Electrochemical DNA nano-biosensor for the detection of genotoxins in water samples简

In the present study, a disposable electrochemical DNA nano-biosensor is proposed for the rapid detection of genotoxic compounds and bio-analysis of water pollution. The DNA nano-biosensor is prepared by immobilizing DNA on Au nanoparticles and a self-assembled monolayer of cysteamine modified Au electrode. The assembly processes of cysteamine, Au nanoparticles and DNA were characterized by cyclic voltammetry （CV）. The Au nanoparticles enhanced DNA immobilization resulting in an increased guanine signal. The interaction of the analyte with the immobilized DNA was measured through the variation of the electrochemical signal of guanine by square wave voltammetry （SWV）. The biosensor was able to detect the known genotoxic compounds： 2-anthramine, acridine orange and 2- naphthylamine with detection limits of 2, 3 and 50 nmol/L, respectively. The biosensor was also used to test actual water samples to evaluate the contamination level. Additionally, the comparison of results from the classical genotoxiciw bioassay has confirmed the applicability of the method for real samoles.     

CE analysis and molecular characterisation of depurinated DNA samples

A DNA sample was partially degraded by scalar heat-acid treatments to study the extent of apurinic-apyrimidinic (A-P) lesions produced along the molecule. A CE-UV method allowed us to measure the rate of depurination at pH 5.0 and 70°C which was calculated to be 5.41×10(-6) s(-1) for adenine and 6.27×10(-6) s(-1) for guanine. CE identified depurination on treated samples when it occurred with a loss of >4% of the basic moieties. The molecular features of the A-P enriched samples were investigated by using molecular assays (agarose gel electrophoresis, UV spectrophotometry and quantitative PCR) and the consistency of the results of the STR typing were compared with the degree of depurination of the PCR template. The treated DNA samples showed molecular features such as fragmentation, altered OD(260) /OD(280) ratios and decreased ability of the quantitative PCR to synthesise the human target, related to the severity of depurination. A satisfactory correlation between the degree of damage and the amount of residual PCR-sensitive target sequences was also demonstrated (r(2) =0.9717). The conventional and mini-STR typing of the samples showed that the genetic outcome was influenced by a depurination damage that exceeded 4% when locus drop-outs and artefactual PCR results were evident. As the success of STR typing depends on the integrity of the DNA recovered from the samples, the CE-UV, physical and molecular assays described here are proposed as a set of useful methods in the analysis of certain forensic and clinical samples, for a critical evaluation of the outcome of the genetic testing.     

Electrochemical Study on DNA Damage Based on the Direct Oxidation of 8‐Hydroxydeoxyguanosine at an Electrochemically Modified Glassy Carbon Electrode

The study of DNA damage induced by Fenton reaction (Fe²⁺/H₂O₂) in vitro was performed based on the direct electrochemical oxidation of 8‐hydroxydeoxyguanosine (8‐OH‐dG), the biomarker of DNA oxidative damage, at an electrochemically modified glassy carbon electrode (GCE). The effects of antioxidants, such as ascorbic acid, and hydroxyl‐radical scavenger (mannitol) on the DNA damage were also investigated. 8‐OH‐dG, the oxidation product of guanine residues in DNA, has shown significantly oxidative peak on the electrochemically modified GCE. The oxidative peak current of 8‐OH‐dG was linear with the damaged DNA concentration in the range of 10–200 mg/L. The experimental results demonstrate that ascorbic acid has ambivalent effect on DNA oxidative stress. It can promote DNA oxidative damage when ascorbic acid concentration is below 1.5 mM and protect DNA from damage in the range of 1.5–2.5 mM. As a hydroxyl‐radical scavenger, mannitol inhibits significantly DNA oxidative damage. The influence of Fe²⁺, as reactant, and EDTA as iron chelator in the system were also studied. The proposed electrochemical method can be used for the estimation of DNA oxidative damage from new point of view.     

Electrochemical Nucleic Acid Biosensors for the Detection of Interaction Between Peroxynitrite and DNA

We studied the reactivity of peroxynitrite and different nucleic acid molecules using DNA electrochemical biosensors. SIN‐1 (3‐morpholinosydnonimine) has been used for the simultaneous generation of NO?and superoxide, i.e., as a peroxynitrite (ONOO^?) donor. Double strand DNA (dsDNA), single strand DNA (ssDNA) and 15 guanine bases oligonucleotide (Oligo(dG)₁₅) were immobilized on a carbon paste electrode to generate the biosensor and DPV was selected as the electroanalytical technique. Results showed that electrochemical biosensors were very sensitive for detecting interaction between ONOO^? and DNA. A down/up effect was observed, i.e., at low ONOO^? concentrations the guanine oxidation signal decreased while at high ONOO^? concentrations the guanine oxidation current increased. Oligo(dG)₁₅ exhibited greater interaction at low ONOO^? concentrations than the other DNA molecules. The reactivity between ONOO^? and DNA was also evaluated in solution phase, showing the same down/up effect. Finally, the capacity of DNA to hybridize was prevented after interaction with ONOO^?.     

