Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Local structural distortions and their role in superconductivity in SmFeAsO1-xFx superconductors

EXAFS studies at the As K edge as a function of temperature were carried out in SmFeAsO1-xFx (x = 0 and 0.2) compounds to understand the role of local structural distortions in superconductivity observed in F-doped compounds. A significant correlation between the thermal variation of local structural parameters such as anion height and superconducting onset is found in the fluorinated compounds. Such a variation in anion height is absent in the non-superconducting compound. An increase in the Fe-As bond distance just below the superconducting onset temperature indicates a similarity between the distortions observed in the high-T-C cuprates and these Fe-based superconductors.

Automatic finite element formulation and assembly of hyperelastic higher order structural models

The formulation of higher order structural models and their discretization using the finite element method is difficult owing to their complexity, especially in the presence of non-linearities. In this work a new algorithm for automating the formulation and assembly of hyperelastic higher-order structural finite elements is developed. A hierarchic series of kinematic models is proposed for modeling structures with special geometries and the algorithm is formulated to automate the study of this class of higher order structural models. The algorithm developed in this work sidesteps the need for an explicit derivation of the governing equations for the individual kinematic modes. Using a novel procedure involving a nodal degree-of-freedom based automatic assembly algorithm, automatic differentiation and higher dimensional quadrature, the relevant finite element matrices are directly computed from the variational statement of elasticity and the higher order kinematic model. Another significant feature of the proposed algorithm is that natural boundary conditions are implicitly handled for arbitrary higher order kinematic models. The validity algorithm is illustrated with examples involving linear elasticity and hyperelasticity. (C) 2013 Elsevier Inc. All rights reserved.

Comparison of structural and luminescence properties of Dy2O3 nanopowders synthesized by co-precipitation and green combustion routes

Dysprosium oxide (Dy2O3) nanopowders were prepared by co-precipitation (CP) and eco-friendly green combustion (GC) routes. SEM micrographs prepared by CP route show smooth rods with various lengths and diameters while, GC route show porous, agglomerated particles. The results were further confirmed by TEM. Thermoluminescence (TL) responses of the nanopowder prepared by both the routes were studied using gamma-rays. A well resolved glow peak at 353 degrees C along with less intense peak at 183 degrees C was observed in GC route while, in CP a single glow peak at 364 degrees C was observed. The kinetic parameters were estimated using Chen's glow peak route. Photoluminescence (PL) of Dy2O3 shows peaks at 481, 577,666 and 756 nm which were attributed to Dy3+ transitions of F-4(9/2)-H-6(15/2), H-6(11/2), H-6(11/2) and H-6(9/2), respectively. Color co-ordinate values were located in the white region as a result the product may be useful for the fabrication of WLED'S. (C) 2014 Elsevier Ltd. All rights reserved.

Structural refinement, optical and electrical properties of Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 ceramics

Samarium doped barium zirconate titanate ceramics with general formula Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 x = 0, 0.01, 0.02, and 0.03] were prepared by high energy ball milling method. X-ray diffraction patterns and micro-Raman spectroscopy confirmed that these ceramics have a single phase with a tetragonal structure. Rietveld refinement data were employed to model BaO12], SmO12], ZrO6], and TiO6] clusters in the lattice. Scanning electron microscopy shows a reduction in average grain size with the increase of Sm3+ ions into lattice. Temperature-dependent dielectric studies indicate a ferroelectric phase transition and the transition temperature decreases with an increase in Sm3+ ion content. The nature of the transition was investigated by the Curie-Weiss law and it is observed that the diffusivity increases with Sm3+ ion content. The ferroelectric hysteresis loop illustrates that the remnant polarization and coercive field increase with an increase in Sm3+ ions content. Optical properties of the ceramics were studied using ultraviolet-visible diffuse reflectance spectroscopy.

