Electrochemical oxidation of guanine: electrode reaction mechanism and tailoring carbon electrode surfaces to switch between adsorptive and diffusional responses

May DNA analyses be biased by hidden oxidative damage? Voltammetric study of temperature and oxidation stress effect

The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on the condition of the genetic material. All potential damage induced by oxidative stress may affect the final results of the analysis of genetic material obtained using commonly used techniques such as polymerase chain reaction or sequencing. The aim of this work was to evaluate the effects of high temperature and pH on DNA structure in the context of the occurrence of oxidative damage, using square-wave voltammetry and two independent research protocols. We resulted in visible oxidation damage registered in acidic conditions after the thermal denaturation process (pH 4.7) with changes in the intensity of guanine and adenine signals. However, using phosphate buffer (pH 7.0) for DNA denaturation negatively affected the DNA structure, but without any oxidized derivatives present. This leads to the conclusion that oxidation occurring in the DNA melting process results in the formation of various derivatives of nucleobases, both electrochemically active and inactive. These derivatives may distort the results of molecular tests due to the possibility of forming complementary bonds with various nucleobases. For example, 8-oxoguanine can form pairs with both cytosine and adenine.

Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA

The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.

Electrochemical Profiling of Plants

The profiling, or fingerprinting, of distinct varieties of the Plantae kingdom is based on the bioactive ingredients, which are systematically segregated to perform their detailed analysis. The secondary products portray a pivotal role in defining the ecophysiology of distinct plant species. There is a crucial role of the profiling domain in understanding the various features, characteristics, and conditions related to plants. Advancements in variable technologies have contributed to the development of highly specific sensors for the non-invasive detection of molecules. Furthermore, many hyphenated techniques have led to the development of highly specific integrated systems that allow multiplexed detection, such as high-performance liquid chromatography, gas chromatography, etc., which are quite cumbersome and un-economical. In contrast, electrochemical sensors are a promising alternative which are capable of performing the precise recognition of compounds due to efficient signal transduction. However, due to a few bottlenecks in understanding the principles and non-redox features of minimal metabolites, the area has not been explored. This review article provides an insight to the electrochemical basis of plants in comparison with other traditional approaches and with necessary positive and negative outlooks. Studies consisting of the idea of merging the fields are limited; hence, relevant non-phytochemical reports are included for a better comparison of reports to broaden the scope of this work.

Understanding Carbon Nanotube Voltammetry: Distinguishing Adsorptive and Thin Layer Effects via "Single-Entity" Electrochemistry

Cyclic voltammetry of ensembles of nanotube-modified electrodes fails to distinguish between signals from electroactive material adsorbed on the tubes from those due to a thin-layer response of analyte material occluded in the pores of the ensemble. We demonstrate that the distinction can be clearly made by combining cyclic voltammetry with single-entity measurements and provide proof of concept for the case of b-MWCNTs and the oxidation of 4-hexylresorcinol (HR), where the increased signals seen at the modified electrode are concluded to arise from thin-layer diffusion and not adsorptive effects. The physical insights are generic to porous, conductive composites.

Defects in graphene-based heterostructures: topological and geometrical effects

The combination of graphene (Gr) and graphene-like materials provides the possibility of using two-dimensional (2D) atomic layer building blocks to create unprecedented architectures. The most attractive characteristics are strongly dependent on the various spatial structures, mainly including in-plane heterostructures butt-joined at the side of an atomic monolayer through covalent bonds, van der Waals (vdW) heterostructures involving a vertically stacked hybrid structure, and their combinations. Heterostructures can not only overcome the limitations inherent to each material but may also obtain new features by appropriate material combination. However, heterostructures made of vdW force superposition or covalent bond splicing are prone to defects. The introduction of external and internal defects causes local deformation and stress in the material, thereby affecting the physical properties of the material, such as its transport properties and mechanical properties. Therefore, research, utilization and control of these defects are highly critical. This paper reviews the vacancy, topological and geometrical effects of defects in modulating the structures and mechanical responses of Gr-based heterostructures. Moreover, the coupling effects of various defects on the Gr-based heterostructures in multi-physics fields are also discussed. This work aims to improve the understanding of the physical mechanism of defective configurations and their association in low dimensions, so as to realize various configurations and to aid the search for new usages.