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.     

Detection of telomere damage as a result of strand breaks in telomeric and subtelomeric DNA

Telomeres are the tandem repetitive DNA sequences at both ends of a chromosome with a repeating unit of TTAGGG. The integrity of a telomere is crucial to chromosomal stability and cellular viability. Damages to telomere DNA disrupt telomere integrity and accelerate telomere shortening. We describe a method for the assessment of strand breaks in the telomere/subtelomere region in cultured cells. Cells were embedded in agarose plugs and subjected to lysis and alkaline treatment to relax the DNA double helix. The telomere fragments as the result of strand breaks in the telomere/subtelomere region were then separated from the genomic DNA by electrophoresis, blotted onto membranes, and detected by a probe specific to the telomere sequence. Because of the large content of the telomere in human cells and the fact that telomere DNA is much more prone to damage than the bulk genomic DNA, the analysis may serve as a good indication of general DNA damage as well.     

A comparison study between a disposable electrochemical DNA biosensor and a Vibrio fischeri-based luminescent sensor for the detection of toxicants in water samples

In the present study, a comparison between a disposable electrochemical DNA biosensor and a Vibrio fischeri-based luminescent sensor for the detection of toxicants in water samples was made.In order to realize this study, a disposable electrochemical DNA biosensor has been reported. The DNA biosensor is assembled by immobilizing double stranded Calf Thymus DNA onto the surface of a disposable carbon screen-printed electrode. The oxidation signal of the guanine base, obtained by a square wave voltammetric scan, is used as analytical signal to detect the DNA damage; the presence of low molecular weight compounds with affinity for nucleic acids is measured by their effect on the guanine oxidation peak.Wastewater samples provided during First European Interlaboratory Exercise on water toxicity in the course of the project SWIFT-WFD were analyzed, and biosensor results were compared with a currently used toxicity test ToxAlert^®100 based on the bioluminescence inhibition of Vibrio fischeri. This test have been used because is rapid, easy handling and cost effectively responses for the toxicity assessment in real water samples.The results showed a promising correlation between two tests used for the detection of toxic compounds in water samples.     

Experimental and theoretical investigation effect of flavonols antioxidants on DNA damage

A new electrochemical biosensor was developed to demonstrate the effect of Acridine Orange (AO) on DNA damage. Then, the biosensor was used to check the inhibitors effect of three flavonols antioxidants (myricetin, fisetin and kaempferol) on DNA damage. Acridine Orange (AO) was used as a damaging agent because it shows a high affinity to nucleic acid and stretch of the double helical structure of DNA. Decreasing on the oxidation signals of adenine and guanine (in the DNA) in the presence of AO were used as probes to study the antioxidants power, using DNA-modified screen printed graphene electrode (DNA/SPGE). The results of our study showed that the DNA-biosensor could be suitable biosensor to investigate the inhibitors ability of the flavonols antioxidants on the DNA damage. The linear dependency was detected in the two regions in the ranges of 1.0–15.0 and 15.0–500.0 pmol L⁻¹. The detection limit was found 0.5 pmol L⁻¹ and 0.6 pmol L⁻¹ for guanine and adenine, respectively. To confirm the electrochemical results, Uv–Vis and fluorescence spectroscopic methods were used too. Finally molecular dynamic (MD) simulation was performed on the structure of DNA in a water box to study any interaction between the antioxidant, AO and DNA.     

A Graphene Oxide‐DNA Electrochemical Sensor Based on Glassy Carbon Electrode for Sensitive Determination of Methotrexate

Methotrexate (MTX) was used as an anti‐cancer drug, but its excessive use can cause serious side effects, it was necessary to monitor MTX in vivo. In this report, DNA was immobilized on a glassy carbon electrode (GCE) modified with graphene oxide (GO) to develop an electrochemical sensor for sensitive determination of MTX for the first time. The adsorptive voltammetric behaviors of MTX on DNA sensor were investigated using differential pulse voltammetry (DPV). The peak current response of guanine in DNA was used as a determination signal of MTX in acetate buffer solution pH 4.6. Voltammetric investigations revealed that the proposed method could determine MTX in the concentration range from 5.5×10⁻⁸ to 2.2×10⁻⁶ mol L⁻¹ with a lower detection limit of 7.6×10⁻9 mol L⁻¹ (S/N=3). The method was applied to detect MTX in human blood serum and diluted urine samples with excellent recoveries of 97.4–102.5 %. Compared with the previous studies, the DNA/GO/GCE electrode constructed by us based on the change rate of guanine current (R%) in DNA, proportionally reflecting the MTX concentration, is simple and sensitive .     

