Electrochemical genosensor for the detection of interaction between methylene blue and DNA

Described here are the chronocoulometric and voltammetric parameters for methylene blue [3,7-bis(dimethylamino)phenothiazin-5-ium chloride, MB] on binding to DNA at carbon paste electrode (CPE) surface. MB, which interacts with the immobilized calf thymus DNA was detected by using single stranded DNA modified CPE (ssDNA modified CPE), bare CPE and double stranded DNA modified CPE (dsDNA modified CPE) in combination with chronocoulometry and differential pulse voltammetry (DPV) techniques. The effect of ionic strength to the behavior of MB with dsDNA and ssDNA was also studied by means of voltammetry. These results demonstrated that MB could be used as an effective electroactive hybridization indicator for DNA biosensors. Performance characteristics of the sensor are described, along with future prospects.     

Electrochemical characteristics of the immobilization of calf thymus DNA molecules on multi-walled carbon nanotubes

Immobilization of DNA on carbon nanotubes plays an important role in the development of new types of miniature DNA biosensors. Electrochemical characteristics of the immobilization of calf thymus DNA molecules on the surfaces of multi-walled carbon nanotubes (MWNTs) have been investigated by cyclic voltammetry and electrochemical impedance analysis. The peak currents for Fe(CN)(6)(3-)/Fe(CN)(6)(4-) redox couple observed in the cyclic voltammograms decrease and the electron-transfer resistance (R(et)) obtained from the Nyquist plots increase due to the immobilization of DNA molecules (dsDNA or ssDNA) on the surfaces of MWNTs. Most of calf thymus DNA are covalently immobilized on MWNTs via diimide-activated amidation between the carboxylic acid groups on the carbon nanotubes and the amino groups on DNA bases, though the direct adsorption of the DNA molecules on MWNTs can be observed. Additionally, the interaction between DNA molecules immobilized on MWNTs and small biomolecules (ethidium bromide) can be observed obviously by cyclic voltammetry and electrochemical impedance analysis. This implies that the DNA molecules immobilized at the surface of MWNTs, with little structure change, still has the ability to interact with small biomolecules.     

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.     

Electrochemical DNA biosensor for polycyclic aromatic hydrocarbon detection

Four DNA electrochemical biosensors using four types of DNA (calf thymus ssDNA, calf thymus dsDNA, salmon testis ssDNA and salmon testis dsDNA) were constructed using graphite screen printed electrodes. These biosensors were exploited as analytical tool to detect polycyclic aromatic hydrocarbons-DNA interactions using benzo(a)anthracene and phenantrene as model analytes, the guanine oxidation peak variation being the signal revealing the interaction between PAHs and immobilized DNA. The salmon testis ssDNA biosensor resulted as the most promising device and was further evaluated for benzo(a)anthracene, fluorene, indeno(1,2,3-cd)pyrene, anthracene, and phenanthrene in 5–40 ng mL^?1 solutions, and for benzo(a)pyrene (5–50 ng mL^?1). A concentration dependent variation of the DNA guanine oxidation peak was observed for all compounds. The effect of benzo(a)pyrene ultraviolet (UV) activation on the benzo(a)pyrene (BaP)-DNA interaction was evaluated at concentration levels of 20 and 50 ng mL^?1, and a 3.5- and 2.7-fold increases of the guanine oxidation peak was measured respectively. The salmon testis ssDNA biosensor was examined with PAHs contaminated samples of Mytilus galloprovincialis. Upon UV irradiation of three sample extracts exceeding the BaP maximum level, a positive variation of the DNA guanine oxidation was obtained. An average 2.4-fold increase of the guanine oxidation peak was detected demonstrating that the sensor can be used to detect toxic degradation products of PAHs.     

高序热解石墨与玻碳电极上DNA的氧化和吸附行为

在高序热解石墨（ＨＯＰＧ）电极上,采用微分脉冲伏安法（ＤＰＶ）和电化学原子显微镜法（ＥＣＡＦＭ）探究小牛胸腺ＤＮＡ（ＣＴ ＤＮＡ）在电极表面的吸附。实验发现,控制电位下预极化对双链ＤＮＡ和ＨＯＰＧ电极上的吸附有很大的影响。而对单链ＤＮＡ影响不大。实验表明,在ＨＯＰＧ电极上ＥＡＦＭ是ＤＮＡ研究领域十分有用的技术,根据ＡＦＭ图象,结合文献上的ＤＮＡ吸附模型提出了ＣＴ ＤＮＡ研究领域十分有用的技术,根据     

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.     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

Investigation of Metal Ion Effect on Specific DNA Sequences and DNA Hybridization

