Investigations of DNA-mediated protein oxidation

<p>DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA &#960;-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt &#960;-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA &#960;-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.</p> <p>Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding <i>E. coli</i> Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.</p> <p>Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with <i>g</i> = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.</p> <p>We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in <i>E. coli</i> Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at <i>g</i> = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.</p> <p>DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.</p> <p>While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.</p> <p>In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.</p>

Chemical and Electrochemical Behavior of Graphene-Covered Silicon Photoanodes

<p>This dissertation describes efforts over the last five years to develop protective layers for semiconductor photoelectrodes based on monolayer or few-layer graphene sheets. Graphene is an attractive candidate for a protective layer because of its known chemical inertness, transparency, ease of deposition, and limited number of electronic states. Monolayer graphene was found to effectively inhibit loss of photocurrent over 1000 seconds at n-Si/aqueous electrolyte interfaces that exhibit total loss over photocurrent over 100 seconds. Further, the presence of graphene was found to effect only partial Fermi level pinning at the Si/graphene interface with respect to a range of nonaqueous electrolytes. Fluorination of graphene was found to extend the stability imparted on n-Si by the monolayer sheet in aqueous Fe(CN)₆^3-/4- electrolyte to over 100,000 seconds. It was demonstrated that the stability of the photocurrent of n-Si/fluorinated graphene/aqueous electrolyte interfaces relative to n-Si/aqueous electrolyte interfaces is likely attributable to the inhibition of oxidation of the silicon surface.</p> <p>This dissertation also relates efforts to describe and define terminology relevant to the field of photoelectrochemistry and solar fuels production. Terminology describing varying interfaces employed in electrochemical solar fuels devices are defined, and the research challenges associated with each are discussed. Methods for determining the efficiency of varying photoelectrochemical and solar-fuel-producing cells from the current-voltage behavior of the individual components of such a device without requiring the device be constructed are described, and a range of commonly employed performance metrics are explored. </p>

The oxidation of CH2O in the intermediate temperature range (943-995 K)

New atmospheric pressure flow reactor data on the oxidation of formaldehyde in the temperature range 943-995 K and over equivalence ratios from 0.013 to 36.7 are reported and discussed. A detailed mechanism assembled from previously published results produced acceptable agreement with the experimental data for the fuel-lean conditions, but failed to predict results for oxidative pyrolysis. Analysis or the very fuel-lean conditions, but failed to modelling results are principally sensitive to CH2O+HO2→HCO+H2O2 (6) and H2O2 +M→OH+OH+M (33). Whereas the specific rate of each reaction cannot be independently determined, it is found that the product k33.k6 is a well defined function of temperature: (3.4±3.0).1028 exp(-(26,800±400)/T). Inadequacies in the mechanism which may be responsible for the disagreement under fuel-rich conditions are discussed. © 1991 Combustion Institute.

Cell adhesion to plasma electrolytic oxidation (PEO) titania coatings, assessed using a centrifuging technique.

The adhesion of bovine chondrocytes and human osteoblasts to three titania-based coatings, formed by plasma electrolytic oxidation (PEO), was compared to that on uncoated Ti-6Al-4V substrates, and some comparisons were also made with plasma sprayed hydroxyapatite (HA) coatings. This was done using a centrifuge, with accelerations of up to 160,000 g, so as to induce buoyancy forces that created normal or shear stresses at the interface. It is shown that, on all surfaces, it was easier to remove cells under normal loading than under shear loading. Cell adhesion to the PEO coatings was stronger than that on Ti-6Al-4V and similar to that on HA. Cell proliferation rates were relatively high on one of the PEO coatings, which was virtually free of aluminium, but low on the other two, which contained significant levels of aluminium. It is concluded that the Al-free PEO coating offers promise for application to prosthetic implants.

Effect of operating conditions and fuel type on crevice hc emissions: Model results and comparison with experiments

A one-dimensional model for crevice HC post-flame oxidation is used to calculate and understand the effect of operating parameters and fuel type (propane and isooctane) on the extent of crevice hydrocarbon and the product distribution in the post flame environment. The calculations show that the main parameters controlling oxidation are: bulk burned gas temperatures, wall temperatures, turbulent diffusivity, and fuel oxidation rates. Calculated extents of oxidation agree well with experimental values, and the sensitivities to operating conditions (wall temperatures, equivalence ratio, fuel type) are reasonably well captured. Whereas the bulk gas temperatures largely determine the extent of oxidation, the hydrocarbon product distribution is not very much affected by the burned gas temperatures, but mostly by diffusion rates. Uncertainties in both turbulent diffusion rates as well as in mechanisms are an important factor limiting the predictive capabilities of the model. However, it seems well suited to sensitivity calculations about a baseline. Copyright © 1999 Society of Automotive Engineers, Inc.

