Impact of iron chelation with deferasirox on telomere length and oxidative stress in hemodialysis patients: A randomized study

BACKGROUND

Recent studies have demonstrated the effectiveness, safety, and tolerability of deferasirox in patients in peritoneal dialysis, however, its effect has not been studied in patients undergoing hemodialysis.

OBJECTIVE

To investigate the impact of iron chelation on telomere length, oxidative stress, and ferritin levels in patients undergoing hemodialysis.

METHODS

This is an open-label study, with a control group of patients undergoing hemodialysis, who will receive treatment with deferasirox 15mg/kg/day for 6 months for iron chelation. Telomere length was measured using real-time PCR. Serum ferritin levels and oxidation markers were evaluated. To evaluate the pharmacokinetics and safety of deferasirox, plasma concentrations were analyzed by HPLC.

RESULTS

Fifty-four patients were included to receive deferasirox, and a control group of 50 patients. Significant differences were observed in serum ferritin levels (p<0.0001), TBARS (thiobarbituric acid reactive substances) (p<0.01). Telomere length had a significant increase after chelation (p<0.001). The serum deferasirox concentration at zero time at 48h was maintained within a range of 2.67-23.78mmol/L.

CONCLUSIONS

Our results demonstrate that iron chelation in hemodialysis patients significantly reduces ferritin and TBARS, resulting in an increase in telomere length. Deferasirox proves to be beneficial for patients with iron overload undergoing hemodialysis.

Encapsulated Ferritin-like Proteins: A Structural Perspective

Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell's interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology.

Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation

Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.

Theranostic Role of Iron Oxide Nanoparticle for Treating Renal Anemia: Evidence of Efficacy and Significance by MRI, Histology and Biomarkers

(1) Background: Increasing attention has been given to applying nanosized iron oxide nanoparticles (IOPs) to treat iron deficiency anemia (IDA). Chronic kidney disease (CKD) patients who suffer from IDA often need long-term iron supplements. We aim to evaluate the safety and therapeutic effect of MPB-1523, a novel IOPs, in anemic CKD mice and to monitor iron storage by magnetic resonance (MR) imaging. (2) Methods: MPB-1523 was intraperitoneally delivered to the CKD and sham mice, and blood were collected for hematocrit, iron storage, cytokine assays, and MR imaging throughout the study. (3) Results: The hematocrit levels of CKD and sham mice dropped initially but increased gradually to reach a steady value 60 days after IOP injection. The body iron storage indicator, ferritin gradually rose and total iron-binding capacity stabilized 30 days after IOP injection. No significant inflammation or oxidative stress were observed in both groups. By T2-weighted MR imaging, the liver signal intensity gradually increased in both groups but was more pronounced in the CKD group, indicating aggressive utilization of MPB-1523. MR imaging, histology and electron microscopy showed MPB-1523 is liver-specific. (4) Conclusions: MPB-1523 can serve as a long-term iron supplement and is monitored by MR imaging. Our results have strong translatability to the clinic.

Risk factors for Barrett's esophagus: Recent advances

Esophageal adenocarcinoma (EAC) is the most common malignant tumor of the esophagus in the West. During the past few decades, its morbidity has been increasing in China. Barrett's esophagus (BE) is defined as the replacement of normal squamous epithelium in the lower esophagus by metaplasia of columnar epithelium. BE is closely related to the occurrence of EAC. Knowledge regarding the risk factors for the occurrence and development of BE is of great significance for early screening and diagnosis of BE and prevention of EAC. In this paper, we review the clinical, demographics-related, lifestyle-related, and medications-related risk factors for BE to provide more valuable scientific evidence for the prevention and treatment of BE.

Uric Acid as a Photosensitizer in the Reaction of Deoxyribonucleosides with UV Light of Wavelength Longer than 300 nm: Identification of Products from 2'-Deoxycytidine

DNA reacts directly with UV light with a wavelength shorter than 300 nm. Although ground surface sunlight includes little of this short-wavelength UV light due to its almost complete absorption by the atmosphere, sunlight is the primary cause of skin cancer. Photosensitization by endogenous substances must therefore be involved in skin cancer development mechanisms. Uric acid is the final metabolic product of purines in humans, and is present at relatively high concentrations in cells and fluids. When a neutral mixed solution of 2'-deoxycytidine, 2'-deoxyguanosine, thymidine, and 2'-deoxyadenosine was irradiated with UV light with a wavelength longer than 300 nm in the presence of uric acid, all the nucleosides were consumed in a uric acid dose-dependent manner. These reactions were inhibited by the addition of radical scavengers, ethanol and sodium azide. Two products from 2'-deoxycytidine were isolated and identified as N⁴-hydroxy-2'-deoxycytidine and N⁴,5-cyclic amide-2'-deoxycytidine, formed by cycloaddition of an amide group from uric acid. A ¹⁵N-labeled uric acid, uric acid-1,3-¹⁵N₂, having two ¹⁴N and two ¹⁵N atoms per molecule, produced N⁴,5-cyclic amide-2'-deoxycytidine containing both ¹⁴N and ¹⁵N atoms from uric acid-1,3-¹⁵N₂. Singlet oxygen, hydroxyl radical, peroxynitrous acid, hypochlorous acid, and hypobromous acid generated neither N⁴-hydroxy-2'-deoxycytidine nor N⁴,5-cyclic amide-2'-deoxycytidine in the presence of uric acid. These results indicate that uric acid is a photosensitizer for the reaction of nucleosides by UV light with a wavelength longer than 300 nm, and that an unidentified radical derived from uric acid with a delocalized unpaired electron may be generated.

Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes

G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavage and/or modification of G4s by functional-NDIs. This is the case of NDI-Cu-DETA, a copper(II) complex able to cleave G4s in the closest proximity to the target binding site. Herein, we present two original Cu(II)-NDI complexes, inspired by NDI-Cu-DETA, differently functionalized with 2-(2-aminoethoxy)ethanol side-chains, to selectively drive redox-catalyzed activity towards parallel G4s. The selective interaction toward parallel G4 topology, controlled by the presence of 2-(2-aminoethoxy)ethanol side chains, was already firmly demonstrated by us using core-extended NDIs. In the present study, the presence of protonable moieties and the copper(II) cavity, increases the binding affinity and specificity of these two NDIs for a telomeric RNA-G4. Once defined the copper coordination relationship and binding constants by competition titrations, ability in G4 stabilization, and ROS-induced cleavage were analyzed. The propensity in the stabilization of parallel topology was highlighted for both of the new compounds HP2Cu and PE2Cu. The results obtained are particularly promising, paving the way for the development of new selective functional ligands for binding and destructuring parallel G4s.

