ds-DNA Biosensor Research Articles

Development of a sensitive ds-DNA/Au NPs/ PGE biosensor for determination of Buprenorphine using electrochemical and molecular dynamic simulation investigation

A sensitive electrochemical DNA biosensor has been developed for the detection of Buprenorphine (Bu), a narcotic pain reliever. To achieve this, double-stranded DNA (ds-DNA) was immobilized on a pencil graphite electrode that was modified with gold nanoparticles (Au NPs/PGE). The gold nanoparticles enhanced the performance of the DNA biosensor. The constructed ds-DNA/Au NPs/ PGE exhibited a linear detection range spanning from 0.05 to 100 μM with an impressive detection limit of 20 nM for Bu detection. Additionally, the DNA biosensor demonstrated good response in real samples evaluations. Finally, the interaction between carbon and gold atoms with DNA was confirmed through molecular dynamics simulation, while the interaction between DNA and the Bu drug was confirmed through molecular docking method. In conclusion, the electrochemical DNA biosensor presented in this study demonstrates exceptional sensitivity and reliability in the detection of buprenorphine. The incorporation of gold nanoparticles, as well as the use of molecular dynamics simulations and docking methods, contributes to a comprehensive understanding of the interactions involved in this detection process.

Bismuth Film along with dsDNA-Modified Electrode Surfaces as Promising (bio)Sensors in the Analysis of Heavy Metals in Soils.

Heavy metals constitute pollutants that are particularly common in air, water, and soil. They are present in both urban and rural environments, on land, and in marine ecosystems, where they cause serious environmental problems since they do not degrade easily, remain almost unchanged for long periods, and bioaccumulate. The detection and especially the quantification of metals require a systematic process. Regular monitoring is necessary because of seasonal variations in metal levels. Consequently, there is a significant need for rapid and low-cost metal determination methods. In this study, we compare and analytically validate absorption spectrometry with a sensitive voltammetric method, which uses a bismuth film-plated electrode surface and applies stripping voltammetry. Atomic absorption spectroscopy (AAS) represents a well-established analytical technique, while the applicability of anodic stripping voltammetry (ASV) in complicated sample matrices such as soil samples is currently unknown. This sample-handling challenge is investigated in the present study. The results show that the AAS and ASV methods were satisfactorily correlated and showed that the metal concentration in soils was lower than the limit values but with an increasing trend. Therefore, continuous monitoring of metal levels in the urban complex of a city is necessary and a matter of great importance. The limits of detection of cadmium (Cd) were lower when using the stripping voltammetry (SWASV) graphite furnace technique compared with those obtained with AAS when using the graphite furnace. However, when using flame atomic absorption spectroscopy (flame-AAS), the measurements tended to overestimate the concentration of Cd compared with the values found using SWASV. This highlights the differences in sensitivity and accuracy between these analytical methods for detecting Cd. The SWASV method has the advantage of being cheaper and faster, enabling the simultaneous determination of heavy elements across the range of concentrations that these elements can occur in Mediterranean soils. Additionally, a dsDNA biosensor is suggested for the discrimination of Cu(I) along with Cu(II) based on the oxidation peak of guanine, and adenine residues can be applied in the redox speciation analysis of copper in soil, which represents an issue of great importance.

SnO2 nanoparticles/waste masks carbon hybrid materials for DNA biosensor application on voltammetric detection of anti-cancer drug pazopanib

This present study is the first investigation of pazopanib-dsDNA binding using bare and modified GCE. The interaction was mainly evaluated based on the decrease of voltammetric signal of deoxyadenosine by differential pulse voltammetry using three different ways, including the incubated solutions, dsDNA biosensor, and nanobiosensor. The nanobiosensor was fabricated with the help of SnO2 nanoparticles and carbon hybrid material. The carbon material is derived from the waste mask, the most used personal protective equipment for the ongoing COVID-19 pandemic. Both materials were synthesized via the green synthesis technique and characterized by various techniques, including BET, TEM, SEM-EDX, AFM, XPS, and XRD. Spectrophotometric and molecular docking studies also evaluated the pazopanib-dsDNA binding. All calculations showed that pazopanib (PZB) was active in the minor grove region of DNA.

