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.     

Voltammetric Studies on the Recognition of a Copper Complex to Single‐ and Double‐Stranded DNA and Its Application in Gene Biosensor

A mixed‐ligands copper complex [Cu(phendione)(DAP)]SO₄ (phendione=1,10‐phenanthroline‐5,6‐dione, DAP=2,3‐diaminophenazine) was synthesized. Cyclic voltammetry showed that the complex underwent an obvious decrease of redox peak currents and positive shift of formal potential after interaction with double‐stranded DNA (dsDNA), suggesting that the copper complex behaved as a typical metallointercalator for dsDNA, The recognition properties of the copper complex to single‐stranded DNA (ssDNA) and dsDNA were assessed using surface‐based electrochemical methods and the results suggested that the complex had obviously different redox signals at ssDNA and dsDNA modified electrodes. The copper complex was further used as an electroactive indicator for the detection of cauliflower mosaic virus (CaMV) 35S promoter gene.     

Direct Electrochemical Oxidation of DNA on Polycrystalline Gold Electrodes

Electrochemical CV and SWV studies were performed with double stranded DNA from salmon testes (dsDNA) and single stranded DNAs, containing 25 nucleotides (ssDNA) directly adsorbed at polycrystalline Au electrodes. A distinct oxidation peak at +730 mV (SWV, scan rate 0.248 V s^?1) or at +730 – +780 mV (CV, scan rate from 0.3 to 1 V s^?1) was obtained with DNA‐modified Au electrodes after a time‐dependent prepolarization step at a positive potential value, i.e., at +500 mV (vs. Ag|AgCl), performed with the DNA‐modified Au electrodes dipped in a blank buffer solution. No electrochemical activity was detected when ssDNA, containing no guanines, was used for adsorptive modification of the Au electrodes. Electrochemical impedance measurements registered a possible reorganization of the adsorbed DNA layer in the course of the prepolarization, accompanied by decreasing in‐phase impedance. The results enable us to relate the oxidation process observed at the DNA‐modified Au electrodes with the oxidation of guanine residues in DNA.     

Determination of Electrochemical Interaction between 2‐(1H‐benzimidazol‐2‐yl) Phenol and DNA Sequences

A benzimidazole derivate, 2‐(1H‐benzimidazol‐2‐yl) phenol (2‐Bip) and its interaction mechanism with sequence specific DNA was examined with Differential Pulse Voltammetry (DPV). We, for the first time, investigated the effect of 2‐Bip on sequence specific DNA with electrochemical methods by evaluating both guanine and 2‐Bip oxidation signal changes. In the study, probe sequences were immobilized to the surface of the electrodes and then hybridization was achieved by sending the complementary target onto the probe modified electrodes. Following the hybridization, 2‐Bip solution was interacted with probe and hybrid sequences to see the effect of 2‐Bip on different DNA sequences. The binding constant (K), toxicity (S%) and thermodynamic parameters, i. e., Gibbs free energy (ΔG°) of 2‐Bip‐DNA complexes were evaluated. K was calculated as 5×10⁵ and the change in the ΔG° was found as ?32.50 kJ mol^?1, which are consistent well with the literature. Furthermore, S% showed that 2‐Bip is moderately toxic to single stranded DNA (ssDNA) and toxic to double stranded DNA (dsDNA). From our experimental data, we made four conclusions (i) 2‐Bip affects both ssDNA and dsDNA, (ii) 2‐Bip interaction mode with DNA could be non‐covalent interactions, (iii) 2‐Bip could be used as new DNA hybridization indicator due to its distinct effects on ssDNA and dsDNA, (iv) 2‐Bip could be used as a drug molecule for its DNA effect.     

Low‐Background,Highly Sensitive DNA Biosensor by Using an Electrically Neutral Cobalt(II) Complex as the Redox Hybridization Indicator

An electrically neutral cobalt complex, [Co(GA)₂(phen)] (GA=glycollic acid, phen=1,10‐phenathroline), was synthesized and its interactions with double‐stranded DNA (dsDNA) were studied by using electrochemical methods on a glassy carbon electrode (GCE). We found that [Co(GA)₂(phen)] could intercalate into the DNA duplex through the planar phen ligand with a high binding constant of 6.2(±0.2)×10⁵ M ^?1. Surface studies showed that the cobalt complex could electrochemically accumulate within the modified dsDNA layer, rather than within the single‐stranded DNA (ssDNA) layer. Based on this feature, the complex was applied as a redox‐active hybridization indicator to detect 18‐base oligonucleotides from the CaMV35S promoter gene. This biosensor presented a very low background signal during hybridization detection and could realize the detection over a wide kinetic range from 1.0×10^?14 M to 1.0×10^?8 M , with a low detection limit of 2.0 fM towards the target sequences. The hybridization selectivity experiments further revealed that the complementary sequence, the one‐base‐mismatched sequence, and the non‐complementary sequence could be well‐distinguished by the cobalt‐complex‐based biosensor.     