The combination of graphene (Gr) and graphene-like materials provides the possibility of using two-dimensional (2D) atomic layer building blocks to create unprecedented architectures.

Kinetics and Mechanism of Plasmon-Driven Dehalogenation Reaction of Brominated Purine Nucleobases on Ag and Au

Plasmon-driven photocatalysis is an emerging and promising application of noble metal nanoparticles (NPs). An understanding of the fundamental aspects of plasmon interaction with molecules and factors controlling their reaction rate in a heterogeneous system is of high importance. Therefore, the dehalogenation kinetics of 8-bromoguanine (BrGua) and 8-bromoadenine (BrAde) on aggregated surfaces of silver (Ag) and gold (Au) NPs have been studied to understand the reaction kinetics and the underlying reaction mechanism prevalent in heterogeneous reaction systems induced by plasmons monitored by surface enhanced Raman scattering (SERS). We conclude that the time-average constant concentration of hot electrons and the time scale of dissociation of transient negative ions (TNI) are crucial in defining the reaction rate law based on a proposed kinetic model. An overall higher reaction rate of dehalogenation is observed on Ag compared with Au, which is explained by the favorable hot-hole scavenging by the reaction product and the byproduct. We therefore arrive at the conclusion that insufficient hole deactivation could retard the reaction rate significantly, marking itself as rate-determining step for the overall reaction. The wavelength dependency of the reaction rate normalized to absorbed optical power indicates the nonthermal nature of the plasmon-driven reaction. The study therefore lays a general approach toward understanding the kinetics and reaction mechanism of a plasmon-driven reaction in a heterogeneous system, and furthermore, it leads to a better understanding of the reactivity of brominated purine derivatives on Ag and Au, which could in the future be exploited, for example, in plasmon-assisted cancer therapy.

Electroanalysis of Biomolecules: Rational Selection of Sensor Construction

Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.

Rational Design of Amphiphilic Diblock Copolymer/MWCNT Surface Modifiers and Their Application for Direct Electrochemical Sensing of DNA

We demonstrate the application of amphiphilic ionic poly(n-butylmethacrylate)-block- poly(2-(dimethylamino)ethyl methacrylate) diblock copolymers (PnBMA₄₀-b-PDMAEMA₄₀, PnBMA₄₀-b-PDMAEMA₁₂₀, PnBMA₇₀-b-PDMAEMA₁₂₀) for dispersing multiwalled carbon nanotubes (MWCNTs) in aqueous media, a subsequent efficient surface modification of screen-printed electrodes (SPEs), and the application of the modified SPEs for DNA electrochemistry. Stable and fine aqueous dispersions of MWCNTs were obtained with PnBMA_x-b-PDMAEMA_y diblock copolymers, regardless of the structure of the copolymer and the amount of MWCNTs in the dispersions. The effect of the diblock copolymer structure was important when the dispersions of MWCNTs were deposited as modifying layers on surfaces of SPEs, resulting in considerable increases of the electroactive surface areas and great acceleration of the electron transfer rate. The SPE/(PnBMA_x-b-PDMAEMA_y + MWCNT) constructs were further exploited for direct electrochemical oxidation of the guanine (G) and adenine (A) residues in a model salmon sperm double-stranded DNA (dsDNA). Two well-defined irreversible oxidation peaks were observed at about +600 and +900 mV, corresponding to the electrochemical oxidation of G and A residues, respectively. A multi-parametric optimization of dsDNA electrochemistry enables one to get the limits of detection (LOD) as low as 5 μg/mL (0.25 μM) and 1 μg/mL (0.05 μM) for G and A residues, respectively. The achieved sensitivity of DNA assay enables quantification of the A and G residues of dsDNA in the presence of human serum and DNA in isolated human leukocytes.