Eco-friendly green synthesis, structural and photoluminescent studies of CeO2:Eu3+ nanophosphors using E. tirucalli plant latex

The investigation involves preparation and photoluminescence properties of CeO2:Eu3+ (1-11 mol%) nano phosphors by eco-friendly green combustion route using Euphorbia tirucalli plant latex as fuel. The final product was characterized by powder X-ray diffraction (PXRD), Scanning electron microcopy (SEM) and Transmission electron microscopy (TEM). The PXRD and SEM results reveals cubic fluorite phase with flaky structure. The crystallite size obtained from TEM was found to be similar to 20-25 nm, which was comparable to W-H plots and Scherrer's method. Photoluminescence (PL) emission of all the Eu3+ doped samples shows characteristic bands arising from the transitions of D-5(0) -> F-5(J) (J = 0, 1, 2, 3, 4) manifolds under excitation at 373 and 467 nm excitation. The D-5(0) -> F-7(2) (613 nm) transition often dominate the emission spectra, indicating that the Eu3+ cations occupy a site without inversion center. The highest PL intensity was recorded for 9 mol% Eu3+ ions with 5 ml latex. PL quenching was observed upon further increase in Eu3+ concentration. The international commission on illumination (CIE) chromaticity co-ordinates were calculated from emission spectra, the values (x, y) were very close to national television system committee (NTSC) standard values of pure red emission. The results demonstrate that the synthesized phosphor material could be very useful for display applications. Further, the phosphor material prepared by this method was found to be non toxic, environmental friendly and could be a potential alternative to economical routes. (C) 2014 Elsevier B.V. All rights reserved.

Self-assembly of Chloro-Bridged Arene-Ruthenium Based Rectangle: Synthesis, Structural Characterization and Sensing Study

Self-assembly of a chloro-bridged half-sandwich p-cymene ruthenium(II) complex Ru-2(mu-Cl-2)(eta(6)-p-cymene)(2)Cl-2] 1 with linear ditopic donor L; trans-1,2-bis(4-pyridyl) ethylene] in presence of 2 eq. AgNO3 in CH3CN yielded a chloro-bridged molecular rectangle 2. The rectangle 2 was isolated as nitrate salt in high yield (90 %) and characterized by infra-red, H-1 NMR spectroscopy including ESI-MS analyses. Molecular structure of 2 was determined by single crystal X-ray diffraction study The diffraction analysis shows that 2 adopts a tetranuclear rectangular geometry with the dimensions of 5.51 angstrom x 13.29 angstrom and forming an infinite supramolecular chain with large internal porosity arising through multiple pi-pi and CH-pi interactions between the adjacent rectangles. Furthermore, rectangle 2 is used as selective receptor for phenolic-nitroaromatic compounds such as picric acid, dinitrophenol and nitrophenol.

Comprehending the Formation of Eutectics and Cocrystals in Terms of Design and Their Structural Interrelationships

The phenomenon of cocrystallization, which encompasses the art of making multicomponent organic solids such as cocrystals, solid solutions, eutectics, etc. for novel applications, has been less studied in terms of reliably and specifically obtaining a desired cocrystallization product and the issues that govern their formation. Further, the design, structural, and functional aspects of organic eutectics have been relatively unexplored as compared to solid solutions and cocrystals well-established by crystal engineering principles. Recently, eutectics were proposed to be designable materials on par with cocrystals, and herein we have devised a systematic approach, based on the same crystal engineering principles, to specifically and desirably make both eutectics and cocrystals for a given system. The propensity for strong homomolecular synthons over weak heteromolecular synthons and vice versa during supramolecular growth was successfully utilized to selectively obtain eutectics and cocrystals, respectively, in two model systems and in two drug systems. A molecular level understanding of the formation of eutectics and cocrystals and their structural interrelationships which is significant from both fundamental and application viewpoints is discussed. On the other hand, the obscurity in establishing a low melting combination as a eutectic or a cocrystal is resolved through phase diagrams.

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

In this study, we combine available high resolution structural information on eukaryotic ribosomes with low resolution cryo-EM data on the Hepatitis C Viral RNA (IRES) human ribosome complex. Aided further by the prediction of RNA-protein interactions and restrained docking studies, we gain insights on their interaction at the residue level. We identified the components involved at the major and minor contact regions, and propose that there are energetically favorable local interactions between 40S ribosomal proteins and IRES domains. Domain II of the IRES interacts with ribosomal proteins S5 and S25 while the pseudoknot and the downstream domain IV region bind to ribosomal proteins S26, S28 and S5. We also provide support using UV cross-linking studies to validate our proposition of interaction between the S5 and IRES domains II and IV. We found that domain IIIe makes contact with the ribosomal protein S3a (S1e). Our model also suggests that the ribosomal protein S27 interacts with domain IIIc while S7 has a weak contact with a single base RNA bulge between junction IIIabc and IIId. The interacting residues are highly conserved among mammalian homologs while IRES RNA bases involved in contact do not show strict conservation. IRES RNA binding sites for S25 and S3a show the best conservation among related viral IRESs. The new contacts identified between ribosomal proteins and RNA are consistent with previous independent studies on RNA-binding properties of ribosomal proteins reported in literature, though information at the residue level is not available in previous studies.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

