DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.

Hole-Phonon Relaxation and Photocatalytic Properties of Titanium Dioxide and Zinc Oxide: First-Principles Approach

First-principles calculations for the temporal characteristics of hole-phonon relaxation in the valence band of titanium dioxide and zinc oxide have been performed. A first-principles method for the calculations of the quasistationary distribution function of holes has been developed. The results show that the quasistationary distribution of the holes in TiO2 extends to an energy level approximately 1eV below the top of the valence band. This conclusion in turn helps to elucidate the origin of the spectral dependence of the photocatalytic activity of TiO2. Analysis of the analogous data for ZnO shows that in this material spectral dependence of photocatalytic activity in the oxidative reactions is unlikely.

Spectroscopy of neutron-rich Dy168,170: Yrast band evolution close to the NpNn valence maximum

The yrast sequence of the neutron-rich dysprosium isotope Dy168 has been studied using multinucleon transfer reactions following collisions between a 460-MeV Se82 beam and an Er170 target. The reaction products were identified using the PRISMA magnetic spectrometer and the γ rays detected using the CLARA HPGe-detector array. The 2+ and 4+ members of the previously measured ground-state rotational band of Dy168 have been confirmed and the yrast band extended up to 10+. A tentative candidate for the 4+→2+ transition in Dy170 was also identified. The data on these nuclei and on the lighter even-even dysprosium isotopes are interpreted in terms of total Routhian surface calculations and the evolution of collectivity in the vicinity of the proton-neutron valence product maximum is discussed. © 2010 The American Physical Society.

Neutron-Proton Asymmetry Dependence of Spectroscopic Factors in Ar Isotopes

Spectroscopic factors have been extracted for proton-rich Ar-34 and neutron-rich Ar-46 using the (p, d) neutron transfer reaction. The experimental results show little reduction of the ground state neutron spectroscopic factor of the proton-rich nucleus Ar-34 compared to that of Ar-46. The results suggest that correlations, which generally reduce such spectroscopic factors, do not depend strongly on the neutronproton asymmetry of the nucleus in this isotopic region as was reported in knockout reactions. The present results are consistent with results from systematic studies of transfer reactions but inconsistent with the trends observed in knockout reaction measurements.

近垒重离子熔合反应和超重核合成机制研究

本论文在同位旋相关的量子分子动力学(IQMD)模型基础上，对相互作用势、核子的费米子属性和两体碰撞做了系统改进，同时考虑原子核的壳效应，发展成为改进的同位旋相关的量子分子动力学(ImIQMD)模型。ImIQMD模型能够很好地描述大量核的基态性质，如结合能、均方根半径、密度分布、动量分布等，并使得基态核的稳定性有了很大提高。基于ImIQMD模型我们系统计算了一系列反应系统的熔合激发函数，并能够与已知实验数据相当好地符合，包括丰中子系统和幻数核系统；分析了各种动力学因素在熔合过程中的作用，发现动力学位垒、位垒分布、颈部动力学行为(颈部的成长，颈部中质比、颈部核子流)等对入射能量和系统的质量不对称度有着密切的依赖关系，分析了垒下熔合区域中壳效应的影响。运用ImIQMD模型，对重系统的俘获动力学过程做了分析，包括俘获截面、动力学位垒、颈部动力学行为等。基于双核系统概念，对熔合－蒸发反应合成超重核形成过程中的俘获、熔合和蒸发三个阶段分别采用了半经验耦合道模型、数值求解主方程(考虑了双核系统的衰变和重碎片的裂变)和统计蒸发理论做了描述，即为双核系统(DNS)模型。基于该模型对超重核的形成机制做了系统研究，并预言了进一步合成超重核最佳的弹靶组合和入射能量

Multilayer structured carbon nanotubes/poly-L-lysine/laccase composite cathode for glucose/O-2 biofuel cell

Multilayer film of laccase, poly-L-lysine (PLL) and multi-walled carbon nanotubes (MWNTs) were prepared by a layer-by-layer self-assembly technique. The results of the UV-vis spectroscopy and scanning electron microscopy studies demonstrated a uniform growth of the multilayer. The catalytic behavior of the modified electrode was investigated. The (MWNTs/PLL/laccase)(n) multilayer modified electrode catalyzed four-electron reduction of O-2 to water, without any mediator.

Electro-assisted precipitation of electrolytes in poly(3,4-ethylenedioxythiophene) film

The electrolyte, NaBF4, can be enriched into the matrix of poly(3,4-ethylenedioxythiophene) (PEDOT) film during the p-doping potential cycling between 0.6 and -0.9 V. It has been demonstrated that this enrichment is originated from the mixed ion transfer between doping and dedoping, i.e. BF4- anion migrate into the PEDOT film during the oxidation process, the Ne cation insert into the film during the reduction process, and then, the electrolyte is accumulated into the film matrix after the multiple CV cycling. The quantitative analysis of energy-dispersive X-ray spectroscopy (EDX) confirmed the enrichment of NaBF4 in the PEDOT film.

