Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-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 π-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 π-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.

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 E. coli 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.

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 g = 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.

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 E. coli 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 g = 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.

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.

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.

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.

Anomalous behaviour of photorefractive grating erasure owing to existence of both negative and positive carriers

In LiNbO3:Fe, anomalous behaviour of grating erasure is observed with different wavelenghts, i.e. rapid grating erasure in the short wavelength range, which deviates from the results predicted by the electron transport band model. The deviation is related to the coexistance of electrons and holes in photorefraction, and charge-transfer process including electrons and hole has been proposed. The electron and hole contributions to photo-excitation coefficient S of the Fe centre on the wavelength.

Channel selective tunnelling through a nanographene assembly.

We report selective tunnelling through a nanographene intermolecular tunnel junction achieved via scanning tunnelling microscope tip functionalization with hexa-peri-hexabenzocoronene (HBC) molecules. This leads to an offset in the alignment between the energy levels of the tip and the molecular assembly, resulting in the imaging of a variety of distinct charge density patterns in the HBC assembly, not attainable using a bare metallic tip. Different tunnelling channels can be selected by the application of an electric field in the tunnelling junction, which changes the condition of the HBC on the tip. Density functional theory-based calculations relate the imaged HBC patterns to the calculated molecular orbitals at certain energy levels. These patterns bear a close resemblance to the π-orbital states of the HBC molecule calculated at the relevant energy levels, mainly below the Fermi energy of HBC. This correlation demonstrates the ability of an HBC functionalized tip as regards accessing an energy range that is restricted to the usual operating bias range around the Fermi energy with a normal metallic tip at room temperature. Apart from relating to molecular orbitals, some patterns could also be described in association with the Clar aromatic sextet formula. Our observations may help pave the way towards the possibility of controlling charge transport between organic interfaces.

Photovoltaic measurements in carbon nanotube - Amorphous silicon core/shell nanowire

Carbon nanotube is one of the promising materials for exploring new concepts in solar energy conversion and photon detection. Here, we report the first experimental realization of a single core/shell nanowire photovoltaic device (2-4μm) based on carbon nanotube and amorphous silicon. Specifically, a multi-walled carbon nanotube (MWNTs) was utilized as the metallic core, on which n-type and intrinsic amorphous silicon layers were coated. A Schottky junction was formed by sputtering a transparent conducting indium-tin-oxide layer to wrap the outer shell of the device. The single coaxial nanowire device showed typical diode ratifying properties with turn-on voltage around 1V and a rectification ratio of 104 when biased at ±2V. Under illumination, it gave an open circuit voltage of ∼0.26V. Our study has shown a simple and useful platform for gaining insight into nanowire charge transport and collection properties. Fundamental studies of such nanowire device are important for improving the efficiency of future nanowire solar cells or photo detectors. © 2012 IEEE.

Graphene nanoribbon blends with P3HT for organic electronics.

In organic field-effect transistors (OFETs) the electrical characteristics of polymeric semiconducting materials suffer from the presence of structural/morphological defects and grain boundaries as well as amorphous domains within the film, hindering an efficient transport of charges. To improve the percolation of charges we blend a regioregular poly(3-hexylthiophene) (P3HT) with newly designed N = 18 armchair graphene nanoribbons (GNRs). The latter, prepared by a bottom-up solution synthesis, are expected to form solid aggregates which cannot be easily interfaced with metallic electrodes, limiting charge injection at metal-semiconductor interfaces, and are characterized by a finite size, thus by grain boundaries, which negatively affect the charge transport within the film. Both P3HT and GNRs are soluble/dispersible in organic solvents, enabling the use of a single step co-deposition process. The resulting OFETs show a three-fold increase in the charge carrier mobilities in blend films, when compared to pure P3HT devices. This behavior can be ascribed to GNRs, and aggregates thereof, facilitating the transport of the charges within the conduction channel by connecting the domains of the semiconductor film. The electronic characteristics of the devices such as the Ion/Ioff ratio are not affected by the addition of GNRs at different loads. Studies of the electrical characteristics under illumination for potential use of our blend films as organic phototransistors (OPTs) reveal a tunable photoresponse. Therefore, our strategy offers a new method towards the enhancement of the performance of OFETs, and holds potential for technological applications in (opto)electronics.

Hybrid bulk heterojunction solar cells from a blend of poly(3-hexylthiophene) and TiO2 nanotubes

Hybrid bulk heterojunction solar cells based on blend of poly(3-hexylthiophene) (P3HT) and TiO2 nanotubes or dye(N719) modified TiO2 nanotubes were processed from solution and characterized to research the nature of organic/inorganic hybrid materials. Compared with the pristine polymer P3HT and TiO2 nanoparticles/P3HT solar cells, the TiO2 nanotubes/P3HT hybrid solar cells show obvious performance improvement, due to the formation of the bulk heterojunction and charge transport improvement. A further improvement in the device performance can be achieved by modifying TiO2 nanotube surface with a standard dye N719 which can play a role in the improvement of both the light absorption and charge dissociation. Compared with the non-modified TiO2 nanotubes solar cells, the modified ones have better power conversion efficiency under 100 mW/cm(2) illumination with 500W Xenon lamp. (C) 2008 Elsevier B. V. All rights reserved.