Depalladation of Neutral Monoalkyne- and Dialkyne-Inserted Palladacycles and Alkyne Insertion/Depalladation Reactions of Cationic Palladacycles Derived from N,N `,N `'-Triarylguanidines as Facile Routes for Guanidine-Containing Heterocycles/Carbocycles: Synthetic, Structural, and Mechanistic Aspects

Depalladation of the monoalkyne-inserted cyclopalldated guanidines (kappa 2(C,N)Pd(2,6-Me2C5H3N)Br] (I and II) in PhCl under reflux conditions and that of the dialkyne-inserted cyclopalladated guanidine kappa(2)(C,N):eta(2)(C=C)PdBr] (III) in pyridine under reflux conditions afforded a guanidine-containing indole (1), imidaziondole (2), and benzazepine (3) in 80%, 67%, and 76%, yields, respectively. trans-L2PdBr2] species (L = 2,6-Me2C5H3N, C5H5N) were also isolated in the aforementioned reactions in 35%, 42%, and 40% yields. Further , the reaction of the cyclopalladated guanidine kappa(2)(C,N)Pd(mu-Br)](2) (IV) with AgBF4 in a CH2Cl2/MeCN mixture afforded the cationic pincer type cyclopalladated guanidine kappa(3)(C,N,O)Pd(MeCN)]BF4] (4) in 85% yield and this palladacycle upon crystallization in MeCN and the reaction of kappa(2)(C,N)Pd(mu-Br)](2) (V) with AgBf(4) in a CH2Cl2/MeCN mixture afforded the cationic palladacycles {kappa(2)(C,N)Pd(MeCN)(2)]BF4](5 and 6) in 89% and 91% yields, respectively. The separate reactions of 4 with 2 equiv of methyl phenylpropiolate (MPP) or diphenylacetylene (DPA) and the reaction of 5 with 2 equiv of MPP in PhCl at 110 degrees C afforded the guanidine-containing quinazolinium tetrafluoroborate 7 in 25-32% yields. The reaction of 6 with 2 equiv of DPA under otherwise identical conditions afforded the unsymmetrically substituted guanidinium tetrafluoroborate 8, containing a highly substituted naphthalene unit, in 82% yield. Compounds 1-8 were characterized by analytical and spectroscopic techniques, and all compounds except 4 were characterized by single-crystal X-ray diffraction. The Molecular structure of 2 and 3 are nove, as the framework in the former arises due to the formation of two C-N bonds upon depalladation while the butadienyl unit in the latter revealed cis,cis stereochemistry, a-feature unprecedented in alkyne insertion chemistry. Plausible pathways for the formation of heterocycles/carbocycles are proposed. the influence of substitutents on the aryl rings fo the cyclopalladated guanidine moiety and those on alkynes upon the nature of the products in addressed. Heterocycles 1 and 7 revealed the presence of two rotamers in about a 1.00:0.43 ratio in CDCl3 and in about a 1.00:0.14 ratio in CD3OD, respectively, as detected by H-1 NMR spectroscopy while in CD3CN and DMSO-d(6) (1) and CD3CN and CDCl3 (7), these heterocycles revealed the presence of a single rotamer. These spectral features are attributed to the restricted C-N single-bond rotation of the CN3 unit of the guanidine moiety, which possibly arises from steric constraint due to the formation of a N-H center dot center dot center dot Cl hydrogen bond with CDCl3 (1) and N-H center dot center dot center dot O and O-D center dot center dot center dot O hydrogen bonds with CD3OD (7).

Optical and structural properties of highly porous shell structured Fe doped TiO2 thin films

TiO2 thin films with 0.2 wt%, 0.4 wt%, 0.6 wt%, and 0.8 wt% Fe were prepared on glass and silicon substrates using sol-gel spin coating technique. The optical cut-off points are increasingly red-shifted and the absorption edge is shifted over the higher wavelength region with Fe content increasing. As Fe content increases, the optical band gap decreases from 3.03 to 2.48 eV whereas the tail width increases from 0.26 to 1.43 eV. The X-ray diffraction (XRD) patterns for doped films at 0.2 wt% and 0.8 wt% Fe reveal no characteristic peaks, indicating that the film is amorphous whereas undoped TiO2 exhibits (101) orientation with anatase phase. Thin films of higher Fe content exhibit a homogeneous, uniform, and nano-structured highly porous shell morphology.

Combustion synthesized tetragonal ZrO2: Eu3+ nanophosphors: Structural and photoluminescence studies

Novel crystalline tetragonal ZrO2: Eu3+ phosphors were prepared by a facile and efficient low temperature solution combustion method at 400 +/- 10 degrees C using oxalyl dihydrazide (ODH) as fuel. The powder X-ray diffraction patterns and Rietveld confinement of as formed ZrO2: Eu3+ (1-11 mol%) confirmed the presence of body centered tetragonal phase. The crystallite size estimated from Scherrer's and W-H plots was found to be in the range of 7-17 nm. These results were in good agreement with transmission electron microscopy studies. The calculated microstrain in most of the planes indicated the presence of tensile stress along various planes of the particles. The observed space group (P4(2)/nmc) revealed the presence of cations in the 2b positions (0.75, 0.25, 0.25) and the anions in the 4d positions (0.25, 0.25, 0.45). The optical band gap energies estimated from Wood and Tauc's relation was found to be in the range 4.3-4.7 eV. Photoluminescence (PL) emission was recorded under 394 and 464 nm excitation shows an intense emission peak at 605 nm along with other emission peaks at 537, 592, 605 and 713 nm. These emission peaks were attributed to the transition of D-5(0) -> F-7(J) (J = 0, 1, 2, 3) of Eu3+ ions. The high ratio of Intensity of (D-5(0) -> F-7(2)) and (D-5(0) -> F-7(1)) infers that Eu3+ occupies sites with a low symmetry and without an inversion center. CIE color coordinates indicated the red regions which could meet the needs of illumination devices. (C) 2014 Elsevier B.V. All rights reserved.

Combinatorial effect of rolling and carbonaceous nanoparticles on the evolution of crystallographic texture and structural properties of ultra high molecular weight polyethylene

Ultra high molecular weight polyethylene (PE) is a structural polymer widely used in biomedical implants. The mechanical properties of PE can be improved either by controlled crystalline orientation (texture) or by the addition of reinforcing agents. However, the combinatorial effect has not received much attention. The objective of this study was to characterize the structure and mechanical properties of PE composites incorporating multiwall carbon nanotubes (MWCNT) and reduced graphene oxide (RGO) subjected to hot rolling. The wide angle X-ray diffraction studies revealed that mechanical deformation resulted in a mixture of orthorhombic and monoclinic crystals. Furthermore, the presence of nanoparticles resulted in lower crystallinity in PE with smaller crystallite size, more so in RGO than in MWCNT composites. Rolling strengthened the texture of both orthorhombic and the monoclinic phases in PE. Presence of RGO weakened the texture of both phases of PE after rolling whereas MWCNT only mildly weakened the texture. This resulted in a reduction in the elastic modulus of RGO composites whereas moduli of neat polymer and the MWCNT composite increased after rolling. This study provides new insight into the role of nanoparticles in texture evolution during polymer processing with implications for processing of structural polymer composites.

Anomalous structural relaxations in PVDF rich blends with PMMA in the presence of surface functionalized CNTs

The structural relaxations in PVDF rich blends with PMMA can be quite interesting in understanding the origin of the different molecular relaxations associated with the crystalline and amorphous phases, crystal-amorphous interphase and the segmental motions. In light of our recent findings, we understood that the origin of these molecular relaxations were strongly contingent on the concentration of PMMA in the blend, crystalline morphology and the surface functional moieties on multiwall carbon nanotubes (CNTs). In addition, for the blends with concentration of PMMA >= 25 wt%, the structural relaxations often merge and are dielectrically indistinguishable. In this study, we attempted to determine the critical width in composition where the structural relaxations can be distinctly realized both in the control as well as blends with amine functionalized CNTs (NH2-CNTs). Intriguingly, we observed that in a narrow zone in composition (with PMMA concentration >= 10 wt% and <= 25 wt%), the molecular relaxations can be dielectrically distinguished and they often merge for all other compositions. Furthermore, we attempted to understand how this critical width in composition is related to the crystalline morphology using small angle X-ray scattering and polarizing optical microscopy and the crystal structure using FTIR and Raman spectroscopy. We now understand that although the formation of beta crystals in the blends has no direct correlation with the observed molecular relaxations, the amorphous miscibility and the interphase regions seem to be dictating the origin of different molecular relaxations in the blends. The latter was observed to be strongly contingent on the concentration of PMMA in the blends.