Guanine Oxidation Research Articles

Controllable Supply-Demand Effect during Superior Fe Single-Atom Catalyst Synthesis for Targeted Guanine Oxidation of Antibiotic Resistance Genes.

Nonradical Fenton-like catalysis offers an opportunity to degrade extracellular antibiotic resistance genes (eARGs). However, high-loading single-atom catalysts (SACs) with controllable configurations are urgently required to selectively generate high-yield nonradicals. Herein, we constructed high-loading Fe SACs (5.4-34.2 wt %) with uniform Fe-N4 sites via an optimized coordination balance of supermolecular assembly for peroxymonosulfate activation. The selectivity of singlet oxygen (1O2) generation and its contribution to eARGs degradation were both >98%. This targeting strategy of oxidizing guanines with low ionization potentials by 1O2 allowed 7 log eARGs degradation within 10 min and eliminated their transformation within 2 min, outperforming most reported advanced oxidation processes. Relevant interactions between 1O2 and guanines were revealed at a single-molecule resolution. The high-loading Fe SACs exhibited excellent universality and stability for different eARGs and water matrices. These findings provide a promising route for constructing high-loading SACs for efficient and selective Fenton-like water treatment.

Theoretical Study of Guanine Oxidation Catalyzed by a Ruthenium Complex with an Oxygen Molecule.

The oxidation of an aromatic ring in guanosine monophosphate by a RuII-aqua complex, [RuII(OH2)(η5-C5Me5)(bpy)]+ (bpy = 2,2'-bipyridine), using O2 gases in an aqueous solution has been reported (Takenaka et al. Chem. Asian J. 2018, 13, 3480-3184). However, its mechanism has not been sufficiently clarified to facilitate the design of optimal catalysts. To clarify the mechanism of aerobic oxidation catalyzed by Ru complexes, we employed density functional theory (DFT) calculations to analyze the oxidation of 9-methyl guanine, as a model of the substrate. Although the ligand-exchange reaction between the H2O and O2 molecules yielded a more stable RuIV-peroxo complex, [RuIV(η2-O2)(η5-C5Me5)(bpy)]+, subsequent reactions were initiated by a RuIII-superoxo complex, [RuIII(η1-O2•-)(η5-C5Me5)(bpy)]+. We confirmed the plausible path for the homolytic cleavage of the O-O bond in [RuIII(η1-O2•-)(η5-C5Me5)(bpy)]+ to form a RuIV-oxo complex, [RuIV(O)(η5-C5Me5)(bpy)]+, with the activation free energy (ΔGa) of 12.2 kcal/mol. The subsequent oxidation of the substrate by [RuIV(O)(η5-C5Me5)(bpy)]+ facilitated the formation of an arenium-like intermediate to form the product compounds, where the energy in the transition state corresponding to the oxidation of the substrate is 21.5 kcal/mol. An additional reaction path for the oxidation of the substrate by [RuIII(η1-O2•-)(η5-C5Me5)(bpy)]+ must exceed the high energy in the transition state (31.7 kcal/mol), indicating that [RuIV(O)(η5-C5Me5)(bpy)]+ catalyzed the oxidation of the substrate as reactive species. Conversely, the Cp*-ligand oxidation, which induced catalyst degradation, requires ΔGa of 21.4 kcal/mol to exceed the transition state. Overall, our DFT study offers insight into the reaction mechanism of aerobic oxidation involving inert chemical bonds, facilitating the design of appropriate catalysts for the reaction.

Determination of the damaging effect of IR radiation on DNA by electrochemical methods and investigation of this effect in the presence of chitosan.

Infrared (IR) rays released from natural and artificial sources reach the layers of the skin and cause different effects. The most important effects of IR rays are the deterioration of the structure of proteins in the skin and the inadequacy of the skin's defense system. Early diagnosis of DNA damage caused by IR rays and discovery of products with antioxidant properties that will reduce the effects of damage are important in the prevention and treatment of possible diseases. This study aimed to determine the harmful effects of IR rays on DNA by measuring the guanine oxidation signal. Within the scope of the study, electrodes with DNA immobilized on their surfaces were exposed to IR irradiation and the change in guanine oxidation was detected electrochemically. A 57% decrease in guanine oxidation signal was observed as a result of IR exposure, and this ratedecreased in the presence of chitosan. The results obtained show that chitosan is effective in preventing DNA damage caused by IR rays and suggest that chitosan-supported products can be used to protect the skin from the harmful effects of sun rays. Furthermore, molecular docking analyses indicated no interaction between chitosan and collagen protein. This suggests that the addition of chitosan to any cosmetic product applied to the skin is unlikely to induce DNA damage attributable to chitosan.