Subsecond detection of guanosine using fast-scan cyclic voltammetry

Guanosine is an important neuromodulator and neuroprotector in the brain and is involved in many pathological conditions, including ischemia and neuroinflammation. Traditional methods to detect guanosine in the brain, like HPLC, offer low limits of detection and are robust; however, subsecond detection is not possible. Here, we present a method for detecting rapid fluctuations of guanosine concentration in real-time using fast-scan cyclic voltammetry (FSCV) at carbon-fiber microelectrodes. The optimized waveform scanned from -0.4 V to 1.3 V and back at a rate of 400 V s-1 and application frequency of 10 Hz. Potential limits were chosen to increase selectivity of guanosine over the structurally similar interferent adenosine. Two oxidation peaks were detected with the optimized waveform: the primary oxidation reaction occurred at 1.3 V and the secondary oxidation at 0.8 V. Guanosine detection was stable over time with a limit of detection of 30 ± 10 nM, which permits its use to monitor low nanomolar fluctuations in the brain. To demonstrate the feasibility of the method for in-tissue detection, guanosine was exogenously applied and detected within live rat brain slices. This paper demonstrates the first characterization of guanosine using FSCV, and will be a valuable method for measuring signaling dynamics during guanosine neuromodulation and protection.

Molecular methods in electrochemical microRNA detection

High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.

Puzzling Aqueous Solubility of Guanine Obscured by the Formation of Nanoparticles

Dissolution of guanine in neutral solutions was obscured by peculiar behavior of guanine, indicating an apparent dependence of solubility on the amount of solid guanine used. Here, we demonstrate that the problem is caused by the formation of tiny guanine nanoparticles that tend to grow forming stable particles of ca. 800 nm size. This effect can be minimalized by using small quantities of guanine powder for dissolution. We also show that assuming a constant, independent of pH, concentration of neutral form of guanine, at 25 °C equal 25.4 μM, and applying known p K_a values related to its dissociation or protonation, it is possible to calculate the concentrations of all conjugate acids and bases of guanine at the given pH value, and by summing them up, the guanine solubility.

Electrochemical impedance-based DNA sensor using pyrrolidinyl peptide nucleic acids for tuberculosis detection

A label-free electrochemical DNA sensor based on pyrrolidinyl peptide nucleic acid (acpcPNA)-immobilized on a paper-based analytical device (PAD) was developed. Unlike previous PNA-based electrochemical PAD (ePAD) sensors where the capture element was placed directly on the electrode, acpcPNA was covalently immobilized onto partially oxidized cellulose paper allowing regeneration by simple PAD replacement. As an example application, a sensor probe was designed for Mycobacterium tuberculosis (MTB) detection. The ePAD DNA sensor was used to determine a synthetic 15-base oligonucleotide of MTB by measuring the fractional change in the charge transfer resistance (R_ct) obtained from electrochemical impedance spectroscopy (EIS). The R_ct of [Fe(CN)₆]^3-/4- before and after hybridization with the target DNA could be clearly distinguished. Cyclic voltammetry (CV) was used to verify the EIS results, and showed an increase in peak potential splitting in a similar stepwise manner for each immobilization step. Under optimal conditions, a linear calibration curve in the range of 2-200 nM and the limit of detection 1.24 nM were measured. The acpcPNA probe exhibited very high selectivity for complementary oligonucleotides over single-base-mismatch, two-base-mismatch and non-complementary DNA targets due to the conformationally constrained structure of the acpcPNA. Moreover, the ePAD DNA sensor platform was successfully applied to detect PCR-amplified MTB DNA extracted from clinical samples. The proposed paper-based electrochemical DNA sensor has potential to be an alternative device for low-cost, simple, label-free, sensitive and selective DNA sensor.