Impedance‐Based DNA Biosensor Employing Molecular Beacon DNA as Probe and Thionine as Charge Neutralizer

In this paper, we present an impedance‐based DNA biosensor using thionine intercalation to amplify DNA hybridization signal. Beacon single‐stranded DNA (ssDNA) probe and mercaptoacetic acid were self‐assembled onto a Au electrode by forming Au? S bonds. These beacon ssDNAs were hybridized with the complementary sequences around the loop structure. Then thionine was intercalated into the double‐stranded DNA (dsDNA) immobilized on the Au electrode surface. Due to the neutralization of the negative charges of dsDNA by the intercalated thionine, the electronic transfer resistance (R_et) of the DNA modified Au electrode was significantly diminished. Herein, the decreased value of R_et resulted from the thionine intercalating into dsDNA was employed as the hybridization signal. SDS was used to reduce the unspecific adsorption between ssDNA and thionine. Several experimental conditions, including the surface coverage of ssDNA probe on Au electrode, the hybridization temperature and time were all optimized. Moreover, the hybridization reactions of the unstructured linear ssDNA probe and the structured beacon ssDNA probe with their complementary sequences were compared in this work. The sensitivity of the presented DNA biosensor highlighted that the intercalation of thionine into dsDNA was an efficient approach to amplify the hybridization signal using impedance detection technique. Additionally, in this DNA biosensing protocol, beacon ssDNA has a good ability to distinguish target DNA sequences. This results in a higher specificity than using traditional unstructured DNA probe.     

Scanning Electrochemical Microscopy for Electrochemical Detection of Single‐base Mismatches by Tagging Ferrocenecarboxylic Acid as a Redox Probe to DNA

Scanning electrochemical microscopy (SECM) was employed for sensitive detection of single base mismatches (SBMs) in a sandwiched dsDNA. Ferrocenecarboxylic acid (Fc), covalently conjugated to the dsDNA, was oxidized to Fc⁺ via the DNA‐mediated charge transfer from the underlying gold substrate, and reduced back to Fc by SECM tip generated ferrocyanide. The electrocatalytic oxidation of SECM tip‐generated ferrocyanide was sensitive to presence, as well as the type of SBMs. Apparent standard rate constants (k⁰_app) values for different SBMs, both near the electrode surface and far from it, were evaluated by SECM. The method can detect SBMs independent of their position in dsDNA.     

The Ag+-G interaction inhibits the electrocatalytic oxidation of guanine--a novel mechanism for Ag+ detection

The heavy metal ions-nucleobases interaction is an important research topic in environmental and biochemical analysis. The presence of the silver ion (Ag⁺) may influence the formation of oxidation intermediate and the electrocatalytic oxidation activity of guanine (G), since Ag⁺ can interact with guanine at the binding sites which are involved in the electrocatalytic oxidation reaction of guanine. According to this principle, a new electrochemical sensor for indirectly detecting Ag⁺ based on the interaction of Ag⁺ with isolated guanine base using differential pulse voltammetry (DPV) was constructed. Among the heavy metal ions examined, only Ag⁺ showed the strongest inhibitory effect on the electrocatalytic oxidation of guanine at the multi-walled carbon nanotubes modified glassy carbon electrode (CNTs/GC). And the quantitative study of Ag⁺ based on Ag⁺-G sensing system gave a linear range from 100 nM to 2.5 μM with a detection limit of 30 nM. In addition, this modified electrode had very good reproducibility and stability. The developed electrochemical method is an ideal tool for Ag⁺ detection with some merits including remarkable simplicity, low-cost, and no requirement for probe preparation.     

Square Wave Stripping Voltammetry of Unlabeled Single‐ and Double‐Stranded DNAs

We show that, in difference to previously applied electrochemical methods working with stationary electrodes, square wave voltammetry produces well‐developed peaks II_SW (specific for dsDNA) and III_SW yielded by ssDNA at hanging mercury drop electrode (HMDE) and solid amalgam electrodes (SAEs). Using these peaks various kinds of DNA structural transitions can be studied, including unwinding of dsDNA at negatively charged electrode surfaces. The sensitivity of the DNA analysis is much better than that obtained with guanine oxidation signals at carbon electrodes. Both carbon electrodes and SAEs appear attractive as transducers in label‐free RNA and DNA sensors.     

