Guanine Oxidation Research Articles

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

The 2-aminoimidazolone is a major and ubiquitous in vitro product of guanine oxidation. The flash-quench method, combining spectroscopy and product analysis, offers a novel and tunable approach to study guanine oxidation on double helical DNA. Herein we found that imidazolone dIz (2-amino-5-[(2-deoxy-β-D-erythro-pentofuranosyl)amino]-4H-imidazole-4-one) and dZ (2,2-diamino-5-[2-deoxy-β-D-erythro-pentofuranosyl)amino]-5(2H)-oxazolone) were the major oxidation products of double-strand DNA from the visible-light irradiation of the well-known DNA intercalating and light-switching Ru(OP)2dppz2+ (OP = 1,10-phenanthroline, dppz = dipyrido [3,2-a:2′,3′-c]phenazine) in the presence of a typical quencher methyl viologen (MV2+). Using ESR spin-trapping method, the radical intermediate MV•+ with typical hyperfine pattern was detected which indicated the successful formation of the corresponding Ru3+ intercalated oxidant. The formation of dIz and dZ decreased markedly with the addition of nitrotetrazolium blue chloride (NBT), a typical O2•- reactant. With a more specific and highly sensitive O2•- probe CT02-H, its ESR signal decayed rapidly in the presence of Ru(OP)2dppz2+ and MV2+, suggesting that O2•- was indeed produced. More interestingly, enantio-selective generation of oxidation products from dsDNA was observed with the two chiral forms of Ru(OP)2dppz2+. This represents the first report that the flash-quench technique with MV2+ as the quencher can oxidize dsDNA effectively to form dIz and dZ via the Ru3+/O2•- mediated mechanism. Our new findings provide a novel method to generate two radicals simultaneously, G (-H)• and O2•-, in close proximity to one another in dsDNA.

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

A novel graphene quantum dots (GQD) / polyfluorene (PF) nanocomposite was deposited on the disposable pencil tip graphite electrode (PGE) and proven to be an efficient nanosensor for analysis of the electrochemical interaction between the antitumor compoundmitomycinC(MC) with double stranded DNA (ds-DNA). This modified electrode (GQD@PF-PGE) was prepared in four steps: hydrothermal, chemical oxidation, ultrasonication and electro-oxidation processes. GQD, PF, GQD@PF and GQD@PF-PGE have been characterized by different analytical techniques such as SEM, TEM, XRD, FTIR, UV–Vis, EIS. Compared to bare PGE, GQD@PF modified PGE performed approximately 56 times more sensitive analysis when evaluating the guanine oxidation signals measured by DPV. CV and EIS measurements also showed that GQD@PF-PGE possesses a fast electron transfer as compared to bare electrode and exhibit a remarkable electrocatalytic activity towards both guanine and MC electrooxidation. Comprehensive optimization studies have also been carried out for the developed new nanobiosensor.

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

Silicon dioxide nanoparticles were synthesized and disposable screen-printed electrodes were modified with these nanoparticles to electrochemically detect the interaction between DNA and patulin, a mycotoxin. Firstly, the synthesized silicon dioxide nanoparticles were chemically characterized by X-ray diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FT-IR). Microscopic characterization of the nanoparticles was performed by Transmission Electron Microscopy (TEM) and Energy-dispersive X-ray spectroscopy (EDX). The surface of the silicon dioxide nanoparticle-modified screen-printed electrode was characterized by Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). SiNP modification resulted in a 2-fold increase in surface area and a 2.3-fold enhancement in the signal. The detection limit (LOD) for the electrochemical patulin determination was calculated as 1.15 µg/mL, and the linear concentration range was found to be 3.2–20 µg/mL. The mode of interaction between patulin and dsDNA was determined through a molecular docking study. After the interaction between patulin and dsDNA, approximately 86 % and 23 % decreases were observed in patulin and guanine oxidation signals, respectively. The S % value for patulin was calculated by utilizing the decrease in the guanine signal after the interaction.

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

The evaluation of antioxidant performance in economic crops is of significant importance due to their potential health benefits and increasing demand for functional foods. In this study, we developed an electrochemical sensor based on guanine binding technology to assess the antioxidant capacity of common economic crops, including tomatoes, blueberries, spinach, grapes, and oranges. The guanine oxidation peak current, measured using square wave voltammetry on a composite film-modified electrode (RGO/G/GCE), served as an indicator of antioxidant activity. Statistical analysis, including one-way analysis of variance (ANOVA) and post-hoc tests, revealed significant differences (p < 0.05) in the guanine oxidation peak currents among the tested crops, highlighting variations in their antioxidant activities. Blueberries exhibited the highest guanine oxidation peak current, indicating the strongest antioxidant capacity, followed by spinach and grapes with significant antioxidant activity. Tomatoes and oranges displayed relatively lower antioxidant capacity. The working/linear range for the electrochemical sensor was determined to be 0.5–4.0 mg/L of ascorbic acid (AA), and the limit of detection (LOD) was calculated as 0.35 mg/L. The proposed electrochemical sensor provides a rapid, sensitive, and cost-effective approach for assessing antioxidant capacity, offering potential applications in quality control, nutraceutical analysis, and functional food development.

