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DNA is the carrier of biological information and damage to DNA has been believed to be responsible for many diseases including aging and cancer. One electron oxidation by charge migration through DNA is one of the processes that lead to DNA damage. It is known that the guanine N1 imino proton can be transferred to the N3 of cytidine that is hydrogen bonded to it. Some reports have implication that this proton transfer and radical cation migration are coupled to each other. We have incorporated 5-fluoro-2 -deoxycytidine (F5dC) in place of normal dC in DNA duplexes. Although, the lower pKa of F5dC should perturb the proton transfer process from the guanine to it, we do not see any change in the charge migration ability compared to the strands having normal cytidines. However, there is a considerable decrease in the guanine damage, when there is F5dC opposite to it. These results indicate that the charge migration is not coupled with proton transfer process, but the change in basicity affects the reactivity of the guanine radical cation. We have also reported a systematic study on the charge migration through adenine (A) and thymidine (T) containing DNA strands. The damage has predominantly seen in thymidine, although from oxidation potentials reaction at adenine was expected. The thymidine reaction has been analyzed thoroughly. It has similar distance dependence property as the well known guanine damage. Study of thymidine damage in presence of radical scavengers, replacement of thymidines by Uracil and HPLC-MS study point toward reactions involving tandem lesion. On the basis of these information and molecular modeling study we have proposed a possible pathway leading to one-electron oxidation at the thymidines.

In sperm chromatin, DNA exists in a highly condensed state reaching a final volume roughly twenty times that of a somatic nucleus. For the vast majority (>90%) of sperm DNA in mammals, somatic-like histones are first replaced by transition proteins which in turn are replaced by arginine-rich protamines. This near crystalline organization of the DNA in mature sperm is thought crucial for both the transport and protection of genetic information since all DNA repair mechanisms are shut down. Recent studies show that increased DNA damage is linked to dysfunctions in replacing histones with protamines resulting in mispackaged DNA. This increased DNA damage correlates not only to infertility but also impacts normal embryonic development. This damage is currently poorly characterized, but is known to involve oxidative base damage by reactive oxygen species (ROS). Using a variety of biophysical methods, the effect of DNA condensation by polycations on the on free radical access and DNA damage in the packaged state was investigated. In Chapter 2, gel electrophoresis was used to quantify the ability of free radicals to damage both unpackaged and packaged DNA. DNA condensed by polycations shows significantly reduced levels of indirect damage from exposure to free radicals. Combining previous work on packaging density, it is also shown that differences in the packaged state, even by a few Angstroms, can result in significantly different degrees of damage to the DNA. In Chapter 3, we investigate the effects of protamine concentration on the ability to condense and protect DNA. Insufficient protamination is known to be a potential source of protamine dysfunction in mammalian sperm chromatin. Using gel retardation assays and UV-Vis studies, we examined the ability for DNA to condense with protamine at varying nitrogen to phosphate (N:P) charge ratios. Initial results on damage as a function of N:P are also discussed. Future work will more quantitatively determine the interrelationship between DNA packaging densities and the resulting accessibility of DNA to reactive oxygen species (ROS).

ABSTRACT DNA in the eukaryotic nucleus is complexed with histone and non-histone proteins into chromatin. Nucleosomes, the basic repeating unit of chromatin, not only package DNA but are also intimately involved the regulation of gene expression. All DNA transactions including replication, transcription, recombination and repair take place in such a chromatin environment. Access to packaged nucleosomal DNA in vivo is mediated at least in part by protein complexes that modify or remodel chromatin. Buried sequences in nucleosomes can also transiently become accessible to DNA binding proteins during cycles of partial, reversible unwrapping of nucleosomal DNA from the histone octamer. We have investigated the ability of the human, bifunctional DNA glycosylase, endonuclease III (hNTH1), to initiate base excision repair (BER) of discretely positioned oxidative lesions in model nucleosomes. hNTH1 was able to process a thymine glycol (Tg) lesion almost as efficiently as naked DNA, when the minor groove of the lesion faced away from the histone octamer. Lesion processing did not require or result in detectable nucleosome disruption, as assayed in gel mobility-shift experiments. Instead, hNTH1 formed a slower migrating enzyme-nucleosome ternary complex that was found to contain processed DNA. Processing of an inward-facing Tg residue located just 5 bp away from the outward-facing lesion was much reduced and processing of a sterically occluded Tg residue positioned closer to the dyad center of the nucleosome was even more reduced. Notably, processing of both inward-facing lesions was found to increase as a function of enzyme concentration. Restriction enzyme protection studies indicated that access to these inward-facing lesions did not entail nucleosomal translocation or sliding. Collectively, these observations are consistent with a model in which hNTH1 binds to lesions during cycles of reversible, partial unwrapping of nucleosomal DNA from the histone octamer core. To further investigate this partial unwrapping hypothesis, we studied the kinetics of hNTH1 processing of sterically occluded lesions in greater detail. Our results suggest that efficiency of processing of inward-facing lesions is a function of both DNA unwrapping and rewrapping rates, and enzyme affinity for the lesion. In addition, we determined that APE1 which catalyzes the second step in BER, exhibited an increasing capacity to process inward-facing furan residues as its concentration was increased. Thus as with hNTH1, we hypothesize that APE1 can capture occluded furan residues during cycles of partial DNA unwrapping. We propose that cellular regulatory factors benefit from this intrinsic, periodic exposure of nucleosomal DNA exposure in vivo, which may be amplified by the downstream recruitment of remodeling and / or modifying proteins to facilitate DNA transactions in the cell.