Investigation of the interaction between anticancer drug ibrutinib and double-stranded DNA by electrochemical and molecular docking techniques

Ibrutinib is Bruton’s tyrosine kinase inhibitor that is generally used in the treatment of lymphoma. The investigation of anticancer drug - double-stranded DNA (dsDNA) interaction is a key issue for cancer treatment. In this study, electrochemical and molecular docking studies were realized to explain the interaction mechanism between ibrutinib and dsDNA. Two interaction methods, including DNA biosensors and incubated solutions, were used in voltammetric studies. The interaction was evaluated based on the voltammetric responses of desoxyguanosine and desoxyadenosine by differential pulse voltammetry in pH 4.70 acetate buffer. The influence of accumulation concentration and time of ibrutinib on the voltammetric responses of these electroactive dsDNA bases were performed. At dsDNA biosensor, the reproducibility results (RSD%) of peak currents of desoxyguanosine and desoxyadenosine were found as 1.95 and 1.74, respectively. The dsDNA biosensor was kept in the range of 2.0 – 20.0 µM of IBR solutions for 5 min. A molecular docking study revealed that binding an ibrutinib molecule with dsDNA suggests a groove-binding mode of interaction, and the dominating interaction force is hydrogen bonding.

Electrochemical investigation of DNA-metal complex interactions and development of a highly sensitive electrochemical biosensor

Metal ion-DNA interactions are important in nature as they often change the genetic material's structure and function. In this work, new Tb complex of TbCl3 (tris(8-hydroxyquinoline-5-sulfonic acid) terbium) (Tb(QS)3) was used as an electrochemical indicator for investigation of DNA-metal interaction and then a new DNA biosensor was designed using this complex. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were used to study the interaction of Tb(QS)3 with double-stranded DNA (ds-DNA). It was found that Tb(QS)3 presented an excellent electrochemical activity on carbon paste electrode (CPE) and could intercalate into the double helix of double-stranded DNA. The interaction mechanism was elucidated in DNA solution and DNA modified carbon paste electrode by using differential pulse voltammetry and cyclic voltammetry. The binding ratio between this complex and ds-DNA was calculated to be 1:1. The extent of hybridization was evaluated on the basis of the difference between signals of Tb(QS)3 with probe DNA before and after hybridization with complementary DNA. With this approach, target DNA could be detected in the range from 0.03 to 0.185 μM with detection limit of 0.021 μM. The interaction mode between Tb(QS)3 and DNA was found to be mainly intercalative interaction.

Electrochemical Detection of 6-Thioguanine and DNA Hybridization with Oligonucleotide Biosensors by Differential Pulse Voltammetry (DPV)

The development of a simple and inexpensive DNA biosensor based on a gold nanoparticle (Au-NPs)/glutathione (GSH) matrix is reported to characterize DNA hybridization. The adhesion and morphological properties of the film were characterized using contact angle measurements and scanning electronic microscopy (SEM), respectively. The modified gold electrode was characterized by differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The results indicate that DNA/AuNPs-GSH/cysteine provides excellent sensitivity for the target DNA in the linear range of response from 7 pM to 5 nM. The interaction of 6-thioguanine (6-tg) with the double stranded DNA (ds-DNA) and single stranded DNA (ss-DNA) modified electrode was investigated using DPV and EIS. Consequently, 6-tg is accumulated onto the modified electrode causing a decrease of the charge transfer resistance (Rct) across the dynamic range from 1 pM to 10 µM. The developed electrochemical DNA biosensor was demonstrated to be efficient to characterize the interactions with drugs and micropollutants in wastewater.

Electrochemical Biosensor Design with Multi‐walled Carbon Nanotube to Display DNA‐Schiff Base Interaction

AbstractThis paper demonstrates a Schiff base i. e. 5‐(diethylamino)‐2‐((2,6‐diethylphenylimino)methyl)phenol (5‐DDMP) that was sensed by DNA biosensor. dsDNA was immobilized onto GCE modified with functionalized multi‐walled carbon nanotubes to prepare a biosensor. The efficiency of dsDNA biosensor was determined and binding of 5‐DDMP with dsDNA was searched by UV‐vis spectrophotometry and differential pulse voltammetry. Molecular docking simulations between 5‐DDMP and dsDNA were explored and as a result, a hydrogen bond and a π‐π contact were observed between 5‐DDMP and deoxyguanosine base (dG22) of the strand B, deoxyadenosine base (dA5) of the strand A, respectively. These studies could be useful for new anticancer drug design and development.

The development of an electrochemical DNA biosensor based on quercetin as a new electroactive indicator for DNA hybridization detection.

