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.

Cryogenic on-chip multiplexer for the study of quantum transport in 256 split-gate devices

We present a multiplexing scheme for the measurement of large numbers of mesoscopic devices in cryogenic systems. The multiplexer is used to contact an array of 256 split gates on a GaAs/AlGaAs heterostructure, in which each split gate can be measured individually. The low-temperature conductance of split-gate devices is governed by quantum mechanics, leading to the appearance of conductance plateaux at intervals of 2e^2/h. A fabrication-limited yield of 94% is achieved for the array, and a "quantum yield" is also defined, to account for disorder affecting the quantum behaviour of the devices. The quantum yield rose from 55% to 86% after illuminating the sample, explained by the corresponding increase in carrier density and mobility of the two-dimensional electron gas. The multiplexer is a scalable architecture, and can be extended to other forms of mesoscopic devices. It overcomes previous limits on the number of devices that can be fabricated on a single chip due to the number of electrical contacts available, without the need to alter existing experimental set ups.

CdS/CdSe lateral heterostructure nanobelts by a two-step physical vapor transport method.

The two-dimensional heterostructure nanobelts with a central CdSe region and lateral CdS structures are synthesized by a two-step physical vapor transport method. The large growth rate difference between lateral CdS structures on both +/- (0001) sides of the CdSe region is found. The growth anisotropy is discussed in terms of the polar nature of the side +/- (0001) surfaces of CdSe. High-resolution transmission electron microscopy reveals the CdSe central region covered with non-uniform CdS layer/islands. From micro-photoluminescence measurements, a systematic blueshift of emission energy from the central CdSe region in accordance with the increase of lateral CdS growth temperature is observed. This result indicates that the intermixing rate in the CdSe region with CdS increases with the increase of lateral CdS growth temperature. In conventional CdSSe ternary nanostructures, morphology and emission wavelength were correlated parameters. However, the morphology and emission wavelength are independently controllable in the CdS/CdSe lateral heterostructure nanobelts. This structure is attractive for applications in visible optoelectronic devices.

Independent Transport and Sorting of Functionally Distinct Protein Families in Tetrahymena thermophila Dense Core Secretory Granules

Dense core granules (DCGs) in Tetrahymena thermophila contain two protein classes. Proteins in the first class, called granule lattice (Grl), coassemble to form a crystalline lattice within the granule lumen. Lattice expansion acts as a propulsive mechanism during DCG release, and Grl proteins are essential for efficient exocytosis. The second protein class, defined by a C-terminal beta/gamma-crystallin domain, is poorly understood. Here, we have analyzed the function and sorting of Grt1p (granule tip), which was previously identified as an abundant protein in this family. Cells lacking all copies of GRT1, together with the closely related GRT2, accumulate wild-type levels of docked DCGs. Unlike cells disrupted in any of the major GRL genes, Delta GRT1 Delta GRT2 cells show no defect in secretion, indicating that neither exocytic fusion nor core expansion depends on GRT1. These results suggest that Grl protein sorting to DCGs is independent of Grt proteins. Consistent with this, the granule core lattice in Delta GRT1 Delta GRT2 cells appears identical to that in wild-type cells by electron microscopy, and the only biochemical component visibly absent is Grt1p itself. Moreover, gel filtration showed that Grl and Grt proteins in cell homogenates exist in nonoverlapping complexes, and affinity-isolated Grt1p complexes do not contain Grl proteins. These data demonstrate that two major classes of proteins in Tetrahymena DCGs are likely to be independently transported during DCG biosynthesis and play distinct roles in granule function. The role of Grt1p may primarily be postexocytic; consistent with this idea, DCG contents from Delta GRT1 Delta GRT2 cells appear less adhesive than those from the wild type.

Band-tail shape and transport near the metal-insulator transition in Si-doped

In the present work, an infrared light-emitting diode is used to photodope molecular-beam-epitaxy-grown Si: Al0.3Ga0.7As, a well-known persistent photoconductor, to vary the effective electron concentration of samples in situ. Using this technique, we examine the transport properties of two samples containing different nominal doping concentrations of Si [1 x 10(19) cm(-3) for sample 1 (S1) and 9 x 10(17) cm(-3) for sample 2 (S2)] and vary the effective electron density between 10(14) and 10(18) cm(-3). The metal-insulator transition for S1 is found to occur at a critical carrier concentration of 5.7 x 10(16) cm(-3) at 350 mK. The mobilities in both samples are found to be limited by ionized impurity scattering in the temperature range probed, and are adequately described by the Brooks-Herring screening theory for higher carrier densities. The shape of the band tail of the density of states in Al0.3Ga0.7As is found electrically through transport measurements. It is determined to have a power-law dependence, with an exponent of -1.25 for S1 and -1.38 for S2.

Electric tunable of electron spin polarization in hybrid magnetic-electric barrier structures

Electron spin-dependent transport properties have been theoretically investigated in two-dimensional electron gas (2DEG) modulated by the magnetic field generated by a pair of anti-parallel magnetization ferromagnetic metal stripes and the electrostatic potential provided by a normal metal Schottky stripe. It is shown that the energy positions of the spin-polarization extremes and the width of relative spin conductance excess plateau could be significantly manipulated by the electrostatic potential strength and width, as well as its position relative to the FM stripes. These interesting features are believed useful for designing the electric voltage controlled spin filters. (C) 2008 Elsevier B.V. All rights reserved.