The work described in this thesis investigates the mechanisms by which copper complexes catalyse the generation of reactive oxygen species (ROS), including the highly reactive hydroxyl radical (.OH), and induce oxidative damage to DNA. An ESR study into the copper-Fenton reaction revealed that, in the presence of buffers and other copper chelators, .OH is generated. In contrast, it is suggested that a Cu(III) species may be formed in the reaction of aqueous, unchelated copper ions. The generation of .OH in the copper-Fenton reaction, under biomimetic conditions, was confirmed by analysis of the products formed following the incubation of DNA components with this system. Preferential binding of Cu(II) to guanosine over the other nucleosides was determined and copper redox cycling at GC sites was found to be more facile than at AT sites. Stability constants for the copper complexes with several other biochemically important ligands such as glutathione (GSH), Quin2 and 1,10-phenanthroline (OP) were also measured. The ease of redox cycling for the copper complexes was found to be of the order: OP ~ Quin2 > GSH. However, OP enhanced both the copper-Fenton reaction and copper-induced DNA damage while both GSH and Quin2 were inhibitory. Gel chromatography studies suggested that ternary complex formation occurs between Cu(I)-DNA and both Quin2 and OP. This implies that the ternary complex with OP is more redox active than that with Quin2. Whilst cysteine enhanced copper-mediated DNA damage at early incubation times, it was more protective than GSH and homocysteine at later stages. The effects at early incubation times are attributed to the ease of copper redox cycling in the presence of thiols while the effects over prolonged incubations reflect Cu(II) stabilisation by the respective disulphides or similar products.

Astronauts in space flight missions are exposed to increased iron (Fe) stores and galactic cosmic radiation, both of which independently induce oxidative stress. Oxidative stress can result in protein, lipid, and DNA oxidation. Recent evidence has linked oxidative stress to bone loss with aging and estrogen deficiency. Whether the increased iron stores and radiation that astronauts face are exacerbating their extreme bone loss while in space is unclear. We hypothesized that elevated iron levels (induced by feeding a high iron diet) and gamma radiation exposure would independently increase markers of oxidative stress and markers of oxidative damage and result in loss of bone mass, with the combined treatment having additive or synergistic effects. Male Sprague-Dawley rats (15-weeks old, n=32) were randomized to receive an adequate (45 mg Fe/kg diet) or high (650 mg Fe/kg diet) Fe diet for 4 weeks and either 3 Gy (8 fractions, 0.375 Gy each) of 137Cs radiation (γRAD) or sham exposure every other day over 16 days starting on day 14. Serum Fe and catalase and liver Fe and glutathione peroxidase (GPX) were assessed by standard techniques. Immunostaining for 8-hydroxy-2-deoxyguanosine (8-OHdG, marker of DNA adducts) quantified the number of cells with oxidative damage in cortical bone. Bone histomorphometry assessed bone cell activity and cancellous bone microarchitecture in the metaphyseal region. Ex vivo pQCT quantified volumetric bone mineral density (vBMD); bone mechanical strength was assessed by 3-pt bending at the midshaft tibia and compression of the femoral neck. High Fe diet increased liver Fe and decreased volume per total volume (BV/TV). γRAD decreased osteoid surface per bone surface (OS/BS) and osteocyte density. The combined treatment increased serum catalase, liver GPX, and serum iron and decreased cancellous vBMD and trabecular number (Tb.N). High Fe diet and γRAD independently increased number of osteocytes stained positive for 8-OHdG, with the combined treatment exhibiting twice as many osteocytes positively stained compared to the control. Higher serum Fe levels were associated with higher oxidative damage (r =0.38) and lower proximal tibial cancellous vBMD (r =–0.38). Higher serum catalase levels were associated with higher oxidative damage (r =0.48), lower BV/TV (r =–0.40) and lower cancellous vBMD (r =–0.39). High dietary iron and fractionated 137Cs γRAD leads to a moderate elevation in iron stores and results in oxidative damage in bone and are associated with decreased cancellous bone density. Moderate elevations in iron stores are not only found in astronauts, but also naturally occur in healthy human populations. This healthy population with elevated iron stores may also have increased levels of oxidative stress in the body. Elevated levels of oxidative stress not only increase one’s risk for accelerated bone loss, but also the risk of developing other chronic diseases such as insulin resistance, hypertension, dyslipidemia, and metabolic syndrome.