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

Acerola (Malpighia emarginata DC) by-product (ABP) has bioactive compounds that can provide antioxidant and hypolipidemic effects in vivo. In this study we aimed to evaluate the antioxidant potential of ABP on oxidative damage along the enterohepatic axis of rats fed a high-fat diet for 7 weeks. In addition, we analysed the phenolic compound profile in the enterohepatic axis, and the lipid accumulation in the liver, colon and liver tissue structure of high-fat diet-fed rats treated with fenofibrate drug (100 mg/kg) or ABP (400 mg/kg) via orogastric administration in the 4th to 7th weeks of the experiment. ABP had increased antioxidant potential in vitro and presented ascorbic acid (2022.06 μg/g), carotenoid (2.63 μg/g), and total phenolic compound (5366.44 μg/g) contents. The high-fat diet-fed rats that received ABP (compared to fenofibrate treatment) presented a non-significant reduction of 9.87% in guanine oxidation product, lower relative liver weight, degree of hepatic steatosis, and aspartate aminotransferase level in their blood. ABP also provided high-fat diet-fed rats: an increased amount of total phenolic compounds in caecal digesta (946.42 µg/g), faeces (3299.07 µg/g), colon (256.15 µg/g) and hepatic tissues (454.80 µg/g); higher total antioxidant capacity in plasma and colon; and lower lipid peroxidation in plasma, colonic and hepatic tissues. The results point to the potential antioxidant activity of ABP against oxidative damage along the enterohepatic axis caused by high-fat diet intake. The ABP had a greater protective effect on the healthy liver compared to fenofibrate treatment due to its bioactive compound content.

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

Atomic Layer Deposition (ALD) enables precise thin-film deposition on electrode substrates for electrochemical sensors. In this work, we present the first example of ALD grown zinc oxide (ZnO) deposition on pencil graphite surfaces for deoxyribonucleic acid (DNA) sensory applications, including its detection and DNA damage investigation. For DNA sensing studies, the use of highly productive materials is essential. In this context, the ZnO modified pencil graphite electrodes (ZnO/PGEs) exhibited good electrochemical properties that make them a suitable substrate. ZnO films were characterized using scanning electron microscopy (SEM), ultraviolet-visible (UV-Vis) spectroscopy, photoluminescence (PL), X-ray photoelectron spectroscopy (XPS), and electrochemical methods. The DNA recognition capability of the thin film coated electrodes was tested by using differential pulse voltammetry (DPV), which showed a linear response ranging from 1 mg L−1 to 200 mg L−1 based on the oxidation of guanine (G) with a limit of detection value (LOD) of 0.53 mg L−1 (n = 3). In addition to this, impedimetric monitoring of oxidative DNA damage was performed in the presence of copper(II)/hydrogen peroxide (Cu(II)/H2O2) reagents, and protection studies were conducted in the presence of ascorbic acid. ZnO thin film-based electrodes exhibited good sensor performance in terms of sensitivity, stability, and reproducibility.

Interaction of Doxorubicin Embedded into Phospholipid Nanoparticles and Targeted Peptide-Modified Phospholipid Nanoparticles with DNA.

The interactions of dsDNA with new targeted drug delivery derivatives of doxorubicin (DOX), such as DOX embedded into phospholipid nanoparticles (NPhs) and DOX with the NGR targeted peptide-modified NPhs were studied electrochemically by differential pulse voltammetry technique. Screen-printed electrodes (SPEs), modified with stable fine dispersions of carbon nanotubes (CNTs), were used for quantitative electrochemical investigations of direct electrochemical oxidation of guanine, adenine, and thymine heterocyclic bases of dsDNA, and their changes in the presence of DOX nanoderivatives. Analysing the shifts of peak potentials of nucleobases in the presence of drug, we have shown that the doxorubicin with NGR targeted peptide changed the mode of interaction in DNA-drug complexes from intercalative to electrostatic. Binding constants (Kb) of DNA-drug complexes were calculated in accordance with adenine, guanine, and thymine oxidation signals. Based on our experiments, we have proven that the surface modification of a drug delivery system with NGR targeted peptide dramatically changed the mechanism of interaction of drug with genetic material. DNA-mediated drug toxicity was calculated based on the concentration-dependent "response" of heterocyclic nucleobases on drug influence. DOX, DOX-loaded phospholipid nanoparticles (NPhs), and DOX with NGR addressed peptide-modified NPhs were moderately toxic in the concentration range of 0.5-290 µM.