An electrochemical DNA biosensor was designed for the detection of a specific target DNA after hybridization with a complementary DNA probe immobilized onto a glassy carbon electrode surface. Quercetin was successfully used as a new electroactive indicator for the hybridization detection. Different interactions of quercetin with single-stranded DNA (ss-DNA) and double-stranded DNA (ds-DNA) led to different electrochemical signals, which were recorded as cyclic and differential pulse voltammograms enabling hybridization detection. Various parameters influencing the biosensor performance were evaluated, and optimized conditions were obtained. Also, the detection limit of 83 pM with a relative standard deviation of 4.6% was obtained for the determination of complementary oligonucleotides. Then, the developed biosensor was applied successively for the detection of short sequences of hepatitis C virus (HCV1). The hybridization between the probe (PHCV1) and its complementary sequence (HCV1a) as the target was studied. Some hybridization experiments with noncomplementary oligonucleotides also showed that the suggested DNA sensor responds selectively to the target.

A new electrochemical DNA biosensor based on modified carbon paste electrode using graphene quantum dots and ionic liquid for determination of topotecan

To study topotecan–DNA interaction and topotecan determination with a modified carbon paste electrode (CPE), a new electrochemical biosensor is introduced. The biosensor was prepared through modification of a CPE with ionic liquid (IL), graphene quantum dots and double stranded DNA (ds-DNA). Compared to reported conventional DNA sensors, the modified electrode displayed high sensitivity and selectivity, respectable reproducibility and satisfactory stability. Moreover, the differential-pulse voltammetric (DPV) peak current was linear to topotecan concentration in the range of 0.35–100.0 μM, with a detection limit (LOD) of 0.1 μM. Applying the proposed method to determine topotecan in blood serum and urine, the use of this screening method for analyzing real sample was studied. In general, the results indicated that this DNA biosensor could be used for the fast, simple, sensitive, and cost effective determination of topotecan in urine and serum samples.

A novel morphine electrochemical biosensor based on intercalative and electrostatic interaction of morphine with double strand DNA immobilized onto a modified Au electrode

The intercalative and electrostatic interaction of morphine with double-stranded DNA (ds-DNA), which was immobilized onto mercapto-benzaldehyde-modified Au electrode, was employed for designing a sensitive biosensor. The interaction of morphine with the immobilized ds-DNA onto the electrode surface has been studied by differential pulse voltammetry (DPV). Under the optimum conditions, a linear dependence for the morphine concentration in the range of 0.05–500μmolL−1 and its oxidation signal were observed and a detection limit of 0.01μmolL−1 for the morphine was obtained. The reproducibility and applicability of the analysis to real samples were also investigated and results demonstrated that this DNA biosensor could be utilized for the sensitive, rapid, simple, and cost effective determination of morphine in urine and blood plasma samples.

Redox mechanism of anticancer drug idarubicin and in-situ evaluation of interaction with DNA using an electrochemical biosensor

Idarubicin (IDA), 4-demethoxydaunorubicin, is an anthracycline derivative and widely used treatment of leukemia. The electrochemical behavior of IDA was examined at a glassy carbon electrode (GCE) in different aqueous supporting electrolyte using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The oxidation process of IDA was found to be pH dependent and irreversible proceeding with a transfer of 1 proton and 1 electron under the diffusion controlled mechanism. The electroactive center is the hydroxyl group on the aromatic ring which produces a final quinonic product. The diffusion coefficient of IDA was calculated to be DIDA=7.47×10−6cm2s−1 in pH=4.3 0.1M acetate buffer.The interaction of IDA and double stranded deoxyribonucleic acid (ds-DNA) was investigated using electrochemical ds-DNA biosensor and incubation solution by means of DPV. The DNA damage was detected following the changes in the oxidation peaks of guanosine and adenosine residues. The results obtained showed that IDA interacts with DNA which causes the change in the DNA morphological structure. In addition to these polynucleotides, PolyG and PolyA, biosensors were also used to confirm the interaction between ds-DNA and IDA. However, no oxidation peaks of the purine base oxidation products, 8-oxoGua and 2,8-oxoAde, were observed.

Label-free supersandwich electrogenerated chemiluminescence biosensor for the determination of the HIV gene

We describe a highly sensitive electrochemiluminescence (ECL) based method for the determination of the human immunodeficiency virus-1 (HIV-1) gene. A long-range self-assembled double strand DNA (ds-DNA) is used as a carrier, and the ruthenium complex Ru(phen)3 2+ as an ECL indicator for signal amplification. The thiolated ss-DNA serving as a capture probe is firstly self-assembled on the surface of a gold electrode. After the target HIV-1 gene is completely hybridized with the capture probe, two previously hybridized auxiliary probes are hybridized with the target HIV-1 gene to form long-range supersandwich ds-DNA polymers on the surface of the electrode. Finally, the ECL indicator is intercalated into the supersandwich ds-DNA grooves. This results in a strongly increased ECL in tripropylamine solution because a large fraction of the intercalator is intercalated into supersandwich ds-DNA. The results showed that the increased ECL intensity is directly related to the logarithm of the concentration of the HIV-1 gene in the range from 0.1 pM to 0.1 nM, with a detection limit of 0.022 pM and using only 10 μL of analyte samples. The method can effectively discriminate target HIV-1 gene (a perfectly matched ss-DNA) from a 2-base mismatched ss-DNA. This work demonstrates that the high sensitivity and selectivity of an ECL DNA biosensor can be largely improved by using supersandwich ds-DNA along with ECL indicators.

