screen-printed electrodes for detection of organophosphorus and carbamic pesticides

Cholinesterase sensors based on screen-printed electrodes modified with polyaniline, 7,7,8,8-tetracyanoquinodimethane (TCNQ), and Prussian blue have been developed and tested for detection of anticholinesterase pesticides in aqueous solution and in spiked grape juice. The influence of enzyme source and detection mode on biosensor performance was explored. It was shown that modification of the electrodes results in significant improvement of their analytical characteristics for pesticide determination. Thus, the slopes of the calibration curves obtained with modified electrodes were increased twofold and the detection limits of the pesticides were reduced by factors of 1.6 to 1.8 in comparison with the use of unmodified transducers. The biosensors developed make it possible to detect down to 2×10^–8 mol L^–1 chloropyrifos-methyl, 5×10^–8 mol L^–1 coumaphos, and 8×10^–9 mol L^–1 carbofuran in aqueous solution and grape juice. The optimal conditions for grape juice pretreatment were determined to diminish interference from the sample matrix.Abbreviations ChE Cholinesterase - TCNQ 7,7,8,8-Tetracyanoquinodimethane - ChO Choline oxidase - AChE Acetylcholinesterase - BChE Butyrylcholinesterase - BSA Bovine serum albumin - 2-PAM 2-Pyridine aldoxime methiodide     

Oxygen evolution on electrodes of different roughness: an electrochemical noise study

Rough and porous Ni layers have been obtained by cathodic deposition from a NiCl₂, NH₄Cl solution, at high current density. Characterisation by SEM has shown that they consisted of micro-dendrites separated by pores with a typical diameter of 1 m. In addition, circular hollows (10–100 m in diameter) were found on the deposit surface; their density varied with the deposition current density and deposition charge. The surface roughness of the Ni deposits, measured by EIS, was found to increase roughly linearly with the deposition charge, and to be little dependent on current density, provided a threshold value was exceeded. The oxygen evolution reaction has been studied on these electrodes by simultaneous real-time measurements of potential and electrolyte resistance fluctuations. The analysis of the electrochemical noise indicated that the dimensions of oxygen bubbles detaching from the electrodes slightly increased with the deposit surface roughness. It is not clear, however, whether or not this increase was associated with the effect of the small (1 m) or the large (10–100 m) features on the electrode-bubble interactions.     

Effect of Plasticizer on the Performance of the Surfactant-Selective Electrode Based on a Poly(Vinyl Chloride) Membrane with no Added Ion-Exchanger

The effect of different plasticizers in the sensing membrane on the performance of a surfactant ISE based on a PVC membrane with no added ion-exchanger was investigated. o-nitrophenyl octyl ether (NPOE), o-nitrophenyl decyl ether (NPDE), o-nitrophenyl dodecyl ether (NPDOE) and o-nitrophenyl tetradecyl ether (NPTE) were used as plasticizers. Electrodes based on NPDE, NPDOE and NPTE produced better results than NPOE-plasticized PVC membrane electrodes in terms of low detection limits. Electrodes based on NPDE, NPDOE and NPTE displayed a Nernstian slope in the concentration range of 10^–6 to 10^–2M. NPOE-plasticized PVC membrane electrodes displayed a Nernstian slope in the concentration range of 10^–5 to 10^–2M. The three electrodes other than the NPOE-plasticized PVC membrane electrode showed a similar performance to that of the NPOE-plasticized PVC membrane electrode concerning low detection limits and slope sensitivity. The four electrodes examined in this study are excellently selective for the dodecyltrimethylammonium ion over inorganic anions, but interference from other cationic surfactants such as tetradecyltrimethylammonium ions is significant. With respect to slope sensitivity, selectivity, response time and pH effect, the four electrodes showed a similar performance.     

Electrochemical reduction of cobalt and nickel complexes with ligands stabilizing metal in low oxidation state

Electrochemical reduction of cobalt(ii) complexes containing -acceptor ligands (L = bpy, Ph₂Ppy) proceeds through three consecutive reversible steps: one-electron transfer to form a more stable Co^IL complex, transfer of two electrons at more negative potentials to form an anionic [NiL]^– complex, and reduction of the ligand to the radical anion. The stability of the cobalt complexes with different ligands decreases in the series Ph₂Ppy > Ph₃P > bpy.     

A low-cost surface plasmon resonance instrument based on detection of resonance excitation wavelength

A laboratory-made surface plasmon resonance (SPR) instrument based on the detection of resonance excitation wavelength has been successfully fabricated. The performance and workability of the SPR instrument was demonstrated as a DNA biosensor. Biotinylated single-stranded oligonucleotides (ssDNA) were chemically immobilized on a gold-film surface of the SPR instrument as a DNA probe for the detection of its fully complementary, half-complementary and non-complementary ssDNA. The immobilization of the ssDNA probe was done by avidin-biotin linkage. The ssDNA used were 12-mer oligonucleotides. The sensing mechanism was based on the shift in resonance wavelength of an excitation light beam as the target ssDNA hybridized with the ssDNA on the gold-film surface. The linear dynamic ranges of the DNA biosensor for fully complementary and half-complementary ssDNA are 0.04-1.2 pM and 0.08-1.1 pM, respectively. The DNA biosensor showed higher sensitivity to fully complementary ssDNA than to half-complementary ssDNA. But no shift of resonance wavelength to the non-complementary ssDNA was observed.     

