Voltammetric determination of all DNA nucleotides

Electron-Induced Damage by UV Photolysis of DNA Attached to Gold Nanoparticles

Photolysis of DNA attached to gold nanoparticles (AuNPs) with ultraviolet (UV) photons induces DNA damage. The release of nucleobases (Cyt, Gua, Ade, and Thy) from DNA was the major reaction (99%) with an approximately equal release of pyrimidines and purines. This reaction contributes to the formation of abasic sites in DNA. In addition, liquid chromatography-mass spectrometry/MS (LC-MS/MS) analysis revealed the formation of reduction products of pyrimidines (5,6-dihydrothymidine and 5,6-dihydro-2'-deoxyuridine) and eight 2',3'- and 2',5'-dideoxynucleosides. In contrast, there was no evidence of the formation of 5-hydroxymethyluracil and 8-oxo-7,8-dihydroguanine, which are common oxidation products of thymine and guanine, respectively. Using appropriate filters, the main photochemical reactions were found to involve photoelectrons ejected from AuNPs by UV photons. The contribution of "hot" conduction band electrons with energies below the photoemission threshold was minor. The mechanism for the release of free nucleobases by photoelectrons is proposed to take place by the initial formation of transient molecular anions of the nucleobases, followed by dissociative electron attachment at the C1'-N glycosidic bond connecting the nucleobase to the sugar-phosphate backbone. This mechanism is consistent with the reactivity of secondary electrons ejected by X-ray irradiation of AuNPs attached to DNA, as well as the reactions of various nucleic acid derivatives irradiated with monoenergetic very-low-energy electrons (∼2 eV). These studies should help us to understand the chemistry of nanoparticles that are exposed to UV light and that are used as scaffolds and catalysts in molecular biology, curative agents in photodynamic therapy, and components of sunscreens and cosmetics.

Electrochemical and theoretical studies of the interaction between anticancer drug ponatinib and dsDNA

In this study, electrochemical and theoretical studies were performed to explain the interaction mechanism between ponatinib (PNT), a third generation tyrosine kinase inhibitor, and dsDNA. The electrochemical part was conducted in phosphate-buffered saline (PBS) at physiological pH of 7.4 and in acetate buffer with a pH of 4.7, using square wave voltammetry. A boron-doped diamond electrode was used in a bulk-incubated solution. The theoretical part was investigated using computational methods, such as the semiempirical method PM7 and density functional theory (DFT). Significant differences in the electrochemical behavior of PNT in the presence of DNA confirmed the occurrence of interactions. The results obtained in the acetate buffer strongly suggested the preferential interaction of PNT with guanine residues. However, at physiological pH, it can be concluded that PNT interacts with dGua and dAdo in the dsDNA molecule. These results are consistent with outcomes from the theoretical studies, where quantum-chemical calculations showed that both electrochemically detectable nucleobases form hydrogen bonds with the drug. These bonds appeared to be stronger with guanine than with adenine. According to the computational studies, the dsDNA major groove is the energetically preferred site for the complexation of PNT.

Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization

We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.

Endogenous Photosensitizers in Human Skin

Endogenous photosensitizers play a critical role in both beneficial and harmful light-induced transformations in biological systems. Understanding their mode of action is essential for advancing fields such as photomedicine, photoredox catalysis, environmental science, and the development of sun care products. This review offers a comprehensive analysis of endogenous photosensitizers in human skin, investigating the connections between their electronic excitation and the subsequent activation or damage of organic biomolecules. We gather the physicochemical and photochemical properties of key endogenous photosensitizers and examine the relationships between their chemical reactivity, location within the skin, and the primary biochemical events following solar radiation exposure, along with their influence on skin physiology and pathology. An important take-home message of this review is that photosensitization allows visible light and UV-A radiation to have large effects on skin. The analysis presented here unveils potential causes for the continuous increase in global skin cancer cases and emphasizes the limitations of current sun protection approaches.

Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate

Novel enzymatic methods are poised to become the dominant processes for de novo synthesis of DNA, promising functional, economic, and environmental advantages over the longstanding approach of phosphoramidite synthesis. Before this can occur, however, enzymatic synthesis methods must be parallelized to enable production of multiple DNA sequences simultaneously. As a means to this parallelization, we report a polymerase-nucleotide conjugate that is cleaved using electrochemical oxidation on a microelectrode array. The developed conjugate maintains polymerase activity toward surface-bound substrates with single-base control and detaches from the surface at mild oxidative voltages, leaving an extendable oligonucleotide behind. Our approach readies the way for enzymatic DNA synthesis on the scale necessary for DNA-intensive applications such as DNA data storage or gene synthesis.

Hybrid Nanomaterial of Graphene Oxide Quantum Dots with Multi-Walled Carbon Nanotubes for Simultaneous Voltammetric Determination of Four DNA Bases

In this proof-of-concept study, a novel hybrid nanomaterial-based electrochemical sensor was developed for the simultaneous detection of four DNA bases. For the modification of the working electrode surface, graphene oxide quantum dots (GOQDs) were synthesized using a solvothermal method. GOQDs were then used for the preparation of a hybrid nanomaterial with multi-walled carbon nanotubes (GOQD-MWCNT) using a solvothermal technique for the first time. Transmission electron microscopy (TEM) was used to characterize the GOQDs-MWCNTs. A glassy carbon electrode (GCE) was modified with the GOQDs-MWCNTs using Nafion™ to prepare a GOQD-MWCNT/GCE for the simultaneous determination of four DNA bases in phosphate buffer solution (PBS, pH 7.0) using differential pulse voltammetry (DPV). The calibration plots were linear up to 50, 50, 500, and 500 µM with a limit of detection at 0.44, 0.2, 1.6, and 5.6 µM for guanine (G), adenine (A), thymine (T) and cytosine (C), respectively. The hybrid-modified sensor was used for the determination of G, A, T, and C spiked in the artificial saliva samples with the recovery values ranging from 95.9 to 106.8%. This novel hybrid-modified electrochemical sensor provides a promising platform for the future development of a device for cost-effective and efficient simultaneous detection of DNA bases in real biological and environmental samples.

Advances in Electrochemical Biosensor Technologies for the Detection of Nucleic Acid Breast Cancer Biomarkers

Breast cancer is the second leading cause of cancer deaths in women worldwide; therefore, there is an increased need for the discovery, development, optimization, and quantification of diagnostic biomarkers that can improve the disease diagnosis, prognosis, and therapeutic outcome. Circulating cell-free nucleic acids biomarkers such as microRNAs (miRNAs) and breast cancer susceptibility gene 1 (BRCA1) allow the characterization of the genetic features and screening breast cancer patients. Electrochemical biosensors offer excellent platforms for the detection of breast cancer biomarkers due to their high sensitivity and selectivity, low cost, use of small analyte volumes, and easy miniaturization. In this context, this article provides an exhaustive review concerning the electrochemical methods of characterization and quantification of different miRNAs and BRCA1 breast cancer biomarkers using electrochemical DNA biosensors based on the detection of hybridization events between a DNA or peptide nucleic acid probe and the target nucleic acid sequence. The fabrication approaches, the biosensors architectures, the signal amplification strategies, the detection techniques, and the key performance parameters, such as the linearity range and the limit of detection, were discussed.

Simultaneous voltammetric determination of 7-methyl-guanine and 5-methyl-cytosine using a cathodically pre-treated boron-doped diamond electrode

Given the importance of identifying the presence of biomarkers of human diseases in DNA samples, the main objective of this work was to investigate, for the first time, the electro-catalytic oxidation of 7-methyl-guanine (7-mGua) and 5-methyl-cytosine (5-mCyt) on a boron doped diamond electrode pre-treated cathodically (red-BDDE), using differential pulse voltammetry (DPV) and cyclic voltammetry (CV). The anodic peak potentials of 7-mGua and 5-mCyt by DPV were at E = 1.04 V and E = 1.37 V at pH = 4.5, indicating excellent peak separation of approximately 330 mV between species. Using DPV, experimental conditions such as supporting electrolyte, pH and influence of interferents were also investigated to develop a sensitive and selective method for individual and simultaneous quantification of these biomarkers. The analytical curves for the simultaneous quantification of 7-mGua and 5-mCyt in the acid medium (pH = 4.5) were: concentration range of 0.50-5.00 μmol L^-1 (r = 0.999), detection limit of 0.27 μmol L^-1 for 7-mGua; from 3.00 to 25.00 μmol L^-1 (r = 0.998), with a detection limit of 1.69 μmol L^-1 for 5-mCyt. A new DP voltammetric method for the simultaneous detection and quantification of biomarkers 7-mGua and 5-mCyt using a red-BDDE is proposed.