Mangiferin DNA biosensor using double-stranded DNA modified pencil graphite electrode based on guanine and adenine signals

In this study a novel biosensor for determination of mangiferin is described. Based on our knowledge there is not any electrochemical sensor or biosensor for determination of mangiferin and this is the first electrochemical report. The interaction of mangiferin with salmon sperm double-stranded DNA (ds-DNA) based on the decreasing of the oxidation signals of guanine and adenine bases was studied electrochemically with a pencil graphite electrode using differential pulse voltammetry (DPV). The decrease in the intensity of the guanine and adenine oxidation signals after interaction with mangiferin were used as indicator signals for the sensitive determination of mangiferin. DPV exhibits a linear dynamic range from 9.0×10−7 to 4.5×10−5M for mangiferin. Finally this modified electrode was used for determination of mangiferin in urine samples.

Sensitive DNA biosensor improved by 1,10-phenanthroline cobalt complex as indicator based on the electrode modified by gold nanoparticles and graphene

A novel and sensitive electrochemical DNA biosensor was constructed based on the gold electrode modified by graphene and gold nanoparticles (AuNPs), whose sensitivity was improved by using 1,10-phenanthroline cobalt ([Co(phen)2(Cl)(H2O)]+) as an electroactive indicator. The gold electrode was firstly modified with sulfur graphene (GR-SH), and then covalently grafted with AuNPs via sulfur–gold affinity. Finally the thiol capped probe DNA was immobilized onto the AuNPs/GR modified electrode. The target DNA could hybridize with the probe DNA to form a double-stranded DNA (ds-DNA), into which [Co(phen)2(Cl)(H2O)]+ can intercalate, which can be confirmed by cyclic voltammetry (CV). The target DNA, from Escherichia coli (E. coil), could be detected in a linear range from 2.50 × 10−11 to 1.25 × 10−9 M (R = 0.9981) with a detection limit of 8.33 × 10−12 M (3σ, n = 11). It was demonstrated that the reported electrochemical DNA biosensor offered a promising approach for the sensitive and selective detection of DNA by using [Co(phen)2(Cl)(H2O)]+ as an electroactive indicator.

A study of the antioxidative behavior of phenolic acids, in aqueous herb extracts, using a dsDNA biosensor

Abstract Electrochemical DNA biosensors are promising tools for the fast, inexpensive and simple in vitro analysis for the determination of free radicals and antioxidants. High concentrations of antioxidants in such compounds as phenolic acids and plant extracts, act as free radical terminators which reduce the effect of the oxidative dam-age on DNA. The electrochemical behavior of three representative phenolic acids, caffeic acid, gallic acid and trolox were studied by cyclic voltammetry. Moreover, the determination of the above antioxidants under the optimized conditions (scan rate, deposition potential and time) using differential pulse voltammetry was also investigated. In vitro studies focused on their antioxidative effect were performed by adsorptive transfer stripping voltammetry and dsDNA biosensor. Using Fenton’s system, with FeSO4 and H2O2 was chosen as a strong oxidative system. This biosensor was applied as a screening antioxidant test in order to estimate the antioxidant capacity of aqueous herb extracts.

Construction of dsDNA biosensor based on dendritic SiO2 nanoparticle and investigation on its interaction with benzo[a]pyrene

In this work, a new dsDNA biosensor was constructed to monitor the interaction of DNA and benzo[a]pyrene (BaP). Firstly, dendritic SiO2 nanoparticles were synthesized by silanization of SiO2 nanoparticles with (γ-(methacryloyloxy)propyl) trimethoxysilane and polymerization with acrylic acid. Then, due to the rich carboxyl groups of these nanoparticles, they were associated with the amino groups of a self-assembly membrane formed on the gold electrode by a sulfur-containing compound, 5-amino-3-mercapto-1,2,4-triazole. Finally, dsDNA was immobilized on the electrode surface by static adsorption with the aid of metallic ion. The whole immobilization steps were characterized by cyclic voltammogram and electrochemical impedance spectrum. After that, using methylene blue as a probe, the interaction of BaP with dsDNA was investigated. A linear relationship between the percentages of current decrease with the logarithm of BaP concentrations was found in the range from 0.33 to 133 μM.