In this article, we investigated the sequence specific interaction of single (ssDNA) and double stranded (dsDNA) with silver ions (Ag⁺) with electrochemical methods. We, for the first time, examined the effect of base sequences, base content and physiochemical properties of different DNA sequences on interaction with Ag⁺ in detail. We used different base contents to show how the composition of nucleic acid influences the electrochemical signals. We first immobilized ssDNA probes on bare graphite electrodes. Then, we showed the sequence effect on oxidation signals of AgDNA complex by sensing Ag⁺ to the probe coated surfaces to interact with different ssDNA sequences. Furthermore, we investigated the effect of Ag⁺ on dsDNA. We measured the oxidation signals obtained from Ag⁺‐ssDNA and Ag⁺‐dsDNA complex at approximately 0.2 V and 1.0 V (vs Ag/AgCl), respectively with Differential Pulse Voltammetry (DPV). We showed that the oxidation signals of the AgDNA complex obtained from dsDNA‐modified electrodes is higher than the electrodes modified with ssDNA. More importantly, we showed that Ag⁺‐ssDNA and Ag⁺ ion‐dsDNA exhibit different electrochemical behaviors.     

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.     

Square wave and elimination voltammetric analysis of azidothymidine in the presence of oligonucleotides and chromosomal DNA

Azidothymidine (AZT, 3'-azido-3'-deoxythymidine, Zidovudine, Retrovir) is an approved and widely used antiretroviral drug for the treatment of human immunodeficiency virus (HIV) infection. Dynamic electrochemical methods have been employed for the fast and inexpensive determination of this drug in natural samples. The electrochemical signal of AZT, resulting from the reduction of azido group, was studied by square wave voltammetry (SWV), linear sweep voltammetry (LSV) and elimination voltammetry with linear scan (EVLS) using a hanging mercury drop electrode (HMDE). This paper explores the possibility of determining AZT in the presence of native (dsDNA) or denatured calf thymus DNA (ssDNA), and/or some synthetic oligodeoxynucleotides (ODNs). The detection limit of AZT in the absence and in the presence of ssDNA (10 microg/ml) is 1 and 250 nM, respectively. It was found that the signal of AZT is not substantially affected by the presence of DNA. We can therefore assume that the electrons are transferred through the adsorption layer of nucleic acids. By using the elimination procedure, both irreversible reduction signals of AZT and DNA are augmented. Moreover, the elimination signal in the peak-counterpeak form may indicate the adsorption of the analytes on the electrode surface preceding an electron transfer.     

Sensitive detection of cyclophosphamide using DNA-modified carbon paste, pencil graphite and hanging mercury drop electrodes

The interaction of cyclophosphamide (CP) with calf thymus double-stranded DNA (dsDNA) and thermally denatured single-stranded DNA (ssDNA) immobilized at the carbon paste (CPE) and pencil graphite electrodes (PGE), was studied electrochemically based on oxidation signals of guanine and adenine using differential pulse voltammetry (DPV).As a result of the interaction of CP with DNA, the voltammetric signals of guanine and adenine increased in the case of dsDNA while a slight increase was observed in ssDNA. The effect of experimental parameters such as the interaction time between CP and DNA forms and the concentration of CP, were studied using DPV with CPE and PGE. Additionally, reproducibility and detection limits were determined using both electrodes. A comparison of the analytical performance between CPE and PGE was done. Our results showed that these two different DNA biosensors could be used for the sensitive, rapid and cost effective detection of CP itself as well as of CP-DNA interaction.Furthermore, the interaction of CP with dsDNA and ssDNA was studied in solution and at the electrode surface by means of alternating current voltammetry (ACV) in 0.3 M NaCl and 50 mM sodium phosphate buffer (pH 8.5) supporting electrolyte, using a hanging mercury drop electrode (HMDE) as working electrode.The conclusions of this study were mainly based on tensammetric peaks I (at −1.183 V) and II (−1.419 V) of DNA. This study involved the interaction of CP with surface-confined and solution phase DNA where experimental parameters, such as the concentration of CP and the interaction time, were studied. By increasing the concentration of CP, an increase of peak II was observed in both ds and ssDNA, while an increase of peak I was observed only in the case of dsDNA. An overall conclusion of the study using HMDE was that the interaction of CP with surface-confined DNA significantly differed from that with solution phase DNA. The increase of peaks I and II was lower in the case of interaction of CP with surface-confined DNA, probably due to steric positioning of DNA at the electrode surface.     