Human Cytochrome P450 (CYP1A2)‐dsDNA Interaction in situ Evaluation Using a dsDNA‐electrochemical Biosensor

Human cytochrome CYP1A2 is one of the major hepatic cytochrome P450s involved in many drugs metabolism, and chemical carcinogens activation. The CYP1A2‐dsDNA interaction in situ evaluation using a DNA‐electrochemical biosensor and differential pulse voltammetry was investigated. A dsDNA‐electrochemical biosensor showed that CYP1A2 interacted with dsDNA causing conformational changes in the double helix chain and DNA oxidative damage. A preferential interaction between the dsDNA guanosine residues and CYP1A2 was found, as free guanine and 8‐oxoguanine, a DNA oxidative damage biomarker, oxidation peaks were detected. This was confirmed using guanine and adenine homopolynucleotides‐electrochemical biosensors. The CYP1A2‐dsDNA interaction and dsDNA conformation changes was also confirmed by UV‐Vis spectrophotometry.     

Coupling of an indicator-free electrochemical DNA biosensor with polymerase chain reaction for the detection of DNA sequences related to the apolipoprotein E

This paper describes a disposable indicator-free electrochemical DNA biosensor applied to the detection of apolipoprotein E (apoE) sequences in PCR samples. In the indicator-free assays, the duplex formation was detected by measuring the electrochemical signal of the guanine base of nucleic acids. The biosensor format involved the immobilisation of an inosine-modified (guanine-free) probe onto a screen-printed electrode (SPE) transducer and the detection of the duplex formation in connection with the square-wave voltammetric measurement of the oxidation peak of the guanine of the target sequence.The indicator-free scheme has been characterised using 23-mer oligonucleotides as model: parameters affecting the hybridisation assay such as probe immobilisation conditions, hybridisation time, use of hybridisation accelerators were examined and optimised.The analysis of PCR samples (244 bp DNA fragments, obtained by amplification of DNA extracted from human blood) required a further optimisation of the experimental procedure. In particular, a lower steric hyndrance of the probe modified surface was essential to allow an efficient hybridisation of the target DNA fragment. Negative controls have been performed using the PCR blank and amplicons unrelated to the immobilised probe. A 10 min hybridisation time allowed a full characterisation of each sample.     

Honey and Pollen Phenolic Composition,Antioxidant Capacity,and DNA Protecting Properties

The phenolic composition, antioxidant capacity, and the dsDNA oxidative damage protecting properties, of ten honey and two pollen samples, from different countries, Portugal, Algeria, Romania, and Greece, using differential pulse voltammetry, DPPH^. spectrophotometric assay, reversed‐phase high performance liquid chromatography with electrochemical detection, and agarose gel electrophoresis, were investigated. The honey samples highest antioxidant capacity was from Multi floral from Greece and the lowest for Mono floral black locust from Romania. The pollen from Romania presented higher antioxidant capacity compared with the pollen from Portugal but both pollen samples have a greater antioxidant capacity compared with the honey samples. In the presence of honey and pollen the DNA oxidative damage, induced by hydroxyl radicals generated through the Fenton reaction, was decreased.     

Antileishmanial Drug Miltefosine‐dsDNA Interaction in situ Evaluation with a DNA‐Electrochemical Biosensor

Leishmaniasis is one of the most important parasitic neglected disease. The electrochemical evaluation of the antileishmanial drug miltefosine‐dsDNA interaction was investigated in incubated solutions and using dsDNA‐electrochemical biosensors, following the changes in the oxidation peaks of guanosine and adenosine residues, and the occurrence of the free guanine residues, electrochemical signal. The electrochemical behaviour of miltefosine was also investigated, at a glassy carbon electrode, using cyclic, differential pulse and square wave voltammetry and no electrochemical redox processes were observed. The interaction mechanism of miltefosine‐dsDNA occurs in two ways: independent of the dsDNA sequence, and leading to the condensation/aggregation of DNA strands, producing a rigid miltefosine‐dsDNA complex structure, and a preferential interaction between the guanine hydrogen atoms in the C−G base pair and miltefosine, causing the release of guanine residues detected on the electrode surface. Miltefosine did not induce oxidative damage to DNA in the experimental conditions used.     