An electrochemical approach for direct detection and discrimination of fully match and single base mismatch double-stranded oligonucleotides corresponding to universal region of hepatitis C virus

Development of an electrochemical DNA biosensor for direct detection and discrimination of HCV core/E1 region corresponding double-stranded DNA (ds-DNA) using a peptide nucleic acid (PNA) oligomer as the probe is described. The PNA probe is a cysteine conjugated 20-mer PNA oligomer, complementary to HCV core/E1 universal region, which is a consensus sequence in almost all HCV genotypes and is not present in other organisms. The significant variation in differential pulse voltammetric response of methylene blue (MB) on the probe modified gold electrode (AuE) upon hybridization with complementary double-stranded oligonucleotide (ds-oligonucleotide) following PNA/ds-DNA hybrid formation is the principle of target ds-DNA detection. No significant variations in MB signal following interaction of the probe with non-complementary and single-base mismatch (SBM) ds-DNAs was observed. This is due to the lack of hybridization between the probe and the non-complementary and SBM ds-DNA samples. Diagnostic performance of the biosensor is described and the detection limit of fully match target ds-DNA was found to be 9.63 × 10−12 M and 4.97 × 10−12 M for 2 h and 20 h hybridization times, respectively. The relative standard deviation over three independently probe modified electrodes measured at 100 pM of target ds-DNA was 2.9% and 2.4% for 2 h and 20 h hybridization times indicating a remarkable reproducibility of the detection method.

Electrochemical Biosensor Assay of the Interaction between [PtCln(NH3)4–n](2–n) (n = 0–4) Complexes and ds‐DNA

AbstractWe report on the results of electrochemical DNA biosensor assay of the interaction between double‐stranded DNA (ds‐DNA) and a series of six neutral, anionic or cationic Pt complexes of the general formula [PtCln(NH3)4–n](2–n) [n = 4, 1; n = 3, 2; n = 2, isomers cisplatin (3) and transplatin (4); n = 1, 5; n = 0, 6]. The ability of the electrophilic PtII agents generated in solution to interact with DNA, and hence to form Pt–DNA adducts, was measured as a function of the decrease in the guanine oxidation signal recorded on a screen‐printed electrode by using square wave voltammetry. Hydrolysis of the platinum complexes was studied by using time‐resolved RP‐HPLC and conductivity measurements to determine the aquation rate, which modulates the formation of the electrophilic agent prone to quickly interact with DNA. Our findings indicate that, if time is allowed for sufficient hydrolysis to occur, the interaction of these PtII complexes with ds‐DNA follows the order 2 > 1 > 3 ≈ 4 > 5 >> 6.

A DNA biosensor based on graphene paste electrode modified with Prussian blue and chitosan

A chemically modified graphene paste electrode was prepared by incorporating appropriate amounts of graphene in a paste mixture, followed by electrodepositing Prussian blue (PB) and coating chitosan on the electrode surface. The electrode was able to bind ssDNA, and gave a better voltammetric response for complement DNA than did ordinary carbon paste electrodes. The response of the electrode was characterized with respect to the paste composition, immobilization time of probe DNA on the chitosan and PB modified graphene paste electrode, and the effect of 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC). The electrochemical behavior of PB assembled on the graphene paste electrode was investigated. The combination of graphene and PB can enhance the current response of the graphene paste electrode. As a consequence of DNA hybridization, a significant change in the current due to daunomycin intercalated with double-stranded DNA (ds-DNA) on the surface of the graphene paste electrode was observed.

A DNA biosensor based on the detection of doxorubicin-conjugated Ag nanoparticle labels using solid-state voltammetry

This report describes an electrochemical biosensor for the detection of short DNA oligonucleotide of the avian flu virus H5N1 with sequence 5′-CCA AGC AAC AGA CTC AAA-3′. To fabricate this DNA biosensor, a gold (Au) electrode surface was modified with thiolated DNA probes with a sequence complementary to the target DNA. This modified Au electrode was incubated in a buffer solution containing the target DNA to form double-stranded DNA (ds-DNA) through hybridization. The ds-DNA on the electrode surface was then labeled with silver nanoparticles conjugated with a well-known DNA intercalator, doxorubicin. By performing cyclic voltammetry in an aqueous KCl solution (0.3M), the silver nanoparticle labels were detected as a result of the highly characteristic solid-state Ag/AgCl redox process. The signal obtained was subsequently used to quantify the amount of DNA. A detection limit of 1pM has been achieved with this new DNA biosensor.