High-performance dye-sensitized solar cells based on solvent-free electrolytes produced from eutectic melts

Low-cost excitonic solar cells based on organic optoelectronic materials are receiving an ever-increasing amount of attention as potential alternatives to traditional inorganic photovoltaic devices. In this rapidly developing field, the dye-sensitized solar cell(1) (DSC) has achieved so far the highest validated efficiency of 11.1% (ref. 2) and remarkable stability(3).

Enhance the optical absorptivity of nanocrystalline TiO2 film with high molar extinction coefficient ruthenium sensitizers for high performance dye-sensitized solar cells

We report two new heteroleptic polypyridyl ruthenium complexes, coded C101 and C102, with high molar extinction coefficients by extending the pi-conjugation of spectator ligands, with a motivation to enhance the optical absorptivity of mesoporous titania film and charge collection yield in a dye-sensitized solar cell. On the basis of this C101 sensitizer, several DSC benchmarks measured under the air mass 1.5 global sunlight have been reached.

Tetrahydrothiophenium-based ionic liquids for high efficiency dye-sensitized solar cells

Binary melts of S-ethyltetrahydrothiophenium iodide and dicyanoamide (or tricyanomethide) have been employed for dye-sensitized solar cells with high power conversion efficiencies up to 6.9% under the illumination of AM 1.5G full sunlight. We have further shown that the transport of triiodide in ionic liquids with high iodide concentration is viscosity-dependent in terms of a physical diffusion coupled bond exchange mechanism apart from the simple physical diffusion.

New Efficiency Records for Stable Dye-Sensitized Solar Cells with Low-Volatility and Ionic Liquid Electrolytes

We report a high molar extinction coefficient heteroleptic polypyridyl ruthenium sensitizer, featuring an electron-rich 3,4-ethylenedioxythiophene unit in its ancillary ligand. A nanocrystalline titania film stained with this sensitizer shows an improved optical absorption, which is highly desirable for practical dye-sensitized solar cells with a thin photoactive layer, facilitating the efficient charge collection.

New Organic Sensitizer for Stable Dye-Sensitized Solar Cells with Solvent-Free Ionic Liquid Electrolytes

We report a high molar extinction coefficient metal-free sensitizer composed of a triarylamine donor in combination with the 2-(2,2'-bithiophen-5-yl)acrylonitrile conjugation unit and cyanoacrylic acid as an acceptor. In conjugation with a volatile acetonitrile-based electrolyte or a solvent-free ionic liquid electrolyte, we have fabricated efficient dye-sensitized solar cells showing a corresponding 7.5% or 6.1% efficiency measured under the air mass 1.5 global sunlight. The ionic liquid cell exhibits excellent stability during a 1000 h accelerated test under the light-soaking and thermal dual stress. Intensity-modulated photocurrent and photovolatge spectroscopies were employed along with the transient photoelectrical decay measurements to detail the electron transport in the mesoporous titania films filled with these two electrolytes.

Energy-Level and Molecular Engineering of Organic D-pi-A Sensitizers in Dye-Sensitized Solar Cells

A series of organic D-pi-A sensitizers composed of different triarylamine donors in conjugation with the thienothiophene unit and cyanoacrylic acid as an acceptor has been synthesized at a moderate yield. Through tuning the number of methoxy substituents on the triphenylamine donor, we have gradually red-shifted the absorption of sensitizers to enhance device efficiencies.

Dye-sensitized solar cells with solvent-free ionic liquid electrolytes

We systematically studied the temperature-dependent physicochemical properties, such as density, conductivity, and fluidity, of 1,3-dialkylimidazolium iodides. In combination with the amphiphilic Z907Na sensitizer, we have found that it is important to use low-viscosity iodide melts with small cations to achieve high-efficiency dye-sensitized solar cells. By employing high-fluidity eutectic-based melts the device efficiencies considerably increased compared to those for cells with the corresponding state of the art ionic liquid electrolytes.

High-Performance Liquid and Solid Dye-Sensitized Solar Cells Based on a Novel Metal-Free Organic Sensitizer

A new metal-free organic sensitizer (see figure) for high-performance and applicable dye-sensitized solar cells is presented. In combination with a solvent-free ionic liquid electrolyte, a similar to 7% cell made with this sensitizer shows all excellent stability measured under thermal and light-soaking dual stress. For the first time a 4.8% efficiency is reached for all-solid-state dye-sensitized solar cells based oil all organic dye.

Crystal packing motifs of oligothiophenes end-capped with N-containing aryls

Oligothiophenes (OThs) end-capped with 3-quinolyl or pyridyl with nitrogen atom at meta-, ortho- or para-position were synthesized. The single-crystal structures of the resulting molecules, i.e., o-PyTh4, m-PyTh4, p-PyTh4, QuTh2, and QuTh3, were successfully determined by single-crystal X-ray analysis. Pyridyl end-capped OThs; o-PyTh4, m-PyTh4, and p-PyTh4, adopt the different herringbone packing arrangement in crystals depending on the position of the nitrogen atom because of the presence of weak C-H center dot center dot center dot N hydrogen bonds. The p-PyTh4 molecules are linked each other along the long axis of the molecules to form the extended chains by C-H center dot center dot center dot N dimer synthon. For m-PyTh4, the C-H center dot center dot center dot N interactions two-dimensionally extend through C-H center dot center dot center dot N trimer synthon.