Electrochemical analysis of the interaction between DNA and abiraterone D4A metabolite

The electroanalytical characteristics of double-stranded DNA (dsDNA) and the complex of dsDNA with the anticancer drug metabolite, abiraterone D4A, in the concentration range of 25–200 μM were investigated using differential pulse voltammetry. The effect of D4A on dsDNA was detected by changes in the intensity of the electrochemical oxidation of the heterocyclic bases guanine, adenine, and thymine. This investigation used screen-printed electrodes modified with carbon nanotubes. Binding constants (Kb) for guanine, adenine, and thymine in the dsDNA/D4A complexes were calculated to be 1.1 × 104, 5.5 × 103, and 2.5 × 103 M–1, respectively. The DNA-mediated electrochemical coefficients of the toxic effect were calculated as the ratio of the signal intensities of guanine and adenine in the presence of D4A compared to those without the drug (T, %). Based on an analysis of electrochemical parameters and binding constant values, an assumption was made regarding the mechanism of the interaction between D4A and DNA, predominantly through electrostatic interactions and the formation of hydrogen bonds with the minor groove. Conclusions about the mechanism of the interaction of the abiraterone D4A metabolite with the dsDNA minor groove, obtained by electrochemical methods, were supported by the molecular simulation of the DNA/D4A complex.

Hole Transfer and the Resulting DNA Damage.

In this review, we focus on the one-electron oxidation of DNA, which is a multipart event controlled by several competing factors. We will discuss the oxidation free energies of the four nucleobases and the electron detachment from DNA, influenced by specific interactions like hydrogen bonding and stacking interactions with neighboring sites in the double strand. The formation of a radical cation (hole) which can migrate through DNA (hole transport), depending on the sequence-specific effects and the allocation of the final oxidative damage, is also addressed. Particular attention is given to the one-electron oxidation of ds-ODN containing G:C pairs, including the complex mechanism of the deprotonation vs. hydration steps of a G:C•+ pair, as well as to the modes of formation of the two guanyl radical tautomers after deprotonation. Among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms, several oxidants react with DNA. The mechanism of stable product formation and their use as biomarkers of guanine oxidation in DNA damage are also addressed.

Spectrum of TP53 Sequence Variants on Chronically Exposed Humans

It is known that ionizing radiation can damage the genetic apparatus of a cell not only through direct exposure, but also through the induction of oxidative stress. Thus, oxidation of guanine (G) nitrogenous base by oxidative stress products can result in G:CT:A and G:CC:G type transversions in the tumor growth suppressor gene TR53. Somatic and inherited variants of the TP53 gene, in its turn, are of great importance in the development of malignant neoplasms. Therefore, the aim of the study was to analyze the G:CT:A and G:CC:G transversions of the TP53 gene in peripheral blood cells of individuals affected by chronic low-dose rate exposure. The paper presents the results of the analysis of the spectrum of TP53 gene sequence variants based on G:CT:A and G:CC:G transversions in peripheral blood cells of the Techa riverside residents of the Chelyabinsk and Kurgan Oblasts, affected by chronic low-dose rate exposure in the 1950s. The range of individual values of the accumulated absorbed dose to red bone marrow due to external gamma radiation and ⁹⁰Sr ranged from 2.1 to 2742.0 mGy (mean value – 605.4 ± 191.9 mGy (M ± SE)). As a result of the study, 7 different variants of the TP53 gene based on the G:CT:A and G:CC:G transversions, which are single nucleotide replacements, were identified in the examined individuals. All detected variants were present in the IARC TP53 Database and had no clinical significance as “pathogenic” or “probably pathogenic”. Differences in the frequencies of carriers of detected TP53 gene variants between the comparison group and the main group did not reach a statistically significant level/ were not statistically significant.

Why the ROS matters: One-electron oxidants focus DNA damage and repair on G-quadruplexes for gene regulation

Why the ROS matters: One-electron oxidants focus DNA damage and repair on G-quadruplexes for gene regulation

Enantioselectively generating imidazolone dIz by the chiral DNA intercalating and “light-switching” Ru(II) polypyridyl complex via a novel flash-quench method

Enantioselectively generating imidazolone dIz by the chiral DNA intercalating and “light-switching” Ru(II) polypyridyl complex via a novel flash-quench method

CO2 protects cells from iron-Fenton oxidative DNA damage in E. coli and humans.

