Functional analysis of DNA bending and unwinding by the high mobility group domain of LEF-1

LEF-1 (lymphoid enhancer-binding factor 1) is a cell type-specific member of the family of high mobility group (HMG) domain proteins that recognizes a specific nucleotide sequence in the T cell receptor (TCR) α enhancer. In this study, we extend the analysis of the DNA-binding properties of LEF-1 and examine their contributions to the regulation of gene expression. We find that LEF-1, like nonspecific HMG-domain proteins, can interact with irregular DNA structures such as four-way junctions, albeit with lower efficiency than with specific duplex DNA. We also show by a phasing analysis that the LEF-induced DNA bend is directed toward the major groove. In addition, we find that the interaction of LEF-1 with a specific binding site in circular DNA changes the linking number of DNA and unwinds the double helix. Finally, we identified two nucleotides in the LEF-1-binding site that are important for protein-induced DNA bending. Mutations of these nucleotides decrease both the extent of DNA bending and the transactivation of the TCRα enhancer by LEF-1, suggesting a contribution of protein-induced DNA bending to the function of TCRα enhancer.

Maintenance of Epstein–Barr virus (EBV) oriP-based episomes requires EBV-encoded nuclear antigen-1 chromosome-binding domains, which can be replaced by high-mobility group-I or histone H1

EBV-encoded nuclear antigen-1 (EBNA-1) binding to a cis-acting viral DNA element, oriP, enables plasmids to persist in dividing human cells as multicopy episomes that attach to chromosomes during mitosis. In investigating the significance of EBNA-1 binding to mitotic chromosomes, we identified the basic domains of EBNA-1 within amino acids 1–89 and 323–386 as critical for chromosome binding. In contrast, the EBNA-1 C terminus (amino acids 379–641), which includes the nuclear localization signal and DNA-binding domain, does not associate with mitotic chromosomes or retain oriP plasmid DNA in dividing cell nuclei, but does enable the accumulation of replicated oriP-containing plasmid DNA in transient replication assays. The importance of chromosome association in episome maintenance was evaluated by replacing EBNA-1 amino acids 1–378 with cell proteins that have similar chromosome binding characteristics. High-mobility group-I amino acids 1–90 or histone H1–2 could substitute for EBNA-1 amino acids 1–378 in mediating more efficient accumulation of replicated oriP plasmid, association with mitotic chromosomes, nuclear retention, and long-term episome persistence. These data strongly support the hypothesis that mitotic chromosome association is a critical factor for episome maintenance. The replacement of 60% of EBNA-1 with cell protein is a significant step toward eliminating the need for noncellular protein sequences in the maintenance of episomal DNA in human cells.

High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor.

The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. However, a single gene, carD, is required for the activation of both light- and starvation-inducible genes. Gene carD has now been sequenced. Its predicted amino acid sequence includes four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA. CarD binds in vitro an A+T-rich element that is required for the proper operation of a carD-dependent promoter in vivo.

Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains.

Transcription factor TFIIIB plays a central role in transcription initiation by RNA polymerase III on genes encoding tRNA, 5S rRNA, and other small structural RNAs. We report the purification of a human TFIIIB-derived complex containing only the TATA-binding polypeptide (TBP) and a 90-kDa subunit (TFIIIB90) and the isolation of a cDNA clone encoding the 90-kDa subunit. The N-terminal half of TFIIIB90 exhibits sequence similarity to the yeast TFIIIB70 (BRF) and the class II transcription factor TFIIB and interacts weakly with TBP. The C-terminal half of TFIIIB90 contains a high-mobility-group protein 2 (HMG2)-related domain and interacts strongly with TBP. Recombinant TFIIIB90 plus recombinant human TBP substitute for human TFIIIB in a complementation assay for transcription of 5S, tRNA, and VA1 RNA genes, and both the TFIIB-related domain and the HMG2-related domain are required for this activity. TFIIIB90 is also required for transcription of human 7SK and U6 RNA genes by RNA polymerase III, but apparently within a complex distinct from the TBP/TFIIIB90 complex.

Specific binding of the mammalian high mobility group protein AT-hook 2 to the minor groove of AT -rich DNAs: Thermodynamic and specificity studies