The combined catalytic action of solid acids with nickel for the transformation of polypropylene into carbon nanotubes by pyrolysis

The effects of both organically modified montmorillonite (OMMT) and Ni2O3 on the carbonization of polypropylene (PP) during pyrolysis were investigated. The results from TEM and Raman spectroscopy showed that the carbonized products of PP were mainly multiwalled carbon nanotubes (MWNTs). Surprisingly, a combination of OMMT and Ni2O3 led to high-yield formation of MWNTs. X-ray powder diffraction (XRD) and GC-MS were used to investigate the mechanism of this combination for the high-yield formation of MWNTs from PP. Bronsted acid sites were created in degraded OMMT layers by thermal decomposition of the modifiers. The resultant carbenium ions play an important role in the carbonization of PP and the formation of MWNTs. The degradation of PP was induced by the presence of carbenium ions to form predominantly products with lower carbon numbers that could be easily catalyzed by the nickel catalyst for the growth of MWNTs. Furthermore, carbenium ions are active intermediates that promote the growth of MWNTs from the degradation products with higher carbon numbers through hydride-transfer reactions. The XRD measurements showed that Ni2O3 was reduced into metallic nickel (Ni) in situ to afford the active sites for the growth of MWNTs.

Electrochemical and spectroscopic study on the interaction of cytochrome c with anionic lipid vesicles

The structure and the electron-transfer of cytochrome c binding on the anionic lipid vesicles were analyzed by electrochemical and various spectroscopic methods. It was found that upon binding to anionic lipid membrane, the formal potential of. cytochrome c shifted 30 mV negatively indicating an eager redox interaction than that in its native state. This is due to the local alteration of the coordination and the heme crevice. The structural Perturbation in which a molten globule-like state is formed during binding to anionic lipid vesicles is more important. This study may help to understand the mechanism of the electron-transfer reactions of cytochrome c at the mitochondrial membrane.

Effect of alkyl group length on the conductivity in the 2,3,7,8,12,13,17,18-octakis(alkyl-thio)tetraazaporphyrins and redox properties of the metallooctakis(hexyl-thio)tetraazaporphyrins

A series of 2,3,7,8,12,13,17,18-octakis(alkyl-thio)tetraazaporphyrins (H(2)OATTAP) with different alkyl chain lengths have been synthesized. Cyclic voltammetry and differential pulse voltammetry have been used to investigate the effect of the controlled lengths of the eight peripheral thioether tails on the redox behavior of the molecules. The electrochemical reduction of octakis(hexyl-thio)tetraazaporphyrins, MOHTTAP (where M = Cu, Ni), was studied in 1,2-dichloroethane at a platinum electrode. The Cu derivative was oxidized in one single-electron-transfer step to yield a pi-cation radical and reduced in three single-electron-transfer steps to yield a pi-anion radical, dianion and trianion, respectively. For the Ni derivative, electron transfer reactions involving both the central metal atom and the macrocyclic ring were observed. Electron transfer pathways are proposed based upon voltammetric and in situ spectroelectrochemical results.

Recent advances in scanning electrochemical microscopy

The basic principle, instrumentation and recent advances of scanning electrochemical microscopy are briefly reviewed with 55 references.

Application of acetone and dimethyl ether chemical ionization reagent gases to structural analysis

Acetone and dimethyl ether( DME) have been shown to be reagent gases of exceptional utitlity and versatility for the characterization of a variety of class of organic compounds. The fragmentation mechanisms of the adduct product ions, formed by ion/molceule reaction of the substrate with the ionized gases, have been studied and substantiated by experiments with acetone-d(6) and DME-d(6).

Investigation of the structures of the product ions produced via self-CI of acetone

The ion-molecule reactions in acetone were investigated which were induced under the chemical ionization. The structural information of the reaction products were obtained by using collision-induced dissociation (CID) technique performed at ion kinetic energies of 30eV.

Synthesis and spectroscopic studies of endohedral metallofullerenes Tb@C-2n

Endohedral metallofullerenes Tb@C-2n were synthesized and extracted with high-yield by K-H carbon-are evaporation and an effective pyridine extraction technique at high-temperature high-pressure. Laser-desorption-ionization time-of-flight (LD-TOF) mass spectrometry, X-ray photoelectron spectroscopy (XPS), solid-state fluorescent emission spectroscopy and gas phase derivation reaction with the self-chemical ionization mass spectrometric ion system of vinyl acetate were employed for studying the electronic structures, fluorescent properties and gas phase reactivities of metallofullerenes Tb@C-2n. The experimental results suggest that endohedral metallofullerenes Tb@C-2n would have the approximate structures of Tb3+@C-2n(3-) similar to other metallofullerenes, good fluorescent emission properties and active reactivities in gas phase ion-molecular reactions.

Determination of the standard heterogeneous rate constant in polyelectrolyte using steady state microdisk voltammograms

The steady state voltammogram at a microdisk electrode is used to measure the diffusion coefficient and standard heterogeneous rate constant (k(s)) of ferrocene in polyelectrolyte PEG + LiClO4. The k(s) obtained is smaller in polyelectrolyte than in liquid medium. It is proposed that the polymer solvent electron transfer dynamics are affected by the relaxation rates of the ether dipole sites on the polymer chains, which are in turn constrained by the rates of polymer chain segment, or local structure, relaxations. The dependence of k(s) on temperature is observed. The k(s) increases with increasing temperature.