Is There Such a Thing as "Anti-Nutrients"? A Narrative Review of Perceived Problematic Plant Compounds

Plant-based diets are associated with reduced risk of lifestyle-induced chronic diseases. The thousands of phytochemicals they contain are implicated in cellular-based mechanisms to promote antioxidant defense and reduce inflammation. While recommendations encourage the intake of fruits and vegetables, most people fall short of their target daily intake. Despite the need to increase plant-food consumption, there have been some concerns raised about whether they are beneficial because of the various ‘anti-nutrient’ compounds they contain. Some of these anti-nutrients that have been called into question included lectins, oxalates, goitrogens, phytoestrogens, phytates, and tannins. As a result, there may be select individuals with specific health conditions who elect to decrease their plant food intake despite potential benefits. The purpose of this narrative review is to examine the science of these ‘anti-nutrients’ and weigh the evidence of whether these compounds pose an actual health threat.

Identification and molecular characterization of peroxiredoxin 6 from noble scallop Chlamys nobilis revealing its potent immune response and antioxidant property

The 1-cyseine peroxiredoxin (Prx6) is an importantly antioxidant enzyme that protects cells from oxidative damage caused by excessive production of reactive oxygen species (ROS). In this study, we described the molecular characteristics of the noble scallop Chlamys nobilis peroxiredoxin 6 (designed as CnPrx6), immune responses and DNA protection activity of the recombinant protein. The complete ORF (696 bp) of CnPrx6 encoded a polypeptide (25.5 kDa) of 231 amino acids, harboring a conserved peroxidase catalytic center (⁴¹PVCTTE⁴⁶) and the catalytic triads putatively involved in peroxidase and phospholipase A2 activities. The deduced amino acid sequence of CnPrx6 shared a relatively high amino acid sequence similarity (more than 50%). The qRT-PCR revealed that the CnPrx6 mRNA was constitutively expressed in all examined tissues, with the highest expression observed in adductor. Upon immunological challenge with Vibrio parahaemolyticus, lipopolysaccharides (LPS) and polyinosinic-polycytidylic acid (Poly I:C), the expression level of CnPrx6 mRNA was significantly up-regulated (P < 0.05). Furthermore, there was a significant difference (P < 0.05) in the expression level of CnPrx6 between golden and brown scallops. The purified recombinant CnPrx6 protein protected the supercoiled plasmid DNA from metal-catalyzed ROS damage. Taken together, these results indicated that the CnPrx6 may play an important role in modulating immune responses and minimizing DNA damage in noble scallop Chlamys nobilis.

A Study on Redox Potential of Phytochemicals and their Impact on DNA

The phytochemicals are endowed with antioxidant activities because of the presence of plentiful polyphenols and many other phytochemicals. However, some recent reports have suggested that phytochemicals from certain plant species exhibit DNA damaging properties mainly due to presence of alkaloids. In the present study, pBR322, Salmonella typhi DNA, insect DNA and human DNA were treated with hexanolic extract of Argemone mexicana and Thevesia peruviana leaves to assess their DNA damaging abilities. Another set of experiments was carried out using the methanolic extracts of Citrus lemon leaves to assess their DNA protecting abilities from damage of DNA by extracts of A. mexicana and T. peruviana at 150000 ppm for all DNAs used. The results indicated that the leaves extract of A. mexicanaand T. peruviana demonstrated significant DNA damaging potential at higher concentrations. In contrast, the extracts from C. limonat 15000 ppm showed maximum DNA protective properties for all DNAs used.

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress

Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H₂O₂ concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H₂O₂ results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H₂O₂ at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H₂O₂ induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H₂O₂ alters the evolution of resistance against oxygen stress. Experimental evolution of H₂O₂ resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients.

Throughout evolution, bacteria were exposed to reactive oxygen species and evolved the ability to scavenge toxic oxygen radicals. Furthermore, multicellular organisms evolved the ability to produce such oxygen species directed against pathogens. Recent studies also suggest that ROS such as H₂O₂ play an important role during host gut colonisation by its microbiota. Traditionally, experiments with different antimicrobials have been carried out using fixed concentrations while in nature, including in intra-host environments, microbes are more likely to experience this type of stress in steps or gradients. Here we show that bacteria treated with sub-lethal concentrations of H₂O₂ (priming) survive far better than non-treated cells when they subsequently encounter a higher concentration. We also found that the 'priming' response has a protective role from lethal mutagenesis. This protection is provided by long-lived proteins that, upon priming, remain at a high level for several generations as determined by time-lapse LC-mass spectrometry. Bacteria that were primed evolved H₂O₂ resistance faster and to a higher level. Moreover, mutations that increase resistance to H₂O₂, as determined by whole-genome sequencing (WGS), do not occur in known scavenger encoding genes but in loci coding for other functions, at least in E. coli.

Dancing with reactive oxygen species generation and elimination in nanotheranostics for disease treatment

Reactive oxygen species (ROS) play important roles in cell signaling and tissue homeostasis, in which the level of ROS is critical through the equilibrium between ROS generating and eliminating events. A disruption of the balance leads to disease development either by a surplus or a dearth of ROS, which requires ROS-modulating strategies to overturn the defect for disease treatment. Over the past decade, there have been tremendous advances in nanomedicine centering ROS generation and/or elimination as major mechanisms to treat a variety of diseases. In this review, we will discuss the research achievements on two opposite approaches of ROS-generating and ROS-eliminating strategies for treating cancer and other related diseases. Importantly, we will highlight the conceptual and strategic advances of ROS-mediated immunomodulation, including macrophage polarization, immunogenic cell death and T cell activation, which are currently rising as one of the mainstreams of cancer therapy. At the end, the future challenges and opportunities of mediating ROS-based mechanisms are envisioned. In light of the pleiotropic roles of ROS in different diseases, we hope this review is timely to deliver a clear logic of designing principles on ROS generation and elimination for different disease treatments.