A highly reusable genosensor for late-life depression diagnosis based on microRNA 184 attomolar detection in human plasma

Late-Life Depression (LLD) is one of the most prevalent psychiatric disorders in elderly, causing significant functional impairments. MicroRNAs are small molecules involved in the post-transcriptional regulation of gene expression. Elderly individuals diagnosed with LLD present down regulation of miR-184 (hsa-miR-184) expression compared to healthy patients. Therefore, this miR-184 can be used as a biomarker to diagnose LLD. Current LLD diagnosis depends primarily on clinical subjective identification, based on symptoms and variable scales. This work introduces a novel and facile approach for the LLD diagnosis based on the development of an electrochemical genosensor for miR-184 detection in plasma, using differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). DPV results presented a 2-Fold increase in current value for healthy patients, compared to individuals with LLD when monitoring ethidium bromide oxidation peak. For EIS, a 1.5-fold increase in charge transfer resistance for healthy elderly subjects was observed in comparison with depressed patients. In addition, the analytical performance of the biosensor was evaluated using DPV, obtaining a linear response ranging from 10^-9 mol L^-1 to 10^-17 mol L^-1 of miR-184 in plasma and a detection limit of 10 atomoles L^-1. The biosensor presented reusability, selectivity and stability, the current response remained 72% up to 50 days of storage. Thus, the genosensor proved to be efficient in the diagnosis of LLD, as well as the accurate quantification of miR-184 in real plasma samples of healthy and depressed patients.

Voltammetric Measurement of Antioxidant Activity by Prevention of Cu(II)-Induced Oxidative Damage on DNA Bases Using a Modified Electrode

The protective effect of antioxidants using electrochemical techniques can be evaluated by examining the oxidative changes in deoxyribonucleic acid (DNA) nucleobases. In this study, a gold nanoparticle (AuNP)-decorated and multiwalled carbon nanotube (MWCNT)-Nafion-modified glassy carbon electrode (GCE/AuNP/MWCNT-Nafion) was developed to evaluate the preventive ability of antioxidants on oxidative DNA damage. A modified working electrode was prepared and characterized by cyclic voltammetry, electrochemical impedance spectroscopy, and scanning electron microscopy. The developed electrochemical method relies on two phenomena: (i) reactive species (RS) produced by dissolved oxygen in the presence of copper(II) partially damage the DNA immobilized on the electrode surface and (ii) antioxidant compounds prevent this damage by scavenging the formed RS. Changes in guanine, adenine, and cytosine oxidation signals resulting from DNA damage were measured using differential pulse stripping voltammetry before/after the interaction of dsDNA with Cu(II) while antioxidants were absent or present. The DNA protective ability of antioxidants was assessed for a number of antioxidant compounds (i.e., ascorbic acid, gallic acid, epicatechin, catechin, epicatechin gallate, glutathione, chlorogenic acid, N-acetyl cysteine, rosmarinic acid, quercetin, and rutin). Quercetin was found to show the highest antioxidant effect, and its limit of detection was determined as 1 μM. The manufactured biosensor was put in an application for the determination of antioxidant activity of herbal teas.

Electrochemical DNA sensors for drug determination

In this review, recent achievements in the development of the DNA biosensors developed for the drug determination have been presented with particular emphasis to the main principles of their assembling and signal measurement approaches. The design of the DNA sensors is considered with characterization of auxiliary components and their necessity for the biosensor operation. Carbon nanomaterials, metals and their complexes as well as electropolymerized polymers are briefly described in the assembly of DNA sensors. The performance of the DNA sensors is summarized within 2017-2022 for various drugs and factors influencing the sensitivity and selectivity of the response are discussed. Special attention is paid to the mechanism of the signal generation and possible drawbacks in the analysis of real samples.