Numerical simulation of post-flame oxidation of hydrocarbons in spark ignition engines

About 50-90 percent of the hydrocarbons that escape combustion during flame passage in spark-ignition engine operation are oxidized in the cylinder before leaving the system. The process involves the transport of unreacted fuel from cold walls towards the hotter burned gas regions and subsequent reaction. In order to understand controlling factors in the process, a transient one-dimensional reactive-diffusive model has been formulated for simulating the oxidation processes taking place in the reactive layer between hot burned gases and cold unreacted air/fuel mixture, with initial and boundary conditions provided by the emergence of hydrocarbons from the piston top land crevice. Energy and species conservation equations are solved for the entire process, using a detailed chemical kinetic mechanism for propane. Simulation results show that the post-flame oxidation process takes place within a reactive layer where intermediate hydrocarbon products are formed at temperatures above 1100-1200 K, followed by a carbon monoxide conversion region closer to the hot burned gases. Model results show that most of hydrocarbons leaving the crevice are completely oxidized inside the cylinder. The largest contribution of remaining hydrocarbons are those leaving the crevice at temperatures below 1400 K. The largest fraction of non-fuel (intermediate) hydrocarbons results from hydrocarbons leaving the crevice when core temperatures are around 1400 K Copyright © 1997 Society of Automotive Engineers, Inc.

Extent of oxidation of hydrocarbons desorbing from the lubricant oil layer in spark-ignition engines

The extent of oxidation of hydrocarbons desorbing from the oil layer has been measured directly in a hydrogen-fueled, spark-ignited engine in which the lubricant oil was doped with a single component hydrocarbon. The amount of hydrocarbon desorbed and oxidized could be measured simultaneously as the dopant was only source of carbon-containing species. The fraction oxidized was strongly dependent on engine load, hydrogen fuel-air ratio and dopant chemical reactivity, but only modestly dependent on spark timing and nitrogen dilution levels below 20 percent. Fast FID measurements at the cylinder exit showed that the surviving hydrocarbons emerge late in the exhaust stroke. © Copyright 1996 Society of Automotive Engineers, Inc.

Superhydrophobic carbon nanotube electrode produces a near-symmetrical alternating current from photosynthetic protein-based photoelectrochemical cells

The construction of protein-based photoelectrochemical cells that produce a variety of alternating currents in response to discontinuous illumination is reported. The photovoltaic component is a protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides which catalyses photochemical charge separation with a high quantum yield. Photoelectrochemical cells formed from this protein, a mobile redox mediator and a counter electrode formed from cobalt disilicide, titanium nitride, platinum, or multi-walled carbon nanotubes (MWCNT) generate a direct current during continuous illumination and an alternating current with different characteristics during discontinuous illumination. In particular, the use of superhydrophobic MWCNT as the back electrode results in a near symmetrical forward and reverse current upon light on and light off, respectively. The symmetry of the AC output of these cells is correlated with the wettability of the counter electrode. Potential applications of a hybrid biological/synthetic solar cell capable of generating an approximately symmetrical alternating current are discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improvement and observation of immunoelectron microscopic method for the localization of frog Rana grylio virus (RGV) in infected fish cells

In this paper, to understand the roles of amorphous structures which were observed within the viromatrix of Rana grylio virus (RGV), an improved immunoelectron microscopy (IEM) method was developed to detect the localization of RGV in carp Epithelipma papulosum cyprinid (EPC) cells. Infected EPC cells were fixed with 4% paraformaldehyde-0.25% glutaraldehyde mixture, dehydrated completely, and embedded in LR White resin. This method allowed good ultrastructural preservation and specific labeling with anti-RGV antibodies. The results of IEM showed that colloidal gold mainly bound to the capsids of viral particles at the stage of viral assembly, while during the viral maturation colloidal gold bound to the envelop of virions. In addition, within the viromatrix, the amorphous structures, including dense floccules, membranous materials and tubules, also had strong colloidal gold signals, revealing that those amorphous structures were participated in RGV assembly. In contrast, no significant gold labeling signals were obtained in negative controls. The present study not only provided further evidence that amorphous structures within the viromatrix were involved in the process of RGV assembly, but also developed an improved IEM method for studying the interaction between iridovirus and host cells. (C) 2006 Elsevier Ltd. All rights reserved.