The aim of this study was to observe levels of oxidative DNA damage in patients with multiple injuries in correlation with the nutritional support that the patients have received during their hospital stay. Oxidative DNA damage was evaluated in two periods of time, first evaluation was performed during standard nutritional support according to the ESPEN guidelines. Second evaluation was performed after a change in nutrition according to individual parameters of metabolism and utilization of nutritional components based on indirect calorimetric measurements. This study included 6 patients with multiple injuries hospitalized in the Intensive Care Unit 1 at the Department of Surgery, University Hospital in Hradec Kralove. In this experiment DNA isolated from peripheral lymphocytes was used to evaluate oxidative DNA damage. This DNA was analyzed using the Comet Assay method. The enzymatic version of the Comet Assay was used to determine the oxidative damage of purines and pyrimidines, and the alkaline version was used for detection of single strand breaks. Mann-Whitney test was used for statistic evaluation the difference between both measuremetns, correlation analysis for relations between Comet Assay results and clinical parameters. Significant correlations between a total amount of nutrients given...

As a hydrophilic biopolymer, a DNA molecule is surrounded by water molecules in aqueous solution. The charge hopping mechanism indicates the competition between radical cation quenching by water molecules and migration along DNA partially determines the distance and efficiency of charge transport in DNA. Lipid can effectively bind DNA to induce hydrophobic environment around the DNA helix and reduce the water contact with bases in the DNA duplex. Therefore, the effect of water molecules on charge transport can be studied by comparison between nature DNA and DNA-lipid complexes. We synthesized several cationic lipids with various lengths of dialkyl chain (2, 8, 18) and spermine (Sp4+) binding core in this research, which posses strong DNA binding affinity due to their multi-charged spermine head-groups. Among those, C8GlySp4+ and C2GlySp4+ can form stable complex with DNA oligomer in aqueous solution, characterized by time dependent UV and CD spectrometry. C2GlySp4+ showed the similar inhibition on oxidative damage in GG steps as spermine while C8GlySp4+ demonstrated much more significant prohibitive effect at the same concentration. Since all the lipids bear the same binding core, they should afford the similar binding affinity towards DNA duplexes. we attributed the observation to the longer length of dialkyl group in C8GlySp4+, which can more effectively shield the DNA duplex from the water molecules than either spermine or C2GlySp4+. A kinetic model based on phonon-assist polaron hopping mechanism was proposed to rationalize the experimental results. The finding may give insight on the protection of DNA oxidative damage by reducing the access of the water molecule to DNA duplex and may have potential impact on the application of DNA as conducting biopolymer and protection of DNA in biological system.

Quercetin (Q), a water-soluble flavonoid that is ubiquitous to foods of plant origin is postulated to protect against colon cancer due to its antioxidant activity. In contrast, we have shown that a dietary combination of fish oil (FO; n-3 fatty acids) and pectin may protect against colon cancer by decreasing endogenous antioxidant enzyme activities leading to increased reactive oxygen species (ROS), an inducer of apoptosis. We hypothesized that adding an antioxidant to a FO diet may negate the beneficial effects of FO by counteracting FO effects on colonocyte redox status. To test this, we provided 40 rats with FO or CO (fiber = pectin) diets with Q being 0 or 0.45% of the diet for 10 wk. All rats were injected with azoxymethane (AOM) on d 21 and 28. Measurements included: aberrant crypt (AC) enumeration (colon cancer marker); apoptosis (TUNEL assay); catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPx) activities; reduced and oxidized glutathione concentrations (GSH/GSSG); and oxidative DNA damage (8-OHdG adducts). AC numbers were lower in FO vs CO rats (p<0.0001), but tended to increase for FO diets containing Q (P<0.098). The apoptotic index was higher (p<0.0001) when Q was added to the FO and CO diets. Total SOD (lipid main effect, p=0.0136) and GPX activity (p=0.0025) was elevated in CO rats. CAT activity was higher (p=0.0204) in FO rats, however Q diminished this effect. GSH was not affected by diet; yet, GSSG accumulated (p=0.0554) in CO rats with Q as compared to CO rats without Q. The GSH/GSSG ratio was lower (p=0.0314) in CO rats than in FO rats. There was no difference in 8-OHdG adduct levels in FO vs CO rats, however, Q decreased 8-OHdG adducts in CO rats (p=0.0428). Despite increasing apoptosis, Q did not significantly lower AC formation. These data suggest that the distinct effects of the CO/Q and FO/Q combinations are functioning through different mechanisms to induce apoptosis. The long-term consequences of adding antioxidants such as Q to a diet thought to exert its anticancer effect through a pro-oxidant mechanism are unknown and deserve further study.

The aim was to determine whether the dietary glycemic index (GI) related to coronary heart disease (CHD) risk and whether oxidized LDL could explain this relation. Nine prospective cohorts of GI or glycemic load (GL) associations were pooled in a meta-analysis and showed an increased risk of CHD for high GI (near significant at RR=1.13, 95%CI; 1.00-1.26) and GL diets (significant at RR=1.40, 95%CI; 1.17-1.68), both with significant evidence of heterogeneity (P<0.07). Sera from 151 type 2 diabetics who completed a 6-month trial of a low GI diet demonstrated no treatment difference in measures of oxidative damage. However, when data from both treatments were pooled, oxidized LDL as a marker of CHD risk inversely related to low GI carbohydrate intake. We conclude that GI and GL relate to CHD and oxidative damage to LDL may explain part of this association.