Photosensitizer Tailored Surface Functionalized Carbon Dots for Visible Light Induced Targeted Cancer Therapy

Herein, a photosensitizer (riboflavin) tailored surface functionalized carbon dot (RCD1s) was designed to utilize it in visible light induced targeted cancer therapy. At first, phenylboronic acid appended biotinylated blue emitting carbon dot (CD1s) was synthesized. Riboflavin having "diol" moiety was covalently linked with this CD1s to prepare RCD1s by using complementary boronate-diol linkage. Lewis acid-base interaction facilitated the covalent linkage formation between the surface functionalizing agent of CD1s and riboflavin to develop water-soluble, green emitting RCD1s. Interestingly, this newly synthesized RCD1s has the ability to produce reactive oxygen species (ROS) such as hydroxyl and superoxide radicals under exposure of visible light (wavelength: 460-490 nm). These ROS also can destroy the structure of DNA by oxidative pathway. Thus, under irradiation of visible light (wavelength: 460-490 nm), RCD1s was found to kill HeLa and B16F10 melanoma cells over noncancer cell NIH3T3 by ∼5-fold higher efficacy through ROS induced oxidative DNA damage. The presence of biotin on the surface of the riboflavin tethered carbon dot is essential for the selective killing of cancer cells over normal cells. In the presence of UV light (340-420 nm), RCD1s showed no notable killing of cancer cells as well as normal cells. Besides, RCD1s in the presence of visible light selectively stained HeLa and B16F10 cells over noncancerous cell NIH3T3 by exploiting its fluorescence and cancer cell targeting moiety, biotin. Hence, the newly developed RCD1s can be utilized in theranostic applications including bioimaging and selective killing of cancer cells in the presence of visible light (460-490 nm).

Identification and molecular characterization of peroxiredoxin 2 in grass carp (Ctenopharyngodon idella)

Peroxiredoxin (Prx), also named thioredoxin peroxidase (TPx), is a selenium independent antioxidant enzyme that can protect organisms from oxidative damage caused by reactive oxygen species (ROS) and is important for immune responses. In this study, the molecular cloning and characterization of a Prx2 homologue (CiPrx2) were described from grass carp (Ctenopharyngodon idella). The full-length cDNA of CiPrx2 was 1163 bp containing 5'-untranslated region (UTR) of 52 bp, a 3'-UTR of 517 bp with the putative polyadenylation consensus signal (AATAAA), an open reading frame (ORF) of 594 bp encoding polypeptides of 197 amino acids with a predicted molecular mass of 21.84 kDa and theoretical isoelectric point of 5.93. The analysis results of multiple sequence alignment and phylogenetic tree confirmed that CiPrx2 belong to the typical 2-Cys Prx subfamily. The CiPrx2 mRNA was ubiquitously expressed in all tested tissues. The temporal expression of CiPrx2 were differentially induced infected with grass carp reovirus (GCRV), polyinosinic:polycytidylic acid (poly I:C) and lipopolysaccharide (LPS) in liver and spleen. Subcellular localization of CiPrx2-GFP fusion proteins were only distributed in the cytoplasm. The purified recombinant CiPrx2 possessed an apparent antioxidant activity and could protect DNA against oxidative damage. Finally, CiPrx2 proteins could obviously inhibit H₂O₂ and heavy metal toxicity. However, further researches are needed to better understand the regulation of CiPrx2 under oxidative stresses.

The cyclopurine deoxynucleosides: DNA repair, biological effects, mechanistic insights, and unanswered questions

Patients with the genetic disease xeroderma pigmentosum (XP) who lack the capacity to carry out nucleotides excision repair (NER) have a dramatically elevated risk of skin cancer on sun exposed areas of the body. NER is the DNA repair mechanism responsible for the removal of DNA lesions resulting from ultraviolet light. In addition, a subset of XP patients develop a progressive neurodegenerative disease, referred to as XP neurologic disease, which is thought to be the result of accumulation of endogenous DNA lesions that are repaired by NER but not other repair pathways. The 8,5-cyclopurine deoxynucleotides (cyPu) have emerged as leading candidates for such lesions, in that they result from the reaction of the hydroxyl radical with DNA, are strong blocks to transcription in human cells, and are repaired by NER but not base excision repair. Here I present a focused perspective on progress into understating the repair and biological effects of these lesions. In doing so, I emphasize the role of Tomas Lindahl and his laboratory in stimulating cyPu research. I also include a critical evaluation of the evidence supporting a role for cyPu lesions in XP neurologic disease, with a focus on outstanding questions, and conceptual and technologic challenges.

CodY Regulates Thiol Peroxidase Expression as Part of the Pneumococcal Defense Mechanism against H2O2 Stress

Streptococcus pneumoniae is a facultative anaerobic pathogen. Although it maintains fermentative metabolism, during aerobic growth pneumococci produce high levels of H₂O₂, which can have adverse effects on cell viability and DNA, and influence pneumococcal interaction with its host. The pneumococcus is unusual in its dealing with toxic reactive oxygen species (ROS) in that it neither has catalase nor the global regulators of peroxide stress resistance. Previously, we identified pneumococcal thiol peroxidase (TpxD) as the key enzyme for enzymatic removal of H₂O₂, and showed that TpxD synthesis is up-regulated upon exposure to H₂O₂. This study aimed to reveal the mechanism controlling TpxD expression under H₂O₂ stress. We hypothesize that H₂O₂ activates a transcription factor which in turn up-regulates tpxD expression. Microarray analysis revealed a pneumococcal global transcriptional response to H₂O₂. Mutation of tpxD abolished H₂O₂-mediated response to high H₂O₂ levels, signifying the need for an active TpxD under oxidative stress conditions. Bioinformatic tools, applied to search for a transcription factor modulating tpxD expression, pointed toward CodY as a potential candidate. Indeed, a putative 15-bp consensus CodY binding site was found in the proximal region of tpxD-coding sequence. Binding of CodY to this site was confirmed by EMSA, and genetic engineering techniques demonstrated that this site is essential for TpxD up-regulation under H₂O₂ stress. Furthermore, tpxD expression was reduced in a ΔcodY mutant. These data indicate that CodY is an activator of tpxD expression, triggering its up-regulation under H₂O₂ stress. In addition we show that H₂O₂ specifically oxidizes the 2 CodY cysteines. This oxidation may trigger a conformational change in CodY, resulting in enhanced binding to DNA. A schematic model illustrating the contribution of TpxD and CodY to pneumococcal global transcriptional response to H₂O₂ is proposed.