Electrochemical Biosensor for the Detection of Interaction Between Arsenic Trioxide and DNA Based on Guanine Signal

The interaction of arsenic trioxide (As₂O₃) with calf thymus double‐stranded DNA (dsDNA), calf thymus single‐stranded DNA (ssDNA) and also 17‐mer short oligonucleotide (Probe A) was studied electrochemically by using differential pulse voltammetry (DPV) with carbon paste electrode (CPE) at the surface and also in solution. Potentiometric stripping analysis (PSA) was employed to monitor the interaction of As₂O₃ with dsDNA in solution phase by using a renewable pencil graphite electrode (PGE). The changes in the experimental parameters such as the concentration of As₂O₃, and the accumulation time of As₂O₃ were studied by using DPV; in addition, the reproducibility data for the interaction between DNA and As₂O₃ was determined by using both electrochemical techniques. After the interaction of As₂O₃ with dsDNA, the DPV signal of guanine was found to be decreasing when the accumulation time and the concentration of As₂O₃ were increased. Similar DPV results were also found with ssDNA and oligonucleotide. PSA results observed at a low DNA concentration such as 1 ppm and a different working electrode such as PGE showed that there could be damage to guanine bases. The partition coefficients of As₂O₃ after interaction with dsDNA and ssDNA in solution by using CPE were calculated. Similarly, the partition coefficients (PC) of As₂O₃ after interaction with dsDNA in solution was also calculated by PSA at PGE. The features of this proposed method for the detection of DNA damage by As₂O₃ are discussed and compared with those methods previously reported for the other type of DNA targeted agents in the literature.     

Quantitative Biodetection of Anticancer Drug Rituxan with DNA Biosensor Modified PAMAM Dendrimer/Reduced Graphene Oxide Nanocomposite

PAMAM dendrimer/reduced graphene oxide nanocomposite modified pencil graphite electrode (PAMAM/RGO/PGE) was used to fabricate an electrochemical DNA biosensor for determination of Rituxan (RTX) at low concentrations, for the first time. The fabricated biosensor was characterized with FE‐SEM, EIS, and CV techniques. The ds‐DNA/PAMAM/RGO/PGE was used as a working electrode to study the interaction between the RTX and salmon sperm ds‐DNA by DPV technique. Because of the interaction between the drug and DNA leads to a decrease in the guanine oxidation peak current, it was used as an indicator for the determination of the RTX. Under the optimized experimental conditions, a wide linear relationship between RTX concentration and guanine signal was obtained within the range of 7.0 to 60.0 μmol L⁻¹ and 60.0 to 300.0 μmol L⁻¹ with a low detection limit (0.56 μmol L⁻¹). To clarify the interaction mechanism between the RTX and the ds‐DNA, DPV and UV‐Vis measurements were used. The reproducibility, stability, and performance of the constructed biosensor was examined by quantitative measuring RTX in pharmaceutical and human serum samples with good precision (RSD; 2.0–6.0 %) and acceptable recoveries (100.04–101.95 %).     

Batch Injection Analysis with Amperometric Detection for DNA Biosensing Applications

In this work, batch injection analysis with the amperometric detection (BIA‐AD), employing a detection cell designed to adapt a screen‐printed carbon electrode (SPCE) was used for the first time as a robust electroanalytical system for DNA biosensing applications. The sensitive amperometric detection was used to evaluate the structural changes in double‐stranded DNA (dsDNA) after UV‐C irradiation of its solution for a given time. Batching of DNA samples was performed by precise electronic pipette microinjection of an irradiated sample aliquot onto the unmodified activated SPCE surface incorporated in the BIA‐AD system. Using the optimized experimental conditions (40 μL of 1 mg mL^?1 dsDNA in a 0.1 M phosphate buffer of pH 7.4 sampled at the injection speed degree of 6 and detected at the potential of +1.5 V vs silver pseudo‐reference electrode), a time‐dependent response (gradual decrease of amperometric signal up to 58 % after 10 min of the irradiation) was found for the detection of damage to low molecular weight salmon sperm dsDNA. The advantages of this low‐dimensional and cost‐effective measuring system can be utilized not only for the quantification of DNA damage/degradation by UV irradiation, but they are also promising for studying other types of DNA interactions.     