Resonance light scattering spectroscopy study of interaction between norfloxacin and calf thymus DNA and its analytical application

The interaction between norfloxacin and calf thymus double-stranded DNA (dsDNA) has been studied by a resonance light scattering (RLS) technique with a common spectrofluorometer. The characteristics of RLS spectra, the effective factors and optimum conditions of the reaction have been investigated. In Britton-Robinson (BR) buffer (pH 5.87), norfloxacin has a maximum peak 405.5 nm and the RLS intensity is remarkably enhanced by trace amount of calf thymus dsDNA due to the interaction between norfloxacin and dsDNA. The binding of norfloxacin to DNA forms large particles, which were characterized by RLS spectrum, scanning electron microscopy (SEM), ultraviolet-visible (UV-vis) spectrum, and fluorescence spectrum. Based on the enhanced RLS intensity, a novel method for sensitive determination of calf thymus dsDNA concentration ranging from 0.02 to 2.3 microg ml(-1) was developed. The determination limit (3 sigma) was 1.2 ng ml(-1). The method is simple, rapid, practical and relatively free from interference generated by coexisting substance, as well as much more sensitive than most of the reported methods. Three synthetic samples of ctDNA were determined with satisfactory results.     

Interaction of the mutagen ethidium bromide with DNA, using a carbon paste electrode and a hanging mercury drop electrode

The interaction of ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide; EB) with double stranded (ds) calf thymus DNA and thermally denatured single stranded (ss) DNA was studied in solution and at the electrode surface by means of transfer voltammetry using a carbon paste electrode (CPE) as working electrode in 0.2 M acetate buffer, pH 5.0. As a result of intercalation of this dye between the base pairs of dsDNA, the characteristic peak of dsDNA, due to the oxidation of guanine residues, decreased and after a particular concentration of EB a new peak at +0.81 V appeared, probably due to the formation of a complex between dsDNA and EB. The non-intercalated EB gives another peak, but at an increased concentration of the dye. A similar behaviour was observed during the interaction of the dye with ssDNA.Furthermore, the interaction of EB with ds, ss and supercoiled (sc) DNA was studied at the hanging mercury drop electrode (HMDE) surface by means of alternating current voltammetry in 0.3 M NaCl and 50 mM sodium phosphate buffer (pH 8.5) as supporting electrolyte. dsDNA yields a smaller peak at −1.42 V (peak III) compared to the one yielded by ssDNA, since the latter is a relaxed and more accessible form. By addition of EB into the buffer solution an increase of peak III was observed in the dsDNA form as well as in ssDNA resulting from their interaction with EB. Furthermore, the appearance of peak III in covalently closed circular scDNA after exposure to increasing concentrations of EB is a result of the introduction of ‘free ends’ in DNA affecting its structural integrity.     

Fluorimetric determinations of nucleic acids using iron, osmium and samarium complexes of 4,7-diphenyl-1,10-phenanthroline

New sensitive, reliable and reproducible fluorimetric methods for determining microgram amounts of nucleic acids based on their reactions with Fe(II), Os(III) or Sm(III) complexes of 4,7-diphenyl-1,10-phenanthroline are proposed. Two complementary single stranded synthetic DNA sequences based on calf thymus as well as their hybridized double stranded were used. Nucleic acids were found to react instantaneously at room temperature in Tris-Cl buffer pH 7, with the investigated complexes resulting in decreasing their fluorescence emission. Two fluorescence peaks around 388 and 567 nm were obtained for the three complexes using excitation lambda(max) of 280 nm and were used for this investigation. Linear calibration graphs in the range 1-6 microg/ml were obtained. Detection limits of 0.35-0.98 microg/ml were obtained. Using the calibration graphs for the synthetic dsDNA, relative standard deviations of 2.0-5.0% were obtained for analyzing DNA in the extraction products from calf thymus and human blood. Corresponding Recovery% of 80-114 were obtained. Student's t-values at 95% confidence level showed insignificant difference between the real and measured values. Results obtained by these methods were compared with the ethidium bromide method using the F-test and satisfactory results were obtained. The association constants and number of binding sites of synthetic ssDNA and dsDNA with the three complexes were estimated using Rosenthanl graphic method. The interaction mechanism was discussed and an intercalation mechanism was suggested for the binding reaction between nucleic acids and the three complexes.     

Packing structures of single-stranded DNA and double-stranded DNA thiolates on Au(111): a molecular simulation study

The packing structures of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) thiolates on implicit gold surfaces were studied in explicit aqueous solutions of 1M NaCl using molecular dynamics simulations. The simulations were based on individual DNA chains placed in hexagonal simulation boxes of different sizes, representing various packing densities. The total potential energy per DNA chain was compared. The optimal packing structures were determined based on the minimal potential energy within the limits of the conditions that were evaluated in this study. The optimal packing density of ssDNA was found to be 0.19 DNA chains/nm(2), which is consistent with that determined experimentally. Furthermore, the optimal packing density of dsDNA was shown to be approximately 58% of the packing density for ssDNA, indicating that the packing of ssDNA should be approximately 58% of its optimal packing in order to achieve the best hybridization.     

