DNA recognition by the first tail-to-tail linked distamycin-like oligopeptide dimers

Sequence-specific bidentate binding to double-stranded (ds)-DNA by 'tail-to-tail' linked dimeric, distamycin analogues is described; compared to their monomeric analogues, these dimers exhibit greater affinity and longer binding site size and open up a novel avenue in the design of minor groove binders that overcome the phasing problem.

Surface chemical characterisation of Paenibacillus polymyxa before and after adaptation to sulfide minerals

A heterotroph Paenibacillus polymyxa bacteria is adapted to pyrite, chalcopyrite, galena and sphalerite minerals by repeated subculturing the bacteria in the presence of the mineral until their growth characteristics became similar to the growth in the absence of mineral. The unadapted and adapted bacterial surface have been chemically characterised by zeta-potential, contact angle, adherence to hydrocarbons and FT-IR spectroscopic studies. The surface free energies of bacteria have been calculated by following the equation of state and surface tension component approaches. The aim of the present paper is to understand the changes in surface chemical properties of bacteria during adaptation to sulfide minerals and the projected consequences in bioflotation and bioflocculation processes. The mineral-adapted cells became more hydrophilic as compared to unadapted cells. There are no significant changes in the surface charge of bacteria before and after adaptation, and all the bacteria exhibit an iso-electric point below pH 2.5. The contact angles are observed to be more reliable for hydrophobicity assessment than the adherence to hydrocarbons. The Lifschitz–van der Waals/acid–base approach to calculate surface free energy is found to be relevant for mineral–bacteria interactions. The diffuse reflectance FT-IR absorbance bands for all the bacteria are the same illustrating similar surface chemical composition. However, the intensity of the bands for unadapted and adapted cells is significantly varied and this is due to different amounts of bacterial secretions underlying different growth conditions.

Thin Films of Titanium Dioxide Prepared by Chemical Routes using Novel Precursors

Novel, volatile, stable, oxo-β-ketoesterate complexes of titanium, whose synthesis requires only an inert atmosphere, as opposed to a glove box, have been developed. Using one of the complexes as the precursor, thin films of TiO2 have been deposited on glass substrates by metalorganic chemical vapor deposition (MOCVD) at temperatures ranging from 400°C to 525°C and characterized by scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. All the films grown in this temperature range are very smooth; those grown above 480°C consist of nearly monodisperse, nanocrystals of the anatase phase. Optical studies show the bandgaps in the range 3.4–3.7 eV for films grown at different temperatures. Thin films of anatase TiO2 have also been grown by spin-coating technique using another ketoesterate complex of titanium, demonstrating that the newly developed complexes can be successfully used for thin film growth by various chemical routes.

Epitaxial Growth of Co3O4 Films by Low Temperature, Low Pressure Chemical Vapor Deposition

The growth of strongly oriented or epitaxial thin films of metal oxides generally requires relatively high growth temperatures or infusion of energy to the growth surface through means such as ion bombardment. We have grown high quality epitaxial thin films of Co3O4 on different substrates at a temperature as low as 450°C by low-pressure metal-organic chemical vapor deposition (MOCVD) using cobalt(II) acetylacetonate as the precursor. With oxygen as the reactant gas, polycrystalline Co3O4 films are formed on glass and Si(100) in the temperature range 350-550°C. Under similar conditions of growth, highly oriented films of Co3O4 are formed on SrTiO3(100) and LaAlO3(100). The film on LaAlO3(100) grown at 450°C show a rocking curve FWHM of 1.61°, which reduces to 1.32° when it is annealed in oxygen at 725°C. The film on SrTiO3(100) has a FWHM of 0.330 (as deposited) and 0.29° (after annealing at 725°C). The ø-scan analysis shows cube-on-cube epitaxy on both these substrates. The quality of epitaxy on SrTiO3(100) is comparable to the best of the pervoskite-based oxide thin films grown at significantly higher temperatures.

Electron Cyclotron Resonance in Strained Si and Si0.94Ge0.06 Channels on Relaxed Si0.62Ge0.38 Buffers Grown by Rapid Thermal Chemical Vapor Deposition

We report the far-infrared measurements of the electron cyclotron resonance absorption in n-type Si/Si0. 62Ge0.38 and Si0.94Ge0.06 /Si0. 62Ge0.38 modulation- doped heterostructures grown by rapid thermal chemical vapor deposition. The strained Si and Si0.94Ge0.06 channels were grown on relaxed Si0.62Ge0.38 buffer layers, which consist of 0.6 μm uniform Si0.62Ge0.38 layers and 0.5 μm compositionally graded relaxed SiGe layers from 0% Ge to 38 % Ge. The buffer layers were annealed at 800 °C for 1 hr to obtain complete relaxation. The samples had 100 Å spacers and 300 Å 2×1019 cm-3 n-type supply layers on the tops of the 75 Å channels. The far-infrared measurements of electron cyclotron resonance were performed at 4K with the magnetic field of 4 – 8 Tesla. The effective masses determined from the slope of center frequency of absorption peak vs applied magnetic field plot are 0.20 mo and 0.19 mo for the two dimensional electron gases in the Si and Si0.94Ge0.06 channels, respectively. The Si effective mass is very close to that of two dimensional electron gas in Si MOSFET (0.198mo). The electron effective mass of Si0.94Ge0.06 is reported for the first time and about 5 % lower than that of pure Si.

Surfactant-mediated Synthesis of Functional Metal Oxide Nanostructures via Microwave Irradiation-assisted Chemical Synthesis

Nanostructured materials have attracted considerable interest in recent years due to their properties which differ strongly from their bulk phase and potential applications in nanoscale electronic and optoelectronic devices. Metal oxide nanostructures can be synthesized by variety of different synthesis techniques developed in recent years such as thermal decomposition, sol-gel technique, chemical coprecipitation, hydrothermal process, solvothermal process, spray pyrolysis, polyol process etc. All the above processes go through a tedious synthesis procedure followed by prolonged heat treatment at elevated temperature and are time consuming. In the present work we describe a rapid microwave irradiation-assisted chemical synthesis technique for the growth of nanoparticles, nanorods, and nanotubes of a variety of metal oxides in the presence of an appropriate surfactant, without the use of any templates The method is simple, inexpensive, and helps one to prepare nanostructures in a very simple way, and in a very short time, measured in minutes. The synthesis procedure employs high quality metalorganic complexes (typically -diketonates) featuring a direct metal-to-oxygen bond in its molecular structure. The complex is dissolved in a suitable solvent, often with a surfactant added, and the solution then subjected to microwave irradiation in a domestic microwave oven operating at 2.45 GHz frequency with power varying from 160-800 W, from a few seconds to a few minutes, leading to the formation of corresponding metal oxides. This method has been used successfully to synthesize nanostructures of a variety of binary and ternary metal oxides such as ZnO, CdO, Fe2O3, CuO, Ga2O3, Gd2O3, ZnFe2O4, etc. There is an observed variation in the morphology of the nanostructures with the change of different parameters such as microwave power, irradiation time, appropriate solvent, surfactant type and concentration. Cationic, anionic, nonionic and polymeric surfactants have been used to generate a variety of nanostructures. Even so, to remove the surfactant, there is either no need of heat treatment or a very brief exposure to heat suffices, to yield highly pure and crystalline oxide materials as prepared. By adducting the metal complexes, the shape of the nanostructures can be controlled further. In this manner, very well formed, single-crystalline, hexagonal nanorods and nanotubes of ZnO have been formed. Adducting the zinc complex leads to the formation of tapered ZnO nanorods with a very fine tip, suitable for electron emission applications. Particle size and their monodispersity can be controlled by a suitable choice of a precursor complex, the surfactant, and its concentration. The resulting metal oxide nanostructures have been characterized by X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, FTIR spectroscopy, photoluminescence, and electron emission measurements.

Growth of nanowires of beta-NaxV2O5 by metalorganic chemical vapor deposition

Films comprised of nanowires of beta-NaxV2O5 measuring 20-200 nm in diameter and 10-30 mum in length have been prepared on glass substrates by metalorganic chemical vapor deposition using the beta-diketonate complex, vanadyl acetyl acetonate, as precursor, but without the use of either templates or catalysts. Films consisting of nanowires of monophasic beta-NaxV2O5 with a preferred orientation along (h0l) are formed only at 550 degreesC, whereas those deposited at 540 degreesC comprise a mixture of nanowires (beta-NaxV2O5) and platelets (V2O5). The films deposited at lower temperatures are less crystalline and comprise a mixture of vanadium oxide phases. From the observations that nanowires are formed only in the narrow temperature range of 540-550 degreesC, and from the critical dependence of the formation of nanowires on the balance between the CVD growth rate and the evaporation rate of the film, it is inferred that the formation of nanowires of beta-NaxV2O5 is due to chemical vapor transport.

Photoluminescence of Sr(2-x)Ln(x)CeO(4+x/2) (Ln = Eu, Sm or Yb) prepared by a wet chemical method

A wet chemical route is developed for the preparation of Sr2CeO4 denoted the carbonate-gel composite technique. This involves the coprecipitation of strontium as fine particles of carbonates within hydrated gels of ceria (CeO2.xH(2)O, 40

Studies on the structural and ionic transport properties at elevated temperatures of La1-xMnO3 +/-delta synthesized by a wet chemical method

Structural transformation and ionic transport properties are investigated on wet-chemically synthesized La1-xMnO3 (X=0.0-0.18) compositions. Powders annealed in oxygen/air at 1000-1080 K exhibit cubic symmetry and transform to rhombohedral on annealing at 1173-1573 K in air/oxygen. Annealing above 1773 K in air or in argon/helium at 1473 K stabilized distorted rhombohedral or orthorhombic symmetry. Structural transformations are confirmed from XRD and TEM studies. The total conductivity of sintered disks, measured by four-probe technique, ranges from 5 S cm(-1) at 298 K to 105 S cm(-1) at 1273 K. The ionic conductivity measured by blocking electrode technique ranges from 1.0X10(-6) S cm(-1) at 700 K to 2.0X10(-3) S cm(-1) at 1273 K. The ionic transference number of these compositions ranges from 3.0X10(-5) to 5.0X10(-5) at 1273 K. The activation energy deduced from experimental data for ionic conduction and ionic migration is 1.03-1.10 and 0.80-1.00 eV, respectively. The activation energy of formation, association and migration of vacancies ranges from 1.07 to 1.44 eV. (C) 2002 Elsevier Science B.V. All rights reserved.

Affinity-Chromatographic Procedure For The Purification Of The Enzyme From Mung-Bean (Phaseolus, Aureus) Seeds And Conformational-Changes On Its Interaction With Ortho-Phosphate

Flavokinase was purified, for the first time from a plant source [mung bean (Phaseolus aureus)] by affinity chromatography in the presence of orthophosphate and by using C-8 ATP-agarose (ATP linked through the C-8 position to beaded agarose), Cibacron Blue and riboflavin--Sepharoses. An altered substrates-saturation pattern was observed in the presence of K2HPO4. The conformational changes of the enzyme in the presence of K2HPO4 were monitored by fluorescence spectroscopy. These results highlight the regulatory nature of this enzyme.

Intercalative pyrimido[4',5':4,5]thieno(2,3-b)quinolines induce apoptosis in leukemic cells: a comparative study of methoxy and morpholino substitution

DNA intercalating molecules are promising anticancer agents. Polycyclic aromatic molecules such as ellipticine intercalate into double-stranded DNA and affect major physiological functions. In the present study, we have characterized two molecules with the same chemical backbone but different side chains, namely 8-methoxy pyrimido[4',5':4,5]thieno (2,3-b)quinoline-4(3H)-one (MPTQ) and 4-morpholino pyrimido[4',5':4,5]thieno(2,3-b)quinoline (morpho-PTQ) at the 8th and 4th position, respectively. Although both MPTQ and morpho-PTQ show similar biophysical properties with high DNA affinity, here we show that they differ in their biological activities. We find that MPTQ is many fold more potent than morpho-PTQ and is cytotoxic against different leukemic cell lines. IC(50) value of methoxy PTQ was estimated between 2-15 A