Heavy Metal Ions Detection Using Nanomaterials-Based Aptasensors

Heavy metals ions as metallic pollutants are a growing global issue due to their adverse effects on the aquatic ecosystem, and human health. Unfortunately, conventional detection methods such as atomic absorption spectrometry exhibit a relatively low limit of detection and hold numerous disadvantages, and therefore, the development of an efficient method for in-situ and real-time detection of heavy metal residues is of great importance. The aptamer-based sensors offer distinct advantages over antibodies and emerged as a robust sensing platform against various heavy metals due to their high sensitivity, ease of production, simple operations, excellent specificity, better stability, low immunogenicity, and cost-effectiveness. The nucleic acid aptamers in conjugation with nanomaterials can bind to the metal ions with good specificity/selectivity and can be used for on-site monitoring of metal ion residues. This review aimed to provide background information about nanomaterials-based aptasensor, recent advancements in aptamer conjunction on nanomaterials surface, the role of nanomaterials in improving signal transduction, recent progress of nanomaterials-based aptasening procedures (from 2010 to 2022), and future perspectives toward the practical applications of nanomaterials-based aptasensors against hazardous metal ions for food safety and environmental monitoring.

An electrochemical assay for sensitive detection of Acinetobacter baumannii gene

A new genosensor, which allows sensitive and selective detection of Acinetobacter baumannii gene sequence was developed herein. In this assay, capture probe of Acinetobacter baumannii was immobilized on the surface of chitosan modified single-use pencil graphite electrodes (c-PGEs) to obtain Acinetobacter baumannii genosensor. Then, Acinetobacter baumannii target DNA sequence was recognized after solid-state hybridization on c-PGE genosensor by measuring guanine signal via differential pulse voltammetry (DPV). In order to improve hybridization efficiency, experimental parameters affecting all assay steps are studied and the analytical performance of the genosensor was tested. The low limit of detection (LOD) for Acinetobacter baumannii target DNA sequence was obtained as 1.86 nM with developed genosensor. The selectivity of the proposed assay was then tested in the presence of 1-base mismatch, or two different type of non-complementary sequences and no interference effect was observed. The proposed electrochemical assay protocol is easy, convenient, and rapid which can be a decent alternative to existing methods.

8-oxoguanine and 8-oxodeoxyguanosine Biomarkers of Oxidative DNA Damage: A Review on HPLC-ECD Determination

Reactive oxygen species (ROS) are continuously produced in living cells due to metabolic and biochemical reactions and due to exposure to physical, chemical and biological agents. Excessive ROS cause oxidative stress and lead to oxidative DNA damage. Within ROS-mediated DNA lesions, 8-oxoguanine (8-oxoG) and its nucleotide 8-oxo-2′-deoxyguanosine (8-oxodG)—the guanine and deoxyguanosine oxidation products, respectively, are regarded as the most significant biomarkers for oxidative DNA damage. The quantification of 8-oxoG and 8-oxodG in urine, blood, tissue and saliva is essential, being employed to determine the overall effects of oxidative stress and to assess the risk, diagnose, and evaluate the treatment of autoimmune, inflammatory, neurodegenerative and cardiovascular diseases, diabetes, cancer and other age-related diseases. High-performance liquid chromatography with electrochemical detection (HPLC–ECD) is largely employed for 8-oxoG and 8-oxodG determination in biological samples due to its high selectivity and sensitivity, down to the femtomolar range. This review seeks to provide an exhaustive analysis of the most recent reports on the HPLC–ECD determination of 8-oxoG and 8-oxodG in cellular DNA and body fluids, which is relevant for health research.