Determination of DNA Hypermethylation Using Anti‐cancer Drug‐Temozolomide

An electrochemical drug‐DNA biosensor was developed for the detection of interaction between the anti‐cancer drug, Temozolomide (TMZ), and DNA sequences by using Differential Pulse Voltammetry at the graphite electrode surfaces. TMZ is a pro‐drug and an alkylating agent that crosses the blood‐brain barrier, so it is mainly used for brain cancers treatment. In this study, we aim to develop a‐proof‐of‐concept study to investigate the effect of TMZ on formerly methylated DNA sequences since TMZ shows its anti‐cancer activity by methylating the DNA. Interaction between TMZ and DNA causes localized distortion of DNA away from an idealized B‐form, resulting in a wider major groove and greater steric accessibility of functional groups in the base of the groove. According to the results, TMZ behaves as a ‘hybridization indicator’ because of its different electrochemical behavior to different strands of DNA. After interaction with TMZ, hybrid (double stranded DNA‐dsDNA) signals decreased dramatically whereas probe (single stranded DNA‐ssDNA) and control signals remain almost unchanged. The signal differences enabled us to distinguish ssDNA and dsDNA without using a label or tag. It is the first study to demonstrate the interaction between the TMZ and dsDNA created from probe and target. We use specific oligonucleotides sequences instead of using long dsDNA sequences.     

抗癌药物4'-O-(α-L-夹竹桃糖基)柔红霉素与小牛胸腺DNA相互作用的荧光光谱法

在pH=7.4的Tris-HCl介质中,利用荧光光谱和紫外吸收光谱法,研究了一种新型蒽环类抗癌药物柔红霉素衍生物(4′-O-(α-L-夹竹桃糖基)柔红霉素,ODNR)与小牛胸腺DNA(ctDNA)的相互作用。 通过离子强度的影响、KI荧光猝灭实验和单双链ctDNA作用的比较实验,分析了ODNR与ctDNA的相互作用模式。 结果表明,ODNR通过嵌插方式与ctDNA发生作用。 ctDNA对ODNR的荧光有明显的猝灭作用,其机理属于静态猝灭。 通过Scatchard方程求得不同温度下的结合常数和结合位点数,由热力学参数确定分子间作用力为疏水作用,也可能存在静电作用。     

ssDNA binding reveals the atomic structure of graphene

We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the π-π stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the π-π stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures.     

Tethered thiazole orange intercalating dye for development of fibre-optic nucleic acid biosensors

Single-stranded DNA (ssDNA) oligonucleotide in solution, or that is immobilized onto a surface to create a biosensor, can be used as a selective probe to bind to a complementary single-stranded sequence. Fluorescence enhancement of thiazole orange (TO) occurs when the dye intercalates into double-stranded DNA (dsDNA). TO dye has been covalently attached to probe oligonucleotides (homopolymer and mixed base 10mer and 20mer) through the 5′ terminal phosphate group using polyethylene glycol linker. The tethered TO dye was able to intercalate when dsDNA formed in solution, and also at fused silica surfaces using immobilized ssDNA. The results indicated the potential for development of a self-contained biosensor where the fluorescent label was available as part of the immobilized oligonucleotide probe chemistry. The approach was shown to be able to operate in a reversible manner for multiple cycles of detection of targeted DNA sequences.     

Conformational change detection of DNA with the fluorogenic reagent of o-phthalaldehyde-beta-mercaptoethanol

o-Phthalaldehyde-beta-mercaptoethanol (OPAME) as a fluorogenic reagent has been found wide applications in the detection of amino acids based on its reaction with primary amino groups. In this contribution, we report our new findings concerning the reactions of OPAME with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), respectively. It has been found that ssDNA can react with OPAME easily as a result of giving rise to strong fluorescence emissions, while dsDNA, prepared by hybridizing ssDNA with its complementary target prior to the reaction, displays inert chemical activity and gives out weak fluorescence emission. Mechanism investigations have shown that the reaction activity between OPAME and DNA depends on the amino groups that are related to the conformation of uncoiled and exposed extent of DNA structure, and thus the inert chemical activity of dsDNA results from screening of the dsDNA bases in the interior of the double strands. Therefore, we could design a way to detect conformation change of DNA with OPAME and further develop a novel, simple label-free sequence detection method for complementary and single-base mismatched ssDNA in the hybridization of DNA.