Electrical control of dynamic spin splitting induced by exchange interaction as revealed by time-resolved Kerr rotation in a degenerate spin-polarized electron gas

Manipulation of the spin degree of freedom has been demonstrated in a spin-polarized electron plasma in a heterostructure by using exchange-interaction-induced dynamic spin splitting rather than the Rashba and Dresselhaus types, as revealed by time-resolved Kerr rotation. The measured spin splitting increases from 0.256 meV to 0.559 meV as the bias varies from -0.3 V to -0.6 V. Both the sign switch of the Kerr signal and the phase reversal of Larmor precessions have been observed with biases, which all fit into the framework of exchange-interaction-induced spin splitting. The electrical control of it may provide a new effective scheme for manipulating spin-selected transport in spin FET-like devices. Copyright (C) EPLA, 2008.

Neutron irradiation effect in two-dimensional electron gas of AlGaN/GaN heterostructures

AlGaN/GaN heterostructures have been irradiated by neutrons with different influences and characterized by means of temperature-dependent Hall measurements and Micro-Raman scattering techniques. It is found that the carrier mobility of two-dimensional electron gas (2DEG) is very sensitive to neutrons. At a low influence of 6.13 x 10(15) cm(-2), the carrier mobility drops sharply, while the sheet carrier density remains the same as that of an unirradiated sample. Moreover, even for a fluence of up to 3.66 x 10(16) cm(-2), the sheet carrier density shows only a slight drop. We attribute the degradation of the figure-of-merit (product of n(s) x mu) of 2DEG to the defects induced by neutron irradiation. Raman measurements show that neutron irradiation does not yield obvious change to the strain state of AlGaN/GaN heterostructures, which proves that degradation of sheet carrier density has no relation to strain relaxation in the present study. The increase of the product of n(s) x mu of 2DEG during rapid thermal annealing processes at relatively high temperature has been attributed to the activation of Ge-Ga transmuted from Ga and the recovery of displaced defects.

Spin current diode based on an electron waveguide with spin-orbit interaction

We propose a spin current diode which can work even in a small applied bias condition (the linear-response regime). The prototypal device consists of a hornlike electron waveguide with Rashba spin-orbit interaction, which is connected to two leads with different widths. It is demonstrated that when electrons are incident from the narrow lead, the generated spin conductance fluctuates around a constant value in a wide range of incident energy. When the transport direction is reversed, the spin conductance is suppressed strongly. Such a remarkable difference arises from spin-flipped transitions caused by the spin-orbit interaction. (c) 2008 American Institute of Physics.

Transport properties in a gated heterostructure with a trapezoidal AlxGa1-xAs barrier layer

By replacing the flat (Ga1-xAlx)As barrier layer with a trapezoidal AlxGa1-xAs barrier layer, a conventional heterostructure can be operated in enhancement mode. The sheet density of two-dimensional electron gas (2DEG) in the structure can be tuned linearly from N-2D = 0.3 x 10(11) cm(-2) to N-2D = 4.3 x 10(11) cm(-2) by changing the bias on the top gate. The present scheme for gated heterostructures is easy to fabricate and does not require the use of self-alignment photolithography or the deposition of insulating layers. In addition, this scheme facilitates the initial electrical contact to 2DEG. Although, the highest electron mobility obtained for the moment is limited by the background doping level of heterostructures, the mobility should be improved substantially in the future. (C) 2009 Elsevier B.V. All rights reserved.

Strong Spin-Orbit Interactions in an InAlAs/InGaAs/InAlAs Two-Dimensional Electron Gas by Weak Antilocalization Analysis

Spin-orbit interactions in a two-dimensional electron gas were studied in an InAlAs/InGaAs/InAlAs quantum well. Since weak anti localization effects take place far beyond the diffusive regime, (i.e., the ratio of the characteristic magnetic field, at which the magnetoresistance correction maximum occurs, to the transport magnetic field is more than ten) the experimental data are examined by the Golub theory, which is applicable to both diffusive regime and ballistic regime. Satisfactory fitting lines to the experimental data have been achieved using the Golub theory. In the strong spin-orbit interaction two-dimensional electron gas system, the large spin splitting energy of 6.08 meV is observed mainly due to the high electron concentration in the quantum well. The temperature dependence of the phase-breaking rate is qualitatively in agreement with the theoretical predictions. (C) 2009 The Japan Society of Applied Physics

Electric-tunable magneto resistance effect in a two-dimensional electron gas modulated by hybrid magnetic-electric barrier nanostructure

The electric-tunable spin-independent magneto resistance effect has been theoretically investigated in ballistic regime within a two-dimensional electron gas modulated by magnetic-electric barrier nanostructure. By including the omitted stray field in previous investigations oil analogous structures, it is demonstrated based on this improved approximation that the magnetoresistance ratio for the considered structure can be efficiently enhanced by a proper electric barrier up to the maximum value depending on the specific magnetic suppression. Besides, it is also shown the introduction of positive electrostatic modulation can effectively overcome the degradation of magnetoresistance ratio for asymmetric configuration and enhance the visibility of periodic pattern induced by the size effect, while for an opposite modulation the system magnetoresistance ratio concerned may change its sign. (C) 2009 Elsevier B.V. All rights reserved.

Anisotropic transport in quantum waveguides due to the spin-orbit interactions

We theoretically investigate the charge transport in the quantum waveguides in the presence of the Rashba spin-orbit interaction and the Dresselhaus spin-orbit interaction. We find that the interplay between the Rashba spin-orbit interaction and Dresselhaus spin-orbit interaction can induce a symmetry breaking and consequently leads to the anisotropic charge transport in the quantum waveguides, the conductance through the quantum waveguides depends sensitively on the crystallographic orientations of the quantum waveguides. The anisotropy of the charge transport can even survive in the presence of disorder effect in realistic systems.