Electrochemical Simulation of the Oxidative Capsaicin Metabolism

Capsaicin, primarily known as the pungent ingredient in hot peppers, is rapidly metabolized in the human body by enzymatic processes altering the pharmacological as well as toxicological properties. Herein, the oxidative transformation of capsaicin was investigated in vitro with electrochemistry as well as human liver microsomal incubations. The reaction mixtures were analyzed with liquid chromatography-mass spectrometry. Structure elucidation involved accurate mass measurements and multistage tandem mass spectrometry experiments. In total, 126 transformation products were detected. Electrochemistry provided evidence for 101 transformation products and the microsomal incubations for 46 species. 21 compounds were observed with both approaches. Identified oxidative pathways likely occurring during the phase I metabolism included dehydrogenation, O-demethylation, and hydroxylation reactions as well as combinations thereof. Furthermore, trapping of reactive intermediates either with glutathione or with electrochemically activated ribonucleosides provided evidence for the possible production of phase II metabolites and covalent adducts with a genetic material. Evidence for the occurrence of some capsaicin metabolites in humans was obtained by urine screening.

DNA electrochemical biosensor for detection of Alicyclobacillus acidoterrestris utilizing Hoechst 33258 as indicator

Alicyclobacillus acidoterrestris is an acidophilic and thermophilic bacterium present in the soil, often associated with the spoilage of acidic juices, such as orange juice. Their spores resist pasteurization and, when reactivated, modify the organoleptic properties of the juice, making it unsuitable for consumption, due mainly to production of guaiacol. Biosensors are detection devices that respond quickly and are easy to handle, with great potential for use in the juice production chain. In this context, this work reports an electrochemical genosensor for detection of A. acidoterrestris, based on a graphite electrode modified with electrochemically reduced graphene oxide, a polymer derived from 3-hydroxybenzoic acid and a specific DNA probe sequence complementary with the genomic DNA of A. acidoterrestris. Detection of the target was performed by monitoring the oxidation peak of the Hoechst 33258, a common DNA stainer. The genosensor detection limit was 12 ng mL^-1 and it kept 77% of response after ten weeks, and a test showed that orange juice does not interfere with bacteria lysate detection. This biosensor is the first platform for electrochemical detection of the genomic DNA of A. acidoterrestris in the literature, and the first to use Hoechst 33258 as indicator with whole genomic DNA molecules.

Direct Detection of DNA and RNA on Carbon Fiber Microelectrodes Using Fast-Scan Cyclic Voltammetry

DNA and RNA have been measured with many techniques but often with relatively long analysis times. In this study, we utilize fast-scan cyclic voltammetry (FSCV) for the subsecond codetection of adenine, guanine, and cytosine, first as free nucleosides, and then within custom synthesized oligos, plasmid DNA, and RNA from the nematode Caenorhabditis elegans. Previous studies have shown the detection of adenosine and guanosine with FSCV with high spatiotemporal resolution, while we have extended the assay to include cytidine and adenine, guanine, and cytosine in RNA and single- and double-stranded DNA (ssDNA and dSDNA). We find that FSCV testing has a higher sensitivity and yields higher peak oxidative currents when detecting shorter oligonucleotides and ssDNA samples at equivalent nucleobase concentrations. This is consistent with an electrostatic repulsion from negatively charged oxide groups on the surface of the carbon fiber microelectrode (CFME), the negative holding potential, and the negatively charged phosphate backbone. Moreover, as opposed to dsDNA, ssDNA nucleobases are not hydrogen-bonded to one another and thus are free to adsorb onto the surface of the carbon electrode. We also demonstrate that the simultaneous determination of nucleobases is not masked even in biologically complex serum samples. This is the first report demonstrating that FSCV, when used with CFMEs, is able to codetect nucleobases when polymerized into DNA or RNA and could potentially pave the way for future uses in clinical, diagnostic, or research applications.