Label‐Free and Label Based Electrochemical Detection of Hybridization by Using Methylene Blue and Peptide Nucleic Acid Probes at Chitosan Modified Carbon Paste Electrodes

A chitosan modified carbon paste electrode (ChiCPE) based DNA biosensor for the recognition of calf thymus double stranded DNA (dsDNA), single stranded DNA (ssDNA) and hybridization detection between complementary DNA oligonucleotides is presented. DNA and oligonucleotides were electrostatically attached by using chitosan onto CPE. The amino groups of chitosan formed a strong complex with the phosphate backbone of DNA. The immobilized probe could selectively hybridize with the target DNA to form hybrid on the CPE surface. The detection of hybridization was observed by using the label‐free and label based protocols. The oxidation signals of guanine and adenine greatly decreased when a hybrid was formed on the ChiCPE surface. The changes in the peak currents of methylene blue (MB), an electroactive label, were observed upon hybridization of probe with target. The signals of MB were investigated at dsDNA modified ChiCPE and ssDNA modified ChiCPE and the increased peak currents were observed, in respect to the order of electrodes. The hybridization of peptide nucleic acid (PNA) probes with the DNA target sequences at ChiCPE was also investigated. Performance characteristics of the sensor were described, along with future prospects.     

Current strategies for electrochemical detection of DNA with solid electrodes

A review of current strategies aimed at detecting nucleic acids (NA) using NA-modified solid electrodes reveals the versatility and potential of electrochemical detection in this field. What emerged at the beginning of 90s as a very promising detection system in DNA technology is now resulting in the first commercial devices. Many aspects of the experimental design, for example surface immobilisation and detection schemes, are outlined and evaluated. Although most approaches use hybridisation as the recognition reaction, those not based on hybridisation are also included. As is finally shown, great advances have been achieved, although further developments are required if electrochemical devices are to be suitable for routine measurement.Abbreviations A Adenine - a.c.V Alternating current voltammetry - Amp. Amperometry - Apo E Apolipoprotein E - BCB Brilliant cresyl blue - BLM Bilayer lipid membrane - bp Base pairs - BPPG Basal planar pyrolytic graphite - bpy 2,2-Bipyridine - C Cytosine - CMV Citomegalovirus - CPE Carbon paste electrode - CPSA Constant-current chronopotentiometric stripping analysis - Cronoamp. Chronoamperometry - CSPE Carbon screen-printed electrode - CV Cyclic voltammetry - dmb 4,4-Dimethyl-2,2-bipyridine - dmphen Dimethylphenanthroline - DPPZ Dipyrido[3,2-a.2,3-c]phenazine - DPV Differential pulse voltammetry - dsDNA Double-stranded DNA - EtBr Ethidium bromide - Fc Ferrocene - Fc-CA Ferrocenecarboxaldehyde - Fc-CTPPZ Di[1-ferrocenecarbamoylpropyl)tetrahydropyrazine-4-(propylcarbamoylpyridine)]phenazine - Fc-NH₂ Aminoferrocene - FET Field-effect transistor - G Guanine - GCE Glassy carbon electrode - HBV Hepatitis B virus - HGH1 Human growth hormone 1 - HIV Human immunodeficiency virus - HRP Horseradish peroxidase - HOPGE Highly oriented pyrolytic graphite electrode - IPA Intermittent pulse amperometry - ISFET Ion-selective field-effect transistor - ITO Tin-doped indium oxide electrode - LSV Linear sweep voltammetry - Nano-Au Au nanoparticles - NMP Nucleotide monophosphate - ODN Oligodeoxynucleotide - ox. Oxidation - PCR Polymerase chain reaction - PET Poly(ethylene terephthalate) - PGE Pyrolytic graphite electrode - phen 1,10-Phenanthroline - PNA Peptide nucleic acid - Ppy Polypyrrole - (PQQ)GDH Pyrroline quinone glucose dehydrogenase - red. Reduction - SAM Self-assembled monolayer - SBP Soybean peroxidase - SNP Single nucleotide polymorphism - ssDNA Single-stranded DNA - SWV Square-wave voltammetry - T Thymine - Th Thionine - TTV TT virus - Ep Difference of peak potential     

Electrocatalytic Response of Electrodes Modified with Metal Phthalocyanines in the Cholinesterase–Thiocholine Ester System

Hydrolysis products in the cholinesterase–thiocholine ester system were determined by voltammetry using electrodes modified with metal phthalocyanines (MPc, M = Fe, Co). Specific features of the electrooxidation of the hydrolysis product (thiocholine) at a carbon-paste electrode and at a chemically modified electrode (CME) were compared. The conditions for the detection of an electrocatalytic signal in the oxidation of thiocholine at the CME were studied. Performance characteristics of the electrocatalytic determination of thiocholine at the CME were determined. The use of electrodes chemically modified with MPc reduces the detection limit for cholinesterase substrates under consideration to n × 10^–6 M.