Structural,Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight

Using density functional theory calculations, we investigated the structural, energetic, electronic, and optical properties of recently synthesized duplex DNA containing metal‐mediated base pairs. The studied duplex DNA consists of three imidazole (Im) units linked through metal (Im‐M‐Im, M=metal) and four flanking A:T base pairs (two on each side). We examined the role of artificial base pairing in the presence of two distinctive metal ions, diamagnetic Ag⁺ and magnetic Cu²⁺ ions, on the stability of duplex DNA. We found that metal‐mediated base pairs form stable duplex DNA by direct metal ion coordination to the Im bases. Our results suggest a higher binding stability of base pairing mediated by Cu²⁺ ions than by Ag⁺ ions, which is attributed to a larger extent of orbital hybridization. We furthermore found that DNA modified with Im‐Ag⁺‐Im shows the low‐energy optical absorption characteristic of π–π*orbital transition of WC A:T base pairs. On the other hand, we found that the low‐energy optical absorption peaks for DNA modified with Im‐Cu²⁺‐Im originate from spin–spin interactions. Additionally, this complex exhibits weak ferromagnetic coupling between Cu²⁺ ions and strong spin polarization, which could be used for memory devices. Moreover, analyzing the role of counter ions (Na⁺) and the presence of explicit water molecules on the structural stability and electronic properties of the DNA duplex modified with Im‐Ag⁺‐Im, we found that the impact of these two factors is negligible. Our results are fruitful for understanding the experimental data and suggest a potential route for constructing effective metal‐mediated base pairs in duplex DNA for optoelectronic applications.     

Label‐Free Detection of Nanomolar Unmodified Single‐ and Double‐Stranded DNA by Using Surface‐Enhanced Raman Spectroscopy on Ag and Au Colloids

Unlabelled single‐ and double‐stranded DNA (ssDNA and dsDNA, respectively) has been detected at concentrations ≥10^?9 M by surface‐enhanced Raman spectroscopy. Under appropriate conditions the sequences spontaneously adsorbed to the surface of both Ag and Au colloids through their nucleobases; this allowed highly reproducible spectra with good signal‐to‐noise ratios to be recorded on completely unmodified samples. This eliminated the need to promote absorption by introducing external linkers, such as thiols. The spectra of model ssDNA sequences contained bands of all the bases present and showed systematic changes when the overall base composition was altered. Initial tests also showed that small but reproducible changes could be detected between oligonucleotides with the same bases arranged in a different order. The spectra of five ssDNA sequences that correspond to different strains of the Escherichia coli bacterium were found to be sufficiently composition‐dependent so that they could be differentiated without the need for any advanced multivariate data analysis techniques.     

灿烂甲酚蓝在DNA修饰金电极上的电化学行为

利用自组装技术将巯基乙醇固定在金电极表面形成巯基乙醇自组装膜修饰金电极, 用乙基-(3-二甲基氨丙基)碳二亚胺盐酸盐(EDC)和N-羟基琥珀酰亚胺(NHS)为偶联试剂, 分别将鲱鱼精单链DNA(ssDNA)和双链DNA(dsDNA)固定于金电极表面形成ssDNA和dsDNA 修饰电极. 考察了灿烂甲酚蓝(BCB)在不同DNA 修饰电极上的电化学行为,结果表明, BCB 在ssDNA 和dsDNA 修饰电极上的吸附常数分别为1.67×10^4和3.22×10^4 L·mol-1, BCB 与ssDNA 主要以静电作用结合, 而与dsDNA作用存在静电和嵌插两种模式. dsDNA 对BCB 具有更高的亲和力, 使BCB 可以作为一种有效的电化学杂交指示剂.     

Impedimetric DNA‐Based Biosensor for Silver Ions Detection with Hemin/G‐Quadruplex Nanowire as Enhancer

A DNA‐based biosensor was reported for detection of silver ions (Ag⁺) by electrochemical impedance spectroscopy (EIS) with [Fe(CN)₆]^4?/3? as redox probe and hybridization chain reaction (HCR) induced hemin/G‐quadruplex nanowire as enhanced label. In the present of target Ag⁺, Ag⁺ interacted with cytosine‐cytosine (C? C) mismatch to form the stable C? Ag⁺? C complex with the aim of immobilizing the primer DNA on electrode, which thus triggered the HCR to form inert hemin/G‐quadruplex nanowire with an amplified EIS signal. As a result, the DNA biosensor showed a high sensitivity with the concentration range spanning from 0.1 nM to 100 µM and a detection limit of 0.05 nM.     

Tin oxide nanoparticles-polymer modified single-use sensors for electrochemical monitoring of label-free DNA hybridization

In this study, SnO₂ nanoparticles (SNPs)-poly(vinylferrocenium) (PVF⁺) modified single-use graphite electrodes were developed for electrochemical monitoring of DNA hybridization. The surfaces of polymer modified and polymer-SNP modified pencil graphite electrodes (PGEs) were firstly characterized by using SEM analysis. The electrochemical behaviours of these electrodes were also investigated using the differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques. The polymer-SNP modified PGEs were then tested for the electrochemical sensing of DNA based on the changes at the guanine oxidation signals. Experimental parameters, such as; different modifications in DNA oligonucleotides, DNA probe concentrations were examined to obtain more sensitive and selective electrochemical signals for nucleic acid hybridization. After optimization studies, DNA hybridization was investigated in the case of complementary of hepatitis B virus (HBV) probe, mismatch (MM), and noncomplementary (NC) sequences.     

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^?.     

Electrochemical DNA biosensor for the detection of Listeria Monocytogenes using toluidine blue as a hybridization indicator

An electrochemical DNA biosensor was established for the determination of actin-assembly inducing protein (actA) gene sequences from Listeria monocytogenes and its polymerase chain reaction (PCR) product. The actA gene probe sequences were covalently immobilized on the surface of the mercaptoacetic acid self-assembled gold electrode with the help of N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), which was further used to hybridize with the target sequence. Toluidine blue (TB) was used as an effective electrochemical indicator for the discrimination of the hybridization reaction on the electrode surface, which had stronger interaction with double-stranded DNA (dsDNA) than single-stranded DNA (ssDNA). The electrochemical parameters of TB on DNA modified electrodes were carefully calculated. Based on the different electrochemical responses of TB on DNA modified electrodes, the actA gene sequences can be detected in the concentration range from 1.0 × 10^-7 to 8.0 × 10^-5 M. The PCR product of Listeria monocytogenes was successfully detected by the proposed electrochemical biosensor.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

A Reusable DNA Single‐Walled Carbon‐Nanotube‐Based Fluorescent Sensor for Highly Sensitive and Selective Detection of Ag+ and Cysteine in Aqueous Solutions

Here we report a reusable DNA single‐walled carbon nanotube (SWNT)‐based fluorescent sensor for highly sensitive and selective detection of Ag⁺ and cysteine (Cys) in aqueous solution. SWNTs can effectively quench the fluorescence of dye‐labeled single‐stranded DNA due to their strong π–π stacking interactions. However, upon incubation with Ag⁺, Ag⁺ can induce stable duplex formation mediated by C–Ag⁺–C (C=cytosine) coordination chemistry, which has been further confirmed by DNA melting studies. This weakens the interactions between DNA and SWNTs, and thus activates the sensor fluorescence. On the other hand, because Cys is a strong Ag⁺ binder, it can remove Ag⁺ from C–Ag⁺–C base pairs and deactivates the sensor fluorescence by rewrapping the dye‐labeled oligonucleotides around the SWNT. In this way, the fluorescence signal‐on and signal‐off of a DNA/SWNT sensor can be used to detect aqueous Ag⁺ and Cys, respectively. This sensing platform exhibits high sensitivity and selectivity toward Ag⁺ and Cys versus other metal ions and the other 19 natural amino acids, with a limit of detection of 1 nM for Ag⁺ and 9.5 nM for Cys. Based on these results, we have constructed a reusable fluorescent sensor by using the covalent‐linked SWNT–DNA conjugates according to the same sensing mechanism. There is no report on the use of SWNT–DNA assays for the detection of Ag⁺ and Cys. This assay is simple, effective, and reusable, and can in principle be used to detect other metal ions by substituting C–C base pairs with other native or artificial bases that selectively bind to other metal ions.     

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.     

Voltammetric Detection of Captopril on Graphite Screen Printed Electrodes

We report the electrochemical detection of captopril on commercially available screen printed electrodes (GSPE); it exploits the silver residue left behind on a GSPE during its manufacturing process and involves the catalytic formation of the silver thiol complex (Ag⁺+RSH→AgSR+H⁺) at potentials corresponding to the oxidation of silver. The oxidation of the silver thiol complex was found to vary linearly with the captopril concentration up to 0.8 mM. A sensitivity of 13.34±0.58 μA mM^?1 is reported with a limit of detection of 4.27±0.18 μM.