DNA Electrochemical Biosensors for In Situ Probing of Pharmaceutical Drug Oxidative DNA Damage

Deoxyribonucleic acid (DNA) electrochemical biosensors are devices that incorporate immobilized DNA as a molecular recognition element on the electrode surface, and enable probing in situ the oxidative DNA damage. A wide range of DNA electrochemical biosensor analytical and biotechnological applications in pharmacology are foreseen, due to their ability to determine in situ and in real-time the DNA interaction mechanisms with pharmaceutical drugs, as well as with their degradation products, redox reaction products, and metabolites, and due to their capacity to achieve quantitative electroanalytical evaluation of the drugs, with high sensitivity, short time of analysis, and low cost. This review presents the design and applications of label-free DNA electrochemical biosensors that use DNA direct electrochemical oxidation to detect oxidative DNA damage. The DNA electrochemical biosensor development, from the viewpoint of electrochemical and atomic force microscopy (AFM) characterization, and the bottom-up immobilization of DNA nanostructures at the electrode surface, are described. Applications of DNA electrochemical biosensors that enable the label-free detection of DNA interactions with pharmaceutical compounds, such as acridine derivatives, alkaloids, alkylating agents, alkylphosphocholines, antibiotics, antimetabolites, kinase inhibitors, immunomodulatory agents, metal complexes, nucleoside analogs, and phenolic compounds, which can be used in drug analysis and drug discovery, and may lead to future screening systems, are reviewed.

Nanostructured material-based electrochemical sensing of oxidative DNA damage biomarkers 8-oxoguanine and 8-oxodeoxyguanosine: a comprehensive review

Oxidative DNA damage plays an important role in the pathogenesis of various diseases. Among oxidative DNA lesions, 8-oxoguanine (8-oxoG) and its corresponding nucleotide 8-oxo-2'-deoxyguanosine (8-oxodG), the guanine and deoxyguanosine oxidation products, have gained much attention, being considered biomarkers for oxidative DNA damage. Both 8-oxoG and 8-oxodG are used to predict overall body oxidative stress levels, to estimate the risk, to detect, and to make prognosis related to treatment of cancer, degenerative, and other age-related diseases. The need for rapid, easy, and low-cost detection and quantification of 8-oxoG and 8-oxodG biomarkers of oxidative DNA damage in complex samples, urine, blood, and tissue, caused an increasing interest on electrochemical sensors based on modified electrodes, due to their high sensitivity and selectivity, low-cost, and easy miniaturization and automation. This review aims to provide a comprehensive and exhaustive overview of the fundamental principles concerning the electrochemical determination of the biomarkers 8-oxoG and 8-oxodG using nanostructured materials (NsM), such as carbon nanotubes, carbon nanofibers, graphene-related materials, gold nanomaterials, metal nanoparticles, polymers, nanocomposites, dendrimers, antibodies and aptamers, and modified electrochemical sensors.

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.

Graphene Oxide Nanoribbons in Chitosan for Simultaneous Electrochemical Detection of Guanine, Adenine, Thymine and Cytosine

Herein, graphene oxide nanoribbons (GONRs) were obtained from the oxidative unzipping of multi-walled carbon nanotubes. Covalent coupling reaction of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxy succinimide (NHS) with amine functional groups (-NH₂) of the chitosan natural polymer (CH) was used for entrapping GONRs on the activated glassy carbon electrode (GCE/GONRs-CH). The nanocomposite was characterized by high-resolution transmission electron microscopy (HRTEM), and field-emission scanning electron microscopy (FESEM). In addition, the modification steps were monitored using FTIR. The nanocomposite-modified electrode was used for the simultaneous electrochemical determination of four DNA bases; guanine (G), adenine (A), thymine (T) and cytosine (C). The nanocomposite-modified GCE displayed a strong, stable and continuous four oxidation peaks during electrochemistry detection at potentials 0.63, 0.89, 1.13 and 1.27 V for G, A, T and C, respectively. The calibration curves were linear up to 256, 172, 855 and 342 μM with detection limits of 0.002, 0.023, 1.330 and 0.641 μM for G, A, T and C, respectively. The analytical performance of the GCE/GONRs-CH has been used for the determination of G, A, T and C in real samples and obtained a recovery percentage from 91.1%-104.7%. Our preliminary results demonstrated that GCE/GONRs-CH provided a promising platform to detect all four DNA bases for future studies on DNA damage and mutations.