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli cells with computationally predicated ethanol-binding proteins and experimentally identified ethanol tolerance genes. Our analysis suggests: (1) ethanol damages cell wall and membrane integrity, causing increased stresses, particularly reactive oxygen species, which damages DNA and reduces the O2 level; (2) decreased cross-membrane proton gradient from membrane damage, coupled with hypoxia, leads to reduced ATP production by aerobic respiration, driving cells to rely more on fatty acid oxidation, anaerobic respiration and fermentation for ATP production; (3) the reduced ATP generation results in substantially decreased synthesis of macromolecules; (4) ethanol can directly bind 213 proteins including transcription factors, altering their functions; (5) all these changes together induce multiple stress responses, reduced biosynthesis, cell viability and growth; and (6) ethanol-adapted E. coli cells restore the majority of these reduced activities through selection of specific genomic mutations and alteration of stress responses, ultimately restoring normal ATP production, macromolecule biosynthesis, and growth. These new insights into the energy and mass balance will inform design of more ethanol-tolerant strains.

Effect of seven Indian plant extracts on Fenton reaction-mediated damage to DNA constituents

The influences of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates, and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from Acacia catechu, Emblica officinalis, Spondias dulcis, Terminalia belerica, Terminalia chebula, as well as gallic acid, epicatechin, chebulagic acid and chebulinic acid enhance the extent of damage in Fenton reactions with all monomeric substrates but protect supercoiled plasmid DNA, compared to standard Fenton reactions. The damage to pyrimidine nucleosides/nucleotides is enhanced by these extracts and compounds to a greater extent than for purine ones in a concentration dependent manner. Dolichos biflorus and Hemidesmus indicus extracts generally do not show this enhancement for the monomeric substrates though they protect plasmid DNA. Compared to standard Fenton reactions for deoxynucleosides with ethanol, the presence of these five plant extracts render ethanol scavenging less effective as the radical is generated in the vicinity of the target. Since substoichiometric amounts of these extracts and the four compounds produce this effect, a catalytic mechanism involving the presence of a ternary complex of the nucleoside/nucleotide substrate, a plant compound and the hydroxyl radical is proposed. Such a mechanism cannot operate for plasmid DNA as the planar rings in the extract compounds cannot stack with the duplex DNA bases. These plant extracts, by enhancing Fenton reaction-mediated damage to deoxynucleoside triphosphates, slow down DNA replication in rapidly dividing cancer cells, thus contributing to their anticancer properties.

Quantification of DNA Damage by Real-Time qPCR

This chapter describes the use of real-time qPCR to quantify damages in genomic DNA. The method is based on the ability of a lesion in one strand to inhibit restriction enzyme digestion of double-stranded DNA. Subsequent amplification of the complementary strand after restriction cleavage gives a quantitative measure of the damage content in that site (Real-time qPCR Analysis of Damage Frequency; RADF). We compare the RADF assay with the commonly used technique to assess damages by their ability to inhibit amplification of a large PCR fragment relative to a short PCR fragment. The RADF method described here is quick, accurate and allows the detection of nuclear and mitochondrial DNA damage in detailed regions.

Identification and molecular characterization of peroxiredoxin 6 from Japanese eel (Anguilla japonica) revealing its potent antioxidant properties and putative immune relevancy

Peroxiredoxins (Prdx) are thiol specific antioxidant enzymes that play a pivotal role in cellular oxidative stress by reducing toxic peroxide compounds into nontoxic products. In this study, we identified and characterized a peroxiredoxin 6 counterpart from Japanese eel (Anguilla japonica) (AjPrdx6) at molecular, transcriptional and protein level. The identified full-length coding sequence of AjPrdx6 (669 bp) coded for a polypeptide of 223 aa residues (24.9 kDa). Deduced protein of AjPrdx6 showed analogy to characteristic structural features of 1-cysteine peroxiredoxin sub-family. According to the topology of the generated phylogenetic reconstruction AjPrdx6 showed closest evolutionary relationship with Salmo salar. As detected by Quantitative real time PCR (qPCR), AjPrdx6 mRNA was constitutively expressed in all the tissues examined. Upon the immune challenges with Edwardsiella tarda, lipopolysaccharides and polyinosinic:polycytidylic acid, expression of AjPrdx6 mRNA transcripts were significantly induced. The general functional properties of Prdx6 were confirmed using purified recombinant AjPrdx6 protein by deciphering its potent protective effects on cultured vero cells (kidney epithelial cell from an African green monkey) against H2O2-induced oxidative stress and protection against oxidative DNA damage elicited by mixed function oxidative (MFO) system. Altogether, our findings suggest that AjPrdx6 is a potent antioxidant protein in Japanese eels and its putative immune relevancy in pathogen stress mounted by live-bacteria or pathogen associated molecular patterns (PAMPs).

Production and removal of superoxide anion radical by artificial metalloenzymes and redox-active metals

Generation of reactive oxygen species is useful for various medical, engineering and agricultural purposes. These include clinical modulation of immunological mechanism, enhanced degradation of organic compounds released to the environments, removal of microorganisms for the hygienic purpose, and agricultural pest control; both directly acting against pathogenic microorganisms and indirectly via stimulation of plant defense mechanism represented by systemic acquired resistance and hypersensitive response. By aiming to develop a novel classes of artificial redox-active biocatalysts involved in production and/or removal of superoxide anion radicals, recent attempts for understanding and modification of natural catalytic proteins and functional DNA sequences of mammalian and plant origins are covered in this review article.

Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA

Oxidation of cytosine is a leading cause of mutations and can lead to cancer. Here we report molecular dynamics simulations that characterized the structure and flexibility of 5-hydroxycytosine damaged DNA. A total of four systems were studied: undamaged DNA, damaged DNA base paired to a matching guanine, damaged DNA base paired to a mismatching adenine, and the corresponding undamaged mismatched strand. The simulations showed high spatial similarity between undamaged and damaged DNA; however, the matched damaged strand had greater overtwisting flexibility, and for both the matched and unmatched strands sugar puckering was much more flexible at the damaged site. The mismatch introduced larger changes, notably a loss in hydrogen bonding and a gain in stacking interactions, as well as effects on base pair and step geometry and solvation. Implications for damage recognition are discussed.

Chloro-benzoquinones cause oxidative DNA damage through iron-mediated ROS production in Escherichia coli

Chloro-benzoquinones (CBQs) are a group of disinfection byproducts that are suspected to be potentially carcinogenic. Here, the mechanism of DNA damage caused by CBQs in the presence of ferrous ions was investigated in an Escherichia coli wild type M5 strain and a mutant L5 (ahpCF katEG mutant) strain that carried an enhanced green fluorescent protein reporter under the control of a SOS response gene (recA) promoter. All tested CBQs (including para-benzoquinone, 2-chloro-para-benzoquinone, and dichloro-para-benzoquinones with different substitutes) caused substantial oxidative DNA damage with EC50 values in the micromolar range. Moreover, 2,5-dichloro-para-benzoquinone (2,5-DCBQ), a typical CBQ, caused substantial ROS production in E. coli mutant cells. And ROS scavengers provided partial protective effects on genotoxicity of 2,5-DCBQ to E. coli mutant cells. The addition of Fe(2+) to the 2,5-DCBQ exposure system caused an increase in DNA oxidative damage; iron-chelating agents could partially prevent these cells from DNA damage. Finally, intracellular AhpCF, catalase E, and catalase G were all found to play an important role in the survival of E. coli cells exposed to CBQs, as indicated by an increased sensitivity of the ahpCF katEG mutant L5 strain to treatment compared with wild type M5 cells. Taken together, these results suggest that CBQs cause oxidative DNA damage in E. coli cells through the participation of iron-mediated ROS production.

Ferritin M of Paralichthys olivaceus possesses antimicrobial and antioxidative properties

Ferritin is an evolutionarily conserved protein that plays a vital role in maintaining iron homeostasis. In this study, we identified a ferritin M (PoFerM) from Japanese flounder (Paralichthys olivaceus) and analyzed its biological property. PoFerM is composed of 176 amino acid residues and contains the conserved ferroxidase diiron center and the ferrihydrite nucleation center typical of M ferritins. Expression of PoFerM occurred in multiple tissues and was most abundant in blood. Bacterial infection upregulated PoFerM expression in head kidney, spleen, and liver in a time-dependent manner. Recombinant PoFerM (rPoFerM) purified from Escherichia coli exhibited iron-chelating activity and inhibited bacterial growth, whereas rPoFerMM, the mutant protein that bears alanine substitution at two conserved residues of the ferroxidase center and the ferrihydrite nucleation center, failed to do so. Oxidative protection analysis showed that rPoFerM, but not rPoFerMM, was able to alleviate the deleterious effect of H2O2-induced free radicals on plasmid DNA and primary flounder cells. Together these results indicate that PoFerM is an iron chelator with antimicrobial and antioxidative properties, all which depend on the conserved ferroxidase center and the ferrihydrite nucleation site.

Comparative real-time study of cellular uptake of a formulated conjugated linolenic acid rich nano and conventional macro emulsions and their bioactivity in ex vivo models for parenteral applications

The objective of the present study was to fabricate and monitor real-time, impact of a stable conjugated linolenic acid, α-eleostearic acid (ESA) rich nanoemulsion (NE) formulation (d < 200 nm) vis-à-vis ESA conventional emulsion (CE) system in ex vivo systems against both endogenous and exogenous reactive oxygen species (ROS). Accordingly, stable nanoemulsion formulation of ESA was engineered with the aid of bitter melon seed oil and non-toxic excipients. Morphology and particle size of the emulsion formulations were studied to validate stability. The real-time rapid uptake of the ESA NE and its increased prophylactic efficacy against induced endogenous and exogenous ROS in terms of cell viability and membrane integrity was evaluated flow-cytometrically and with fluorescence microscopic analysis of different primary cells. It was found that the fabricated non-toxic ESA NE had stable parameters (hydrodynamic mean diameter, particle size distribution and zeta potential) for over 12 weeks. Further, ESA NE at a concentration of ∼ 70 μM exhibited maximum efficacy in protecting cells from oxidative damage against both endogenous and exogenous ROS in lymphocytes and hepatocytes as compared to its corresponding presence in the CE formulation. This study provides a real-time empirical evidence on the influence of nano formulation in enhancing bioavailability and antioxidative properties of ESA.

Molecular profile and functional characterization of the ferritin H subunit from rock bream (Oplegnathus fasciatus), revealing its putative role in host antioxidant and immune defense

Ferritins are iron binding proteins made out of 24 subunits, involved in iron homeostasis and metabolism in cellular environments. Here, we sought to identify and functionally characterize a one type of subunits of ferritin (ferritin H-like subunit) from rock bream (Oplegnathus fasciatus; RbFerH). The complete coding sequence of RbFerH was 531 bp in length, encoding a 177-amino acid protein with a predicted molecular mass of 20.8 kDa. The deduced protein structure possessed the domain architecture characteristic of known ferritin H subunits, including metal ligands for iron binding, a ferroxidase center, and two iron-binding region signatures. As expected, the 5' untranslated region of the RbFerH cDNA sequence contained a putative iron response element region, a characteristic regulatory element involved in its translation. The RbFerH gene comprised 5 exons and 4 introns spanning a 4195 bp region. Overexpressed recombinant RbFerH protein demonstrated prominent Fe(II) ion depriving activity, bacteriostatic properties, and protective effects against oxidative double-stranded DNA damage. Using quantitative polymerase chain reaction (qPCR), we found that RbFerH was expressed ubiquitously in the majority of physiologically important tissues in rock bream. A greater abundance of the mRNA transcripts were detected in blood and liver tissues. Upon administering different microbial pathogens and pathogen-derived mitogens, RbFerH transcription was markedly elevated in the blood of rock bream. Taken together, our findings suggest that RbFerH acts as a potent iron sequestrator in rock bream and may actively participate in antimicrobial as well as antioxidative defense.