ZnO nanoflowers modified pencil graphite electrode for voltammetric DNA detection and investigation of Gemcitabine–DNA interaction

In this study, ZnO nanoflowers (ZnONFs) were synthesized using sonochemical method, which is a simple, environmentally friendly, low-cost and rapid method. ZnONFs was characterized by using FE-SEM, EDS, elemental mapping, FTIR and XRD techniques. Single use pencil graphite electrode (PGE) modified with ZnONFs was characterized using FE-SEM, EDS, elemental mapping, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods. This developed electrode was used for the first time for the determination of calf thymus double-stranded DNA (dsDNA) and the chemotherapeutic drug Gemcitabine (GEM) using differential pulse voltammetry (DPV). The detection limits (DLs) of dsDNA and GEM were calculated as 1.91 μg/mL and 2.47 μg/mL, respectively. The interaction of GEM and dsDNA at different times was investigated by measuring the changes in both GEM and guanine oxidation signals by DPV technique. The developed nanoflower-based biosensor responded in as short as 5 min in the DNA-anticancer drug interaction study. The study provides advantages such as low cost, biocompatibility, and easy synthesis of the used nanomaterial synthesis, as well as low detection limit and short interaction time at the sensor stage.

An integrated approach to evaluate acetamiprid-induced oxidative damage to tRNA in human cells based on oxidized nucleotide and tRNA profiling

Acetamiprid is poisonous to mammals due to severe acetamiprid-induced oxidative stress that could cause mitochondrial dysfunctions, lipid and protein oxidation, inflammation, apoptosis, and DNA damage. Evidence has accumulated for the role of oxidative stress in changing structures and functions of transfer RNAs (tRNAs) by inducing tRNA cleavage, reprogramming tRNA modifications and impairing aminoacyl-tRNA synthetase editing sites. However, the impact of acetamiprid-induced oxidative stress on tRNA is still unknown. Here, we investigated the effects of acetamiprid on cell viability, reactive oxygen species (ROS) levels, DNA damage, cellular oxidized nucleotide concentrations, and oxidative damage to tRNA in HepG2 cells and LO2 cells. Acetamiprid can cause the significant increment of ROS and DNA oxidative damage. In this study, an integrated approach was established to simultaneously study the network of oxidized nucleotides and explore the tRNA oxidative damage after acetamiprid exposure. A simple and high-throughput liquid chromatography with tandem mass spectrometry (LC-MS/MS) method coupled with (trimethylsilyl)diazomethane (TMSD) derivatization was successfully developed to quantify 12 cellular oxidized nucleotides that cannot be detected using traditional detection methods because of the huge interferences from naturally abundant nucleotides. Meanwhile, the accumulation rate and the locating sites of 8-oxo-2, 7-dihydro-guanine (8-oxo-G) in tRNA were inspected using the established N-(tert-Butyldimethylsilyl)-N-methyl-trifluoroacetamide (MTBSTFA) labeling-based tRNA profiling method. After acetamiprid treatment, the increment of oxidized nucleoside triphosphates is smaller than that of their corresponding mono- and diphosphates, as well as the dephosphorylated nucleosides, on account of the existence of sanitization enzymes. Several tRNA fragments, CUC[m1A]Gp, CACGp, [Cm]C[m2G]p, and DDGp, are significantly downregulated in acetamiprid-treated HepG2 cells, while only [Cm]C[m2G]p in acetamiprid-treated LO2 cells. According to the profiling results, the significantly changed fragment CUC[m1A]Gp might be caused by the oxidation of guanine (G) to form 8-oxo-G at position 15 in human tRNAphe([Gm]AA), providing more information about the effect of oxidized nucleobases on tRNA’s functions.