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a small transcriptional factor involved in cell development and oncogenesis. It contains three "AT-hook" DNA binding domains, which specifically recognize the minor groove of AT-rich DNA sequences. It also has an acidic C-terminal motif. Previous studies showed that HMGA2 mediates all its biological effects through interactions with AT-rich DNA sequences in the promoter regions. In this dissertation, I used a variety of biochemical and biophysical methods to examine the physical properties of HMGA2 and to further investigate HMGA2's interactions with AT-rich DNA sequences. The following are three avenues perused in this study: (1) due to the asymmetrical charge distribution of HMGA2, I have developed a rapid procedure to purify HMGA2 in the milligram range. Preparation of large amounts of HMGA2 makes biophysical studies possible; (2) Since HMGA2 binds to different AT-rich sequences in the promoter regions, I used a combination of isothermal titration calorimetry (ITC) and DNA UV melting experiment to characterize interactions of HMGA2 with poly(dA-dT) 2 and poly(dA)poly(dT). My results demonstrated that (i) each HMGA2 molecule binds to 15 AT bp; (ii) HMGA2 binds to both AT DNAs with very high affinity. However, the binding reaction of HMGA2 to poly(dA-dT) 2 is enthalpy-driven and the binding reaction of HMGA2 with poly(dA)poly(dT) is entropy-driven; (iii) the binding reactions are strongly depended on salt concentrations; (3) Previous studies showed that HMGA2 may have sequence specificity. In this study, I used a PCR-based SELEX procedure to examine the DNA binding specificity of HMGA2. Two consensus sequences for HMGA2 have been identified: 5'-ATATTCGCGAWWATT-3' and 5'-ATATTGCGCAWWATT-3', where W represents A or T. These consensus sequences have a unique feature: the first five base pairs are AT-rich, the middle four to five base pairs are GC-rich, and the last five to six base pairs are AT-rich. All three segments are critical for high affinity binding. Replacing either one of the AT-rich sequences to a non-AT-rich sequence causes at least 100-fold decrease in the binding affinity. Intriguingly, if the GC-segment is substituted by an AT-rich segment, the binding affinity of HMGA2 is reduced approximately 5-fold. Identification of the consensus sequences for HMGA2 represents an important step towards finding its binding sites within the genome.

Magnetoresistance in a High Mobility Two-Dimensional Electron System as a Function of Sample Geometry

In a high mobility two-dimensional electron gas (2DEG) realized in a GaAs/Al0.3Ga0.7As quantum well we observe changes in the Shubnikov-de Haas oscillations (SdHO) and in the Hall resistance for different sample geometries. We observe for each sample geometry a strong negative magnetoresistance around zero magnetic field which consists of a peak around zero magnetic field and of a huge magnetoresistance at larger fields. The peak around zero magnetic field is left unchanged for different geometries.

The cross layer RMPA handover: a reliable mobility pattern aware handover strategy for broadband wireless communication in a high-speed railway domain

Enhancing the handover process in broadband wireless communication deployment has traditionally motivated many research initiatives. In a high-speed railway domain, the challenge is even greater. Owing to the long distances covered, the mobile node gets involved in a compulsory sequence of handover processes. Consequently, poor performance during the execution of these handover processes significantly degrades the global end-to-end performance. This article proposes a new handover strategy for the railway domain: the RMPA handover, a Reliable Mobility Pattern Aware IEEE 802.16 handover strategy "customized" for a high-speed mobility scenario. The stringent high mobility feature is balanced with three other positive features in a high-speed context: mobility pattern awareness, different sources for location discovery techniques, and a previously known traffic data profile. To the best of the authors' knowledge, there is no IEEE 802.16 handover scheme that simultaneously covers the optimization of the handover process itself and the efficient timing of the handover process. Our strategy covers both areas of research while providing a cost-effective and standards-based solution. To schedule the handover process efficiently, the RMPA strategy makes use of a context aware handover policy; that is, a handover policy based on the mobile node mobility pattern, the time required to perform the handover, the neighboring network conditions, the data traffic profile, the received power signal, and current location and speed information of the train. Our proposal merges all these variables in a cross layer interaction in the handover policy engine. It also enhances the handover process itself by establishing the values for the set of handover configuration parameters and mechanisms of the handover process. RMPA is a cost-effective strategy because compatibility with standards-based equipment is guaranteed. The major contributions of the RMPA handover are in areas that have been left open to the handover designer's discretion. Our simulation analysis validates the RMPA handover decision rules and design choices. Our results supporting a high-demand video application in the uplink stream show a significant improvement in the end-to-end quality of service parameters, including end-to-end delay (22%) and jitter (80%), when compared with a policy based on signal-to-noise-ratio information.

Phthalocyanato tin(IV) dichloride: An air-stable, high-performance, n-type organic semiconductor with a high field-effect electron mobility

Phthalocyanato tin(IV) dichloride, an axially dichloriniated MPc, is an air-stable high performance n-type organic semiconductor with a field-effect electron mobility of up to 0.30 cm(2) V-1 s(-1). This high mobility together with good device stability and commercial availability makes it a most suitable n-type material for future organic thin-film transistor applications.

Characteristics of high-performance ambipolar organic field-effect transistors based on a diketopyrrolopyrrole-benzothiadiazole copolymer

In this paper, we report the device characteristics of ambipolar thin-film transistors (TFTs) based on a diketopyrrolopyrrole-benzothiadiazole copolymer. This polymer semiconductor exhibits the largest comparable electron and hole mobility values in a single organic semiconductor. The key to realizing such high mobility values, which are $0.5&cm}{2}/\hbox{V}̇\hbox{s, is molecular design, i.e., the use of suitable surface treatments of the source/drain contact electrodes and device architectures, particularly top-gate configurations. The subthreshold characteristics of the TFT devices are greatly improved by the use of dual-gate device geometry. We also report the first measurement of the velocity distribution of electron and hole velocities in an ambipolar organic semiconductor.