Electrochemical Study of the Interaction of the Alkylating Agent Busulfan with Double Strand DNA

Damage of salmon sperm double strand ss dsDNA in solution or immobilized on screen‐printed carbon electrode (SPCE) induced by incubation of DNA with the antineoplastic alkylating agent busulfan (BUS) at various conditions was detected for the first time by simple electrochemical methods. Chemical changes in DNA bases can be detected through the altered electroactivity of the DNA. Electrochemical voltammetric sensing of damage caused by BUS to dsDNA in solution was monitored by the appearance of peaks diagnostic of the oxidation of guanine and adenine. Moreover, crystal violet, which interacts with the DNA immobilized on SPCEs, was used as an effective electroactive indicator, in combination with cyclic voltammetry and differential pulse voltammetry techniques to monitor the cross‐links or damage to DNA. The interaction between BUS and DNA were determined by the changes in the voltammetric peak of crystal violet. The effects of various conditions upon the crystal violet signal were investigated.     

Voltammetric Behavior of the Alizarin Red S Interaction with DNA and Damage to DNA

The electrochemical behavior and the interaction of alizarin red S (ARS) with calf thymus DNA was investigated on a bare glassy carbon electrode (GCE) and DNA modified GCE (DNA/GCE), respectively. ARS showed a pair of redox peaks at ?0.445 V and ?0.414 V on a bare GCE. On addition of DNA into the ARS solution, the peak current of ARS decreased and the peak potential positively shifted, but without new redox peaks appeared. The ARS reduction peak current increased with immersion time on a DNA/GCE. The results showed that ARS could interact with DNA molecules by intercalative binding mode. The equilibrium constant, binding number and the ratio of binding constant for oxidized and reduced ARS forms were obtained. The DNA damage was directly detected by appearance of guanosine and adenosine bases oxidation signal. The influence of experimental conditions on DNA damage extent was discussed in detail.     

Mechanisms of oxidation of guanine in DNA by carbonate radical anion, a decomposition product of nitrosoperoxycarbonate

Peroxynitrite is produced during inflammation and combines rapidly with carbon dioxide to yield the unstable nitrosoperoxycarbonate, which decomposes (in part) to CO(3) (.-) and (.)NO(2) radicals. The CO(3) (.-) radicals oxidize guanine bases in DNA through a one-electron transfer reaction process that ultimately results in the formation of stable guanine oxidation products. Here we have explored these mechanisms, starting with a spectroscopic study of the kinetics of electron transfer from 20-22mer double-stranded oligonucleotides to CO(3) (.-) radicals, together with the effects of base sequence on the formation of the end-products in runs of one, two, or three contiguous guanines. The distributions of these alkali-labile lesions were determined by gel electrophoresis methods. The cascade of events was initiated through the use of 308 nm XeCl excimer laser pulses to generate CO(3) (.-) radicals by an established method based on the photodissociation of persulfate to sulfate radicals and the oxidation of bicarbonate. Although the Saito model (Saito et al., J. Am. Chem. Soc. 1995, 117, 6406-6407) predicts relative ease of one-electron oxidations in DNA, following the trend 5'-GGG > 5'-GG > 5'-G, we found that the rate constants for CO(3) (.-)-mediated oxidation of guanines in these sequence contexts (k(5)) showed only small variation within a narrow range [(1.5-3.0)x10(7) M(-1) s(-1)]. In contrast, the distributions of the end-products are dependent on the base sequence context and are higher at the 5'-G in 5'-GG sequences and at the first two 5'-guanines in the 5'-GGG sequences. These effects are attributed to a combination of initial hole distributions among the contiguous guanines and the subsequent differences in chemical reaction yields at each guanine. The lack of dependence of k(5) on sequence context indicates that the one-electron oxidation of guanine in DNA by CO(3) (.-) radicals occurs by an inner-sphere mechanism.     

High-sensitivity capillary gel electrophoretic analysis of DNA fragments on an electrophoresis microchip using electrokinetic injection with transient isotachophoretic preconcentration

The research adopted a single-channel microchip as the probe, and focused electrokinetic injection combined with transient isotachophoresis preconcentration technique on capillary electrophoresis microchip to improve the analytical sensitivity of DNA fragments. The channel length, channel width and channel depth of the used microchip were 40.5 mm, and 110 and 50 μm, respectively. The separation was detected by CCD (charge-coupled device) (effective LENGTH=25 mm, 260 nm). A 1/100 diluted sample (0.2 mg/l of each DNA fragment) of commercially available stepladder DNA sample could be baseline separated in 120 s with S/N=2–5. Compared with conventional chip gel electrophoresis, the proposed method is ideally suited to improve the sensitivity of DNA analysis by chip electrophoresis.