The Optimization of a Label-Free Electrochemical DNA Biosensor for Detection of Sus scrofa mtDNA as Food Adulterations

Fast, sensitive, and easy-to-use methods for detecting DNA related to food adulteration, health, religious, and commercial purposes are evolving. In this research, a label-free electrochemical DNA biosensor method was developed for the detection of pork in processed meat samples. Gold electrodeposited screen-printed carbon electrodes (SPCEs) were used and characterized using SEM and cyclic voltammetry. A biotinylated probe DNA sequence of the Cyt b S. scrofa gene mtDNA used as a sensing element containing guanine substituted by inosine bases. The detection of probe-target DNA hybridization on the streptavidin-modified gold SPCE surface was carried out by the peak guanine oxidation of the target using differential pulse voltammetry (DPV). The optimum experimental conditions of data processing using the Box–Behnken design were obtained after 90 min of streptavidin incubation time, at the DNA probe concentration of 1.0 µg/mL, and after 5 min of probe-target DNA hybridization. The detection limit was 0.135 µg/mL, with a linearity range of 0.5–1.5 µg/mL. The resulting current response indicated that this detection method was selective against 5% pork DNA in a mixture of meat samples. This electrochemical biosensor method can be developed into a portable point-of-care detection method for the presence of pork or food adulterations.

A novel electrochemical biosensor based on palladium nanoparticles decorated on reduced graphene oxide-polyaminophenol matrix for the detection and discrimination of mitomycin C-DNA and acyclovir-DNA interaction

Both the design of molecules that will interact specifically with DNA and the determination of the mechanism of action of this drug on DNA are important as they allow the control of gene expression. In particular, rapid and precise analysis of this type of interaction is a vital element for pharmaceutical studies. In the present study, a novel reduced graphene oxide/ palladium nanoparticles/ poly(2-amino-4-chlorophenol) (rGO/Pd@PACP) nanocomposite was synthesized by chemical process to modify pencil graphite electrode (PGE) surface. Here, the performance of the newly developed nanomaterial-based biosensor for drug-DNA interaction analysis has been demonstrated. For this purpose, it was determined whether this system, which was developed by selecting a drug molecule (Mitomycin C; MC) known to interact with DNA and a drug molecule (Acyclovir; ACY) that does not interact with DNA, performs a reliable/accurate analysis. Here, ACY was used as a negative control. Compared to bare PGE, the rGO/Pd@PACP nanomaterial modified sensor exhibited 17 times higher sensitivity performance in terms of guanine oxidation signal measured by differential pulse voltammetry (DPV). Moreover, the developed nanobiosensor system provided a highly specific determination between the anticancer drug MC and ACY by discrimination the interactions of these drugs with double-stranded DNA (dsDNA). ACY was also preferred in studies for the optimization of the new nanobiosensor developed. ACY was detected in a concentration as low as 0.0513 μM (51.3 nM) (LOD), and limit of quantification (LOQ) was 0.1711 μM with a linear range from 0.1 to 0.5 μM.

Oxidative Probing of the G4 DNA Structure by ZnP1 Porphyrin within Sequences of &lt;i&gt;MYC&lt;/i&gt; and &lt;i&gt;TERT&lt;/i&gt; Promotors

The formation of G4 structures in a DNA double helix competes with the complementary strand, which can change the equilibrium G4 structures studied on single-strand models by classical structural methods. A relevant task is to develop methods for detecting and localizing G4 in extended double-stranded (ds) DNA in the promoter regions of the genome. The porphyrin derivative ZnP1 selectively binds and leads to photo-induced oxidation of guanine in G4 structures on single-stranded (ss) and dsDNA model systems. In this research, we show the oxidative effect of ZnP1 on native sequences of MYC and TERT oncogene promoters that potentially capable to form G4 structures. Single strand breaks in the guanine rich sequence caused by ZnP1 oxidation and subsequent cleavage of the DNA strand by Fpg glycosylase were identified and assigned to the nucleotide sequence. The detected break sites corresponded to sequences potentially capable of forming G4 structures. New data were obtained on the possibility of folding G4 structures in the presence of a complementary strand in the context of the DNA double helix of the natural sequence.

Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs.

Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. Here, we show that DNA dynamics determine the frequency of misincorporating the A•G mismatch, and altered dynamics explain the high frequency of 8-oxoguanine (8OG) A•8OG misincorporation. NMR measurements revealed that Aanti•Ganti (population (pop.) of >91%) transiently forms sparsely populated and short-lived Aanti+•Gsyn (pop. of ~2% and kex = kforward + kreverse of ~137 s-1) and Asyn•Ganti (pop. of ~6% and kex of ~2,200 s-1) Hoogsteen conformations. 8OG redistributed the ensemble, rendering Aanti•8OGsyn the dominant state. A kinetic model in which Aanti+•Gsyn is misincorporated quantitatively predicted the dA•dGTP misincorporation kinetics by human polymerase β, the pH dependence of misincorporation and the impact of the 8OG lesion. Thus, 8OG increases replicative errors relative to G because oxidation of guanine redistributes the ensemble in favor of the mutagenic Aanti•8OGsyn Hoogsteen state, which exists transiently and in low abundance in the A•G mismatch.