Can the mechanical activation (polishing) of screen-printed electrodes enhance their electroanalytical response?

The mechanical activation (polishing) of screen-printed electrodes (SPEs) is explored and shown to exhibit an improved voltammetric response (in specific cases) when polished with either commonly available alumina slurry or diamond spray. Proof-of-concept is demonstrated for the electrochemical sensing of nitrite where an increase in the voltammetric current is found using both polishing protocols, exhibiting an improved limit of detection (3σ) and a two-fold increase in the electroanalytical sensitivity compared to the respective un-polished counterpart. It is found that mechanical activation/polishing increases the C/O ratio which significantly affects inner-sphere electrochemical probes only (whereas outer-sphere systems remain unaffected). Mechanical activation/polishing has the potential to be a simple pre-treatment technique that can be extended and routinely applied towards other analytes for an observable improvement in the electroanalytical response.

DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids

Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.

Paper-Based Sensing Device for Electrochemical Detection of Oxidative Stress Biomarker 8-Hydroxy-2'-deoxyguanosine (8-OHdG) in Point-of-Care

This work presents a cost-effective, label-free in point-of-care (POC) biosensor for the sensitive detection of 8-hydroxy-2′-deoxyguanosine (8-OHdG), the most abundant oxidative product of DNA, that may allow a premature assessment of cancer disease, thereby improving diagnosis, prognostics and survival rates. The device targets the direct detection of 8-OHdG by using for the first time a carbon-ink 3-electrode on a paper substrate coupled to Differential Pulse Voltammetry readings. This design was optimized by adding nanostructured carbon materials to the ink and the conducting polymer PEDOT, enhancing the electrocatalytic properties of the sensor towards 8-OHdG detection. Meanwhile, the ability of this oxidative stress biomarker to undertake an oxidation reaction enabled the development of the sensing electrochemical device without the need of chemical probes and long incubation periods. This paper-modified sensor presented high electrochemical performance on the oxidation of 8-OHdG with a wide linear range (50–1000 ng/ml) and a low detection limit (14.4 ng/ml). Thus, our results showed the development of a direct and facile sensor with good reproducibility, stability, sensitivity and more importantly, selectivity. The proposed carbon-based electrochemical sensor is a potential candidate to be miniaturized to small portable size, which make it applicable for in-situ 8-OHdG sensing in real biological samples.

Boron-Enhanced Growth of Micron-Scale Carbon-Based Nanowalls: A Route toward High Rates of Electrochemical Biosensing

In this study, we have demonstrated the fabrication of novel materials called boron-doped carbon nanowalls (B:CNWs), which are characterized by remarkable electrochemical properties such as high standard rate constant (k°), low peak-to-peak separation value (ΔE) for the oxidation and reduction processes of the [Fe(CN)₆]^3-/4- redox system, and low surface resistivity. The B:CNW samples were deposited by the microwave plasma-assisted chemical vapor deposition (CVD) using a gas mixture of H₂/CH₄/B₂H₆ and N₂. Growth results in sharp-edged, flat, and long CNWs rich in sp² as well as sp³ hybridized phases. The achieved high values of k° (1.1 × 10^-2 cm s^-1) and ΔE (85 mV) are much lower compared to those of the glassy carbon or undoped CNWs. The enhanced electrochemical performance of the B:CNW electrode facilitates the simultaneous detection of DNA purine bases: adenine and guanine. Both separated oxidation peaks for the independent determination of guanine and adenine were observed by means of cyclic voltammetry or differential pulse voltammetry. It is worth noting that the determined sensitivities and the current densities were about 1 order of magnitude higher than those registered by other electrodes.

Guanosine radical reactivity explored by pulse radiolysis coupled with transient electrochemistry

We follow the reactivity of a guanosine radical created by a radiolytic electron pulse both by spectroscopic and electrochemical methods. This original approach allows us to demonstrate that there is a competition between oxidation and reduction of these intermediates, an important result to further analyse the degradation or repair pathways of DNA bases.