Simultaneous Determination of Four DNA bases at Graphene Oxide/Multi-Walled Carbon Nanotube Nanocomposite-Modified Electrode

In this study, we developed a modified glassy carbon electrode (GCE) with graphene oxide, multi-walled carbon nanotube hybrid nanocomposite in chitosan (GCE/GO-MWCNT-CHT) to achieve simultaneous detection of four nucleobases (i.e., guanine (G), adenine (A), thymine (T) and cytosine (C)) along with uric acid (UA) as an internal standard. The nanocomposite was characterized using TEM and FT-IR. The linearity ranges were up to 151.0, 78.0, 79.5, 227.5, and 162.5 µM with a detection limit of 0.15, 0.12, 0.44, 4.02, 4.0, and 3.30 µM for UA, G, A, T, and C, respectively. Compared to a bare GCE, the nanocomposite-modified GCE demonstrated a large enhancement (~36.6%) of the electrochemical active surface area. Through chronoamperometric studies, the diffusion coefficients (D), standard catalytic rate constant (K_s), and heterogenous rate constant (K_h) were calculated for the analytes. Moreover, the nanocomposite-modified electrode was used for simultaneous detection in human serum, human saliva, and artificial saliva samples with recovery values ranging from 95% to 105%.

Fabrication of WO2/W@C core-shell nanospheres for voltammetric simultaneous determination of thymine and cytosine

Pomegranate-like multicore WO₂/W nanocrystals wrapped with layers of multiporous carbon were fabricated via carbonization of a copper(II)-organic framework host and a tungsten-based polyoxometalates guest, and subsequent etching off the metallic copper. The WO₂/W@C core-shell nanospheres were employed to modify an electrode for the analysis of the DNA bases thymine (T) and cytosine (C) by differential pulse voltammetry. The WO₂/W@C exhibited strongly increased oxidation signal of T and C. Under optimized conditions, the enhanced peak current represented excellent analytical performance for determination of T and C. This is attributed to the synergic effects of the porous multicore-shell microstructure and the use of tungsten-based materials with their excellent electrocatalytic activity for T and C, with typical peaks voltages near 1.26 V and 1.44 V. The calibration plots for T and C extend from 1 to 4000 μM and from 1 to 3000 μM, respectively, and both detection limits are 0.2 μM. The method was successfully applied to the determination of T and C in spiked blood and urine samples, and the recoveries are form 97.3 to 105.0%. Graphic abstractCore-shell nanospheres of type WO2/W-carbon were prepared for highly sensitive simultaneous voltammetric determination of thymine and cytosine.

The Dynamics of Hole Transfer in DNA

High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.

Highly selective sensing and measurement of microRNA-541 based on its sequence-specific digestion by the restriction enzyme Hinf1

In this study, a genosensor is introduced to detect microRNA-541 through an enzymatic digestion method and using a restriction enzyme (RE). Hinf1 is a type of RE which can cut the double helix DNA at specific sequences. The hybridization event and the corresponding enzymatic reactions are studied through guanine signal tracing on a pencil graphite electrode modified with graphene quantum dots (GQDs/PGE). The stages of fabricating the electrode are monitored by atomic force microscopy, and its electrochemical behavior is studied by cyclic voltammetry. The results indicate that the guanine current response of a 25-mer oligonucleotide of 7-guanine immobilized on the electrode surface decreases after hybridization despite an increase in the number of the guanine bases. Also, after enzyme treatment, the current decreases further due to the separation of a number of guanine bases from ds-DNA. A comparison of the analytical parameters of the proposed method with those of the conventional guanine oxidation method indicates that the linear concentration range in the proposed method, i.e. 1.0 fM to 1.0 nM, is lower than that in the conventional method, i.e. 10.0 pM-1.0 μM. On the basis of these findings, it is concluded that the use of Hinf1 enzyme makes it possible to measure microRNA at a femtomolar level. The selectivity of the designed biosensor has been proved using a non-complementary sequence with a one-base mismatch in the recognition site, rather than a complementary sequence. Finally, the proposed genosensor can be satisfactorily applied to measure microRNA-541 in human plasma samples.