Whereas hydroxyl radical is commonly named as the Fenton product responsible for DNA and RNA damage in cells, here we demonstrate that the cellular reaction generates carbonate radical anion due to physiological levels of bicarbonate. Analysis of the metabolome, transcriptome and, in human cells, the nuclear genome shows a consistent buffering of H2O2-induced oxidative stress leading to one common pathway, namely guanine oxidation. Particularly revealing are nanopore-based studies of direct RNA sequencing of cytosolic and mitochondrial ribosomal RNA along with glycosylase-dependent qPCR studies of oxidative DNA damage in telomeres. The focusing of oxidative modification on one pathway is consistent with the highly evolved base excision repair suite of enzymes and their involvement in gene regulation in response to oxidative stress.

Electrochemical DNA-nano biosensor for the detection of Goserelin as anticancer drug using modified pencil graphite electrode.

Goserelin is an effective anticancer drug, but naturally causes several side effects. Hence the determination of this drug in biological samples, plays a key role in evaluating its effects and side effects. The current studies have concentrated on monitoring Goserelin using an easy and quick DNA biosensor for the first time. In this study, copper(II) oxide nanoparticles were created upon the surface of multiwalled carbon nanotubes (CuO/MWCNTs) as a conducting mediator. The modified pencil graphite electrode (ds-DNA/PA/CuO/MWCNTs/PGE) has been modified with the help of polyaniline (PA), ds-DNA, and CuO/MWCNTs nanocomposite. Additionally, the issue with the bio-electroanalytical guanine oxidation signal in relation to ds-DNA at the surface of PA/CuO/MWCNTs/PGE has been examined to determination Goserelin for the first time. It also, established a strong conductive condition to determination Goserelin in nanomolar concentration. Thus, Goserelin's determining, however, has a 0.21 nM detection limit and a 1.0 nM-110.0 µM linear dynamic range according to differential pulse voltammograms (DPV) of ds-DNA/PA/CuO/MWCNTs/PGE. Furthermore, the molecular docking investigation highlighted that Goserelin is able to bind ds-DNA preferentially and supported the findings of the experiments. The determining of Goserelin in real samples has been effectively accomplished in the last phase using ds-DNA/PA/CuO/MWCNTs/PGE.

Pharmacogenomic Studies of Antiviral Drug Favipiravir.

In this work, we conducted a study of the interaction between DNA and favipiravir (FAV). This chemotherapeutic compound is an antiviral drug for the treatment of COVID-19 and other infections caused by RNA viruses. This paper examines the electroanalytical characteristics of FAV. The determined concentrations correspond to therapeutically significant ones in the range of 50-500 µM (R2 = 0.943). We have shown that FAV can be electro-oxidized around the potential of +0.96 V ÷ +0.98 V (vs. Ag/AgCl). A mechanism for electrochemical oxidation of FAV was proposed. The effect of the drug on DNA was recorded as changes in the intensity of electrochemical oxidation of heterocyclic nucleobases (guanine, adenine and thymine) using screen-printed graphite electrodes modified with single-walled carbon nanotubes and titanium oxide nanoparticles. In this work, the binding constants (Kb) of FAV/dsDNA complexes for guanine, adenine and thymine were calculated. The values of the DNA-mediated electrochemical decline coefficient were calculated as the ratio of the intensity of signals for the electrochemical oxidation of guanine, adenine and thymine in the presence of FAV to the intensity of signals for the electro-oxidation of these bases without drug (S, %). Based on the analysis of electrochemical parameters, values of binding constants and spectral data, intercalation was proposed as the principal mechanism of the antiviral drug FAV interaction with DNA. The interaction with calf thymus DNA also confirmed the intercalation mechanism. However, an additional mode of interaction, such as a damage effect together with electrostatic interactions, was revealed in a prolonged exposure of DNA to FAV.

Automated determination of 8-OHdG in cells and tissue via immunofluorescence using a specially created antibody

Despite powerful DNA repair systems, oxidative damage/modification to DNA is an inevitable side effect of metabolism, ionizing radiation, lifestyle habits, inflammatory pathologies such as type-2 diabetes or metabolic syndrome, cancer and natural aging.One of the most common oxidative DNA modifications is 8-OHdG (8‑hydroxy-2′-deoxyguanosine), which is the most widely used marker in research and clinical diagnostics. 8-OHdG is easily and specifically detectable in various samples such as urine, plasma, cells and tissues via a large variety of methods like ELISA, HPLC, chromatographic methods, and immunochemistry.Formed by oxidation of guanine and being representative for the degree of DNA damage, 8-OHdG can be also used as biomarker for risk assessment of various cancers as well as degenerative diseases.Here, we present a highly specific, self-developed 8-OHdG antibody in successful comparison to a commercially one, tested in cells (FF95, HCT116, and HT22) and intestinal tissue, focusing on automatized evaluation via fluorescence/confocal microscopy.