Electrochemical investigations of 8-hydroxydeoxyguanosine and its determination at an edge plane pyrolytic graphite electrode

Electrochemical oxidation of 8-hydroxydeoxyguanosine (8-OHdG) and its detection with low detection limit is reported at pyrolytic graphite electrode.

Recent Advances in Voltammetry

Recent progress in the theory and practice of voltammetry is surveyed and evaluated. The transformation over the last decade of the level of modelling and simulation of experiments has realised major advances such that electrochemical techniques can be fully developed and applied to real chemical problems of distinct complexity. This review focuses on the topic areas of: multistep electrochemical processes, voltammetry in ionic liquids, the development and interpretation of theories of electron transfer (Butler-Volmer and Marcus-Hush), advances in voltammetric pulse techniques, stochastic random walk models of diffusion, the influence of migration under conditions of low support, voltammetry at rough and porous electrodes, and nanoparticle electrochemistry. The review of the latter field encompasses both the study of nanoparticle-modified electrodes, including stripping voltammetry and the new technique of 'nano-impacts'.

Functionalized solid electrodes for electrochemical biosensing of purine nucleobases and their analogues: a review

Interest in electrochemical analysis of purine nucleobases and few other important purine derivatives has been growing rapidly. Over the period of the past decade, the design of electrochemical biosensors has been focused on achieving high sensitivity and efficiency. The range of existing electrochemical methods with carbon electrode displays the highest rate in the development of biosensors. Moreover, modification of electrode surfaces based on nanomaterials is frequently used due to their extraordinary conductivity and surface to volume ratio. Different strategies for modifying electrode surfaces facilitate electron transport between the electrode surface and biomolecules, including DNA, oligonucleotides and their components. This review aims to summarize recent developments in the electrochemical analysis of purine derivatives, as well as discuss different applications.

Direct electrochemical oxidation of S-captopril using gold electrodes modified with graphene-AuAg nanocomposites

In this paper, we present a novel approach for the electrochemical detection of S-captopril based on graphene AuAg nanostructures used to modify an Au electrode. Multi-layer graphene (Gr) sheets decorated with embedded bimetallic AuAg nanoparticles were successfully synthesized catalytically with methane as the carbon source. The two catalytic systems contained 1.0 wt% Ag and 1.0 wt% Au, while the second had a larger concentration of metals (1.5 wt% Ag and 1.5 wt% Au) and was used for the synthesis of the Gr-AuAg-1 and Gr-AuAg-1.5 multicomponent samples. High-resolution transmission electron microscopy analysis indicated the presence of graphene flakes that had regular shapes (square or rectangular) and dimensions in the tens to hundreds of nanometers. We found that the size of the embedded AuAg nanoparticles varied between 5 and 100 nm, with the majority being smaller than 20 nm. Advanced scanning transmission electron microscopy studies indicated a bimetallic characteristic of the metallic clusters. The resulting Gr-AuAg-1 and Gr-AuAg-1.5 samples were used to modify the surface of commonly used Au substrates and subsequently employed for the direct electrochemical oxidation of S-captopril. By comparing the differential pulse voltammograms recorded with the two modified electrodes at various concentrations of captopril, the peak current was determined to be well-defined, even at relatively low concentration (10(-5) M), for the Au/Gr-AuAg-1.5 electrode. In contrast, the signals recorded with the Au/Gr-AuAg-1 electrode were poorly defined within a 5×10(-6) to 5×10(-3) M concentration range, and many of them overlapped with the background. Such composite materials could find significant applications in nanotechnology, sensing, or nanomedicine.

Electrochemical detection of adenine and guanine using a self-assembled copper(ii)–thiophenyl-azo-imidazole complex monolayer modified gold electrode

A self-assembled copper(ii)–thiophenyl-azo-imidazole complex monolayer modified gold electrode exhibits an excellent electrochemical sensing ability towards adenine and guanine at physiological pH.