The influence of animal mobility on the assumption of uniform distances in aerial line-transect surveys

Line-transect distance sampling is a widely used method for estimating animal density from aerial surveys. Analysis of line-transect distance data usually relies on a requirement that the statistical distribution of distances of animal groups from the transect line is uniform. We show that this requirement is satisfied by the survey design if all other assumptions of distance sampling hold, but it can be violated by consistent survey problems such as responsive movement of the animals towards or away from the observer. We hypothesise that problems with the uniform requirement are unlikely to be encountered for immobile taxa, but might become substantial for species of high mobility. We test evidence for non-uniformity using double-observer distance data from two aerial surveys of five species with a spectrum of mobility capabilities and tendencies. No clear evidence against uniformity was found for crabeater seals or emperor penguins on the pack-ice in East Antarctica, while minor non-uniformity consistent with responsive movement up to 30 m was found for Adelie penguins. Strong evidence of either non-uniformity or a failure of the capture-recapture validating method was found for eastern grey kangaroos and red kangaroos in Queensland.

New type of high field electrooptic response in nematics

We have made concurrent measurements of ionic current and optical transmission between crossed polarisers on several nematics with positive dielectric anisotropy under the action of applied low frequency (< 1KHz) square wave voltages. When the field E is low, the measured current is linear in E and there is no electrooptic response. Beyond some value of the field (E(0)similar to 100 esu), the current becomes independent of the field (phenomenon of limiting current). Further an electrooptic signal is measured at twice the frequency of the applied voltage, which exhibits a peak as a function of the field. The width of the peak is 3 to 4 times the value of E-0, and the signal level at the peak decreases as the frequency is increased. These measurements have been made on three highly polar compounds with cyano end groups. Careful observations do not show any evidence of electrohydrodynamic instabilities in the sample. It is argued that the observations can be understood if at the onset of the phenomenon of the limiting current, a strong electric field gradient is established near one of the electrodes due to the sweeping of an ionic species with high mobility. The field gradient produces a flexoelectric deformation of the director field, which in turn gives rise to the electrooptic effect. At higher fields, the stabilising dielectric torque takes over to suppress this instability.

Noncontact measurement of charge carrier lifetime and mobility in GaN nanowires

The first noncontact photoconductivity measurements of gallium nitride nanowires (NWs) are presented, revealing a high crystallographic and optoelectronic quality achieved by use of catalyst-free molecular beam epitaxy. In comparison with bulk material, the NWs exhibit a long conductivity lifetime (>2 ns) and a high mobility (820 ± 120 cm 2/(V s)). This is due to the weak influence of surface traps with respect to other III-V semiconducting NWs and to the favorable crystalline structure of the NWs achieved via strain-relieved growth. © 2012 American Chemical Society.

Room temperature mobility above 2100 cm2/Vs in Al0.3Ga0.7N/AIN/GaN heterostructures grown on sapphire substrates by MOCVD

Al0.3Ga0.7N/AlN/GaN HEMT structures with significantly high mobility have been grown by metalorganic chemical vapor deposition (MOCVD) on sapphire substrates. At room temperature (RT) a Hall mobility of 2104 cm(2)/Vs and a two-dimensional electron gas (2DEG) density of 1.1x10(13) cm(-2) are achieved, corresponding to a sheet resistance of 277.8 Omega/sq. The elimination of V-shaped defects were observed on Al0.3Ga0.7N/AlN/GaN HEMT structures and correlated with the increase of 2DEG mobility. (c) 2006 WILEY-VCH Verlag GmbH & Co KGaA, Weinheim.

On the mobility of a one-dimensional damped Frenkel-Kontorova chain: Commensurate versus incommensurate

The mobility of a one-dimensional damped Frenkel-Kontorova chain under a de driving force is studied numerically and analytically For the commensurate case, the particles in the chain me synchronized st high driving force. For the incommensurate chain, a single mode solution dominates st high mobility regime. We are able to calculate the mobilities for both the cases analytically, and a good agreement with numerical results is found. The mobility hysteresis for the incommensurate chain is explained by the existence of two branches of physical solutions, and transitions occur when one of them breaks up.

High current density and drift velocity in templated conducting polymers

Conducting polymers prepared by a templated vapour phase polymerisation process involving solid phase transition metal complexes are found to produce polymers with charge carriers that exhibit maximum drift velocity in the range of 1 m/s. This super-mobility seems to be related to a high degree of ordering in the materials as evidenced by the X-ray diffraction data. This may result from a templated polymerisation process. The high mobility manifests itself as a capacity to sustain very high current densities (>10000 A/cm2); such high current densities are of importance in thin film conductor applications.