Quenching of G4-DNA intrinsic fluorescence by ligands.

G-quadruplex (G4) structures formed by the guanine-rich DNA regions exhibit several distinctive optical properties, including UV absorption and circular dichroism spectra. Some G4 DNA possess intrinsic UV fluorescence whose origin is not completely clear to date. In this work, we study the effect of TMPyP4 and Methylene Blue on the intrinsic fluorescence of the dimeric G4 DNA structure formed by two d(G3T)4 sequences. We demonstrate that binding of the ligands results in quenching of the intrinsic fluorescence, although the conformation of the G4 DNA and its dimeric structure remain preserved. The binding sites of the ligands were suggested by the photoinduced oxidation of guanines and analysis of binding isoterms. We discuss how DNA-ligand complexes can affect the intrinsic fluorescence of G4 DNA.

Graphene quantum dots-polyfluorene hybrid nanobiosensor for mitomycin C-DNA interaction sensing

Graphene quantum dots-polyfluorene hybrid nanobiosensor for mitomycin C-DNA interaction sensing

Electrochemical DNA Sensor Designed Using the Pencil Graphite Electrode to Detect Listeria monocytogenes.

In the present work, a novel electrochemical DNA sensor was designed to detect L. monocytogenes. Two different gene fragments were selected for the sensor design. One is a 702bp long fragment of the hlyA gene, encoding the synthesis of listeriolysin O toxin, which is unique only to pathogenic strains of L. monocytogenes and is essential for pathogenicity. The other is a 209bp long fragment of the 16S RNA gene found in all species of the Listeria genus. As the working electrode, the pencil graphite electrode was modified in various ways (activated or covered with polypyrrole), and six different combinations were constituted using three types of the modified working electrode and two different gene fragments. The developed system is based on differential pulse voltammetric transduction of guanine oxidation after hybridization between the selected gene fragment (38µg/mL) and the selected fragment-specific inosine-modified probe (1.8 µmol/L) immobilized on a pencil graphite electrode surface. The comparison of all combinations demonstrates that the best results are obtained with the combination formed from a polypyrrole-coated pencil graphite electrode (prepared at 2 scans) and 702bp fragment of the hlyA gene. The analysis time is less than 1 hour, and the necessary DNA concentrations for the analysis have been determined as 8.2 × 10-11M DNA and 2.7 × 10-10M DNA respectively, for the hlyA gene and 16S RNA gene.

Integrative blood-based characterization of oxidative mitochondrial DNA damage variants implicates Mexican American’s metabolic risk for developing Alzheimer’s disease

Alzheimer’s Disease (AD) continues to be a leading cause of death in the US. As the US aging population (ages 65 +) expands, the impact will disproportionately affect vulnerable populations, e.g., Hispanic/Latino population, due to their AD-related health disparities. Age-related regression in mitochondrial activity and ethnic-specific differences in metabolic burden could potentially explain in part the racial/ethnic distinctions in etiology that exist for AD. Oxidation of guanine (G) to 8-oxo-guanine (8oxoG) is a prevalent lesion and an indicator of oxidative stress and mitochondrial dysfunction. Damaged mtDNA (8oxoG) can serve as an important marker of age-related systemic metabolic dysfunction and upon release into peripheral circulation may exacerbate pathophysiology contributing to AD development and/or progression. Analyzing blood samples from Mexican American (MA) and non-Hispanic White (NHW) participants enrolled in the Texas Alzheimer’s Research & Care Consortium, we used blood-based measurements of 8oxoG from both buffy coat PBMCs and plasma to determine associations with population, sex, type-2 diabetes, and AD risk. Our results show that 8oxoG levels in both buffy coat and plasma were significantly associated with population, sex, years of education, and reveal a potential association with AD. Furthermore, MAs are significantly burdened by mtDNA oxidative damage in both blood fractions, which may contribute to their metabolic vulnerability to developing AD.

Disposable nanosensor for the electrochemical determination of the interaction between DNA, and a mycotoxin, patulin

Disposable nanosensor for the electrochemical determination of the interaction between DNA, and a mycotoxin, patulin

Evaluation of antioxidant performance of economic crops by electrochemical sensors using guanine as a probe

Evaluation of antioxidant performance of economic crops by electrochemical sensors using guanine as a probe

Antioxidant potential of acerola by-product along the enterohepatic axis of rats fed a high-fat diet

Antioxidant potential of acerola by-product along the enterohepatic axis of rats fed a high-fat diet

Atomic layer deposited zinc oxide thin film on pencil graphite for DNA sensor applications

Atomic layer deposited zinc oxide thin film on pencil graphite for DNA sensor applications