Iron, oxidative stress and gestational diabetes

Both iron deficiency and hyperglycemia are highly prevalent globally for pregnant women. Iron supplementation is recommended during pregnancy to control iron deficiency. The purposes of the review are to assess the oxidative effects of iron supplementation and the potential relationship between iron nutrition and gestational diabetes. High doses of iron (~relative to 60 mg or more daily for adult humans) can induce lipid peroxidation in vitro and in animal studies. Pharmaceutical doses of iron supplements (e.g., 10× RDA or more for oral supplements or direct iron supplementation via injection or addition to the cell culture medium) for a short or long duration will induce DNA damage. Higher heme-iron intake or iron status measured by various biomarkers, especially serum ferritin, might contribute to greater risk of gestational diabetes, which may be mediated by iron oxidative stress though lipid oxidation and/or DNA damage. However, information is lacking about the effect of low dose iron supplementation (≤60 mg daily) on lipid peroxidation, DNA damage and gestational diabetes. Randomized trials of low-dose iron supplementation (≤60 mg daily) for pregnant women are warranted to test the relationship between iron oxidative stress and insulin resistance/gestational diabetes, especially for iron-replete women.

In vivo detection of a novel endogenous etheno-DNA adduct derived from arachidonic acid and the effects of antioxidants on its formation

Previous studies showed that 7-(1',2'-dihydroxyheptyl)-substituted etheno DNA adducts are products of reactions with the epoxide of (E)-4-hydroxy-2-nonenal, an oxidation product of ω-6 polyunsaturated fatty acids (PUFAs). In this work, we report the detection of 7-(1',2'-dihydroxyheptyl)-1,N(6)-ethenodeoxyadenosine (DHHedA) in rodent and human tissues by two independent methods: a (32)P-postlabeling/HPLC method and an isotope dilution liquid chromatography-electrospray ionization-tandem mass spectrometry method, demonstrating for the first time that DHHedA is a background DNA lesion in vivo. We showed that DHHedA can be formed upon incubation of arachidonic acid with deoxyadenosine, supporting the notion that ω-6 PUFAs are the endogenous source of DHHedA formation. Because cyclic adducts are derived from the oxidation of PUFAs, we subsequently examined the effects of antioxidants, α-lipoic acid, Polyphenon E, and vitamin E, on the formation of DHHedA and γ-hydroxy-1,N(2)-propanodeoxyguanosine (γ-OHPdG), a widely studied acrolein-derived adduct arising from oxidized PUFAs, in the livers of Long Evans Cinnamon (LEC) rats. LEC rats are afflicted with elevated lipid peroxidation and prone to the development of hepatocellular carcinomas. The results showed that although the survival of LEC rats was increased significantly by α-lipoic acid, none of the antioxidants inhibited the formation of DHHedA, and only Polyphenon E decreased the formation of γ-OHPdG. In contrast, vitamin E caused a significant increase in the formation of both γ-OHPdG and DHHedA in the livers of LEC rats.

Improved yield of high molecular weight DNA coincides with increased microbial diversity access from iron oxide cemented sub-surface clay environments

Despite over three decades of progress, extraction of high molecular weight (HMW) DNA from high clay soils or iron oxide cemented clay has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage. Several DNA extraction procedures were compared from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions offered no improvement in nucleic acid recovery. Lysis by liquid N₂ grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22±2.33 µg DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46±0.25 µg DNA/g clay with the Powerlyzer system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots of 16S rRNA (V1–V3 region) pyrosequencing from A-horizon and clay soils showed an ∼80% and ∼400% larger accessed diversity compared to the Powerlyzer soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered.

Quantitative and in situ detection of oxidatively generated DNA damage 8,5'-cyclo-2'-deoxyadenosine using an immunoassay with a novel monoclonal antibody

Xeroderma pigmentosum (XP) is a genetic disorder associated with defects in nucleotide excision repair, which eliminates a wide variety of helix-distorting types of DNA damage including sunlight-induced pyrimidine dimers. In addition to skin disease, approximately 30% of XP patients develop progressive neurological disease, which has been hypothesized to be associated with the accumulation of a particular type of oxidatively generated DNA damage called purine 8,5'-cyclo-2'-deoxynucleosides (purine cyclonucleosides). However, there are no currently available methods to detect purine cyclonucleosides in DNA without the need for DNA hydrolysis. In this study, we generated a novel monoclonal antibody (CdA-1) specific for purine cyclonucleosides in single-stranded DNA that recognizes 8,5'-cyclo-2'-deoxyadenosine (cyclo-dA). An immunoassay using CdA-1 revealed a linear dose response between known amounts of cyclo-dA in oligonucleotides and the antibody binding to them. The quantitative immunoassay revealed that treatment with Fenton-type reagents (CuCl(2)/H(2)O(2)/ascorbate) efficiently produces cyclo-dA in DNA in a dose-dependent manner. Moreover, immunofluorescent analysis using CdA-1 enabled the visualization of cyclo-dA in human osteosarcoma cells, which had been transfected with oligonucleotides containing cyclo-dA. Thus, the CdA-1 antibody is a valuable tool for the detection and quantification of cyclo-dA in DNA, and may be useful for characterizing the mechanism(s) underlying the development of XP neurological disease.

DNA-templated Ag nanoclusters as fluorescent probes for sensing and intracellular imaging of hydroxyl radicals

We have developed a simple, rapid and label-free sensor for the essential biological OH radicals based on the fluorescence quenching of DNA-templated Ag nanoclusters (DNA-Ag NCs). The OH radicals generated from the Fenton reagent attack and cleave the DNA template, which disturbs the microenvironments around Ag NCs, resulting in spontaneous aggregation due to the lack of stabilization and further the quenching of the Ag NCs fluorescence. These changes in fluorescence intensity allow sensing of OH radicals with good sensitivity and selectivity under optimal conditions. The sensor can be also applied for quantifying the radical scavenging action of antioxidants. Various characterizations including absorption spectra, fluorescence lifetimes, light scattering (LS) spectra, transmission electron microscopy (TEM), dark field light scattering imaging, and circular dichroism (CD) spectrometry have been employed to illustrate the proposed sensing mechanism. Further investigations demonstrate that the fluorescent probe could penetrate into intact cell membranes to selectively detect intracellular OH radicals induced by the phorbol myristate acetate (PMA) stimulation. These advantageous characteristics make the fluorescent DNA-Ag NCs potentially useful as a new candidate to monitor OH in broad biosystems.

Comparative proteomic analysis of Streptomyces lividans Wild-Type and ppk mutant strains reveals the importance of storage lipids for antibiotic biosynthesis

Streptomyces lividans TK24 is a strain that naturally produces antibiotics at low levels, but dramatic overproduction of antibiotics occurs upon interruption of the ppk gene. However, the role of the Ppk enzyme in relation to the regulation of antibiotic biosynthesis remains poorly understood. In order to gain a better understanding of the phenotype of the ppk mutant, the proteomes of the wild-type (wt) and ppk mutant strains, grown for 96 h on R2YE medium limited in phosphate, were analyzed. Intracellular proteins were separated on two-dimensional (2D) gels, spots were quantified, and those showing a 3-fold variation or more were identified by mass spectrometry. The expression of 12 proteins increased and that of 29 decreased in the ppk mutant strain. Our results suggested that storage lipid degradation rather than hexose catabolism was taking place in the mutant. In order to validate this hypothesis, the triacylglycerol contents of the wt and ppk mutant strains of S. lividans as well as that of Streptomyces coelicolor M145, a strain that produces antibiotics at high levels and is closely related to S. lividans, were assessed using electron microscopy and thin-layer chromatography. These studies highlighted the large difference in triacylglycerol contents of the three strains and confirmed the hypothetical link between storage lipid metabolism and antibiotic biosynthesis in Streptomyces.

MECHANISMS FOR THE DECOMPOSITION OF HYDROXYL-RADICAL-INDUCED CYTOSINE HYDROPEROXIDES: A COMPUTATIONAL STUDY

Hydroxyl-radical-induced damage to cytosine leads to a multitude of base modifications, which contribute to the natural processes of aging, mutagenesis and carcinogenesis. The stable products resulting from the main hydroxyl-radical-induced cytosine hydroperoxide, 5-hydroxy-6-hydroperoxyl-5,6-dihydrocytosine (5-OH-6-OOH-DHC), have been mapped out in the present work for the first time using ab initio calculations. Optimized geometries of all stationary structures in the gas phase were determined at the MP2 and B3LYP using the 6-31G(d) basis set and at the B3LYP/6-311++G(d,p) levels of theory. Energies were also determined at the G3MP2 level of theory. Meanwhile, full optimization of all stationary points were also performed in aqueous solution at the B3LYP/CPCM/6-31G(d) level of theory to evaluate the solvent effect. Three distinct possible pathways, pathways A–C, were evaluated. For pathway C, four channels, channels D–G, were characterized in turn. In each pathway, both the direct and the water-mediated processes were considered. The calculated results clearly manifest that (i) pathway C is kinetically favored over pathways A and B and is the most energetically feasible decomposition process of 5-OH-6-OOH-DHC; (ii) for pathway C, channels D, E and G are energetically feasible mechanisms and 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione, 1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine, and biuret therefore are predicted to be the kinetically favored decomposition products of 5-OH-6-OOH-DHC; (iii) channel G may be kinetically favored over channels D and E and have the highest possibility to occur; (iv) the thermal decomposition of 5-OH-6-OOH-DHC can be significantly promoted by the presence of one explicit water molecule. Apart from characterizing the experimental products well, the main striking result of the present DFT computational study is the identification of a new theoretical optimum decomposition product, i.e. 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione. The data and insights presented here have elucidated the chemical properties of 5-OH-6-OOH-DHC in free radical reactions and should facilitate to assess their mutagenic features.

Identification of the Treponema pallidum subsp. pallidum TP0092 (RpoE) regulon and its implications for pathogen persistence in the host and syphilis pathogenesis

Bacteria often respond to harmful environmental stimuli with the induction of extracytoplasmic function (ECF) sigma (σ) factors that in turn direct RNA polymerase to transcribe specific groups of response genes (or regulons) to minimize cellular damage and favor adaptation to the changed extracellular milieu. In Treponema pallidum subsp. pallidum, the agent of syphilis, the TP0092 gene is predicted to code for the pathogen's only annotated ECF σ factor, homologous to RpoE, known in Escherichia coli to control a key transduction pathway for maintenance of envelope homeostasis in response to external stress and cell growth. Here we have shown that TP0092 is highly transcribed during experimental syphilis. Furthermore, TP0092 transcription levels significantly increase as infection progresses toward immune clearance of the pathogen, suggesting a role for TP0092 in helping T. pallidum respond to harmful stimuli in the host environment. To investigate this hypothesis, we determined the TP0092 regulon at two different time points during infection using chromatin immunoprecipitation followed by high-throughput sequencing. A total of 22 chromosomal regions, all containing putative TP0092-binding sites and corresponding to as many T. pallidum genes, were identified. Noteworthy among them are the genes encoding desulfoferrodoxin and thioredoxin, involved in detoxification of reactive oxygen species (ROS). Because T. pallidum does not possess other enzymes for ROS detoxification, such as superoxide dismutase, catalase, or glutathione peroxidase, our results suggest that the TP0092 regulon is important in protecting the syphilis spirochete from damage caused by ROS produced at the site of infection during the inflammatory response.

Intravenous ferric chloride hexahydrate supplementation induced endothelial dysfunction and increased cardiovascular risk among hemodialysis patients

Background

The association between intravenous (IV) iron administration and outcomes in hemodialysis (HD) patients is still debated. Therefore, this study was aimed to assess the relationship between the IV administration of ferric chloride hexahydrate (Atofen®) and cardiovascular (CV) outcome and the interaction between iron-induced oxidative stress and endothelial dysfunction in chronic HD patients.

Methodology/Principal Findings

A cohort of 1239 chronic HD patients was recruited. In a follow-up of 12 months, Kaplan-Meier survival curves showed that higher doses of IV Atofen associated with higher risks for CV events and deaths in HD patients. In multivariate Cox models, compared to no iron supplementation, IV Atofen administration was an independent predictor for CV events and overall mortality. However, the nature of the observational cohort study possibly bears selection bias. We further found that IV Atofen enhanced the superoxide production of mononuclear cells (MNCs), the levels of circulating soluble adhesion molecules, and the adhesion of MNCs to human aortic endothelial cells (HAECs). In vitro experiments showed that Atofen increased the expression of intracellular cell adhesion molecule-1 and vascular cell adhesion molecule-1 in HAECs and aggravated the endothelial adhesiveness in a dose-dependent manner. These iron-induced changes were significantly attenuated by the co-treatment of HAECs with N-acetylcysteine and inhibitors of NADPH oxidase, nuclear factor κB, and activator protein-1.

Conclusion

A cumulative dose of IV Atofen >800 mg within 6 months was associated with an adverse CV outcome and a higher mortality among chronic HD patients. The detrimental effects of IV iron supplementation were partly due to the increased oxidative stress and induction of MNC adhesion to endothelial cells, a pivotal index of early atherogenesis.

Oxidative damage to DNA constituents by iron-mediated Fenton reactions: the deoxyadenosine family

The effect of exposing 2'-deoxyadenosine (dA), 5'-dAMP, 3'-dAMP, dApA, dA(pdA)(19,) and poly(dA): oligo(dT) to iron/H(2)O(2) in the presence and absence of ethanol or NADH has been studied. HPLC retention times, enzyme treatments, radio-labeled substrates, UV absorption spectra, and fast atom bombardment mass spectrometry (FABMS) have been used to distinguish 20 products arising from the reaction, of which 16 have been identified and four anomers proposed by comparison with earlier gamma radiation studies. The radical responsible for the reactions seems to be analogous to radiation-derived [Formula: see text], has many products in common, but has some novel ones probably specific for Fenton-induced damage. Two new dimeric adducts arising from the generation of hydroxylamine at N7 and its subsequent condensation with two known sugar damage products, dR-adenine-N1-oxide, and two isomers of dR-FAPy arising from radical attacks at C4 and C5, may be considered novel in the present study. Unlike radiation-derived [Formula: see text], the radical under study is difficult to eliminate due to its generation in the proximity of the substrate molecules. It is proposed that the iron binds to the phosphate group and generates the radical in its vicinity. Strand breaks in dA(pdA)(11) resulting from the Fenton reaction are of two types, spontaneous and alkali-labile. Duplex DNA is less sensitive to attack by this radical, as its various degradation products are a subset of those obtained with monomer substrates and only dR-FAPy production is relatively enhanced for poly (dA): oligo (dT) as compared to those from other substrates.

Thermodynamic signature of DNA damage: characterization of DNA with a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair

Oxidation of DNA due to exposure to reactive oxygen species is a major source of DNA damage. One of the oxidation lesions formed, 5-hydroxy-2'-deoxycytidine, has been shown to miscode by some replicative DNA polymerases but not by error prone polymerases capable of translesion synthesis. The 5-hydroxy-2'-deoxycytidine lesion is repaired by DNA glycosylases that require the 5-hydroxycytidine base to be extrahelical so it can enter into the enzyme's active site where it is excised off the DNA backbone to afford an abasic site. The thermodynamic and nuclear magnetic resonance results presented here describe the effect of a 5-hydroxy-2'-deoxycytidine·2'-deoxyguanosine base pair on the stability of two different DNA duplexes. The results demonstrate that the lesion is highly destabilizing and that the energy barrier for the unstacking of 5-hydroxy-2'-deoxycytidine from the DNA duplex may be low. This could provide a thermodynamic mode of adduct identification by DNA glycosylases that requires the lesion to be extrahelical.

Characterization of 2'-deoxyguanosine oxidation products observed in the Fenton-like system Cu(II)/H2O2/reductant in nucleoside and oligodeoxynucleotide contexts

Reactive oxygen species attack both base and sugar moieties in DNA with a preference among the bases for reaction at guanine. In the present study, 2'-deoxyguanosine (dG) was oxidized by a copper-mediated Fenton reaction with the reductants ascorbate or N-acetyl-cysteine, yielding oxidation on both the base and the sugar. The primary oxidized lesions observed in these studies include the 2'-deoxyribonucleosides of 8-oxo-7,8-dihydroguanosine (dOG), spiroiminodihydantoin (dSp), guanidinohydantoin (dGh), oxazolone (dZ), and 5-carboxamido-5-formamido-2-iminohydantoin (d2Ih), as well as the free base guanine. d2Ih was the major product observed in the nucleoside, single- and double-stranded oligodeoxynucleotide contexts and is proposed to arise from oxidation at C5 of guanine. Product distribution studies provide insight into the role of the reductant in partitioning of dG base oxidation along the C5 and C8 pathways.

The DNA-binding activity of the Neisseria gonorrhoeae LexA orthologue NG1427 is modulated by oxidation

Neisseria gonorrhoeae is a human-specific organism that is not usually exposed to UV light or chemicals but is likely to encounter reactive oxygen species during infection. Exposure of N. gonorrhoeae to sublethal hydrogen peroxide revealed that the ng1427 gene was upregulated sixfold. N. gonorrhoeae was thought to lack an SOS system, although NG1427 shows amino acid sequence similarity to the SOS response regulator LexA from Escherichia coli. Similar to LexA and other S24 peptidases, NG1427 undergoes autoproteolysis in vitro, which is facilitated by either the gonococcal or E. coli RecA proteins or high pH, and autoproteolysis requires the active and cleavage site residues conserved between LexA and NG1427. NG1427 controls a three gene regulon: itself; ng1428, a Neisseria-specific, putative integral membrane protein; and recN, a DNA repair gene known to be required for oxidative damage survival. Full NG1427 regulon de-repression requires RecA following methyl methanesulphonate or mitomycin C treatment, but is largely RecA-independent following hydrogen peroxide treatment. NG1427 binds specifically to the operator regions of the genes it controls, and DNA binding is abolished by oxidation of the single cysteine residue encoded in NG1427. We propose that NG1427 is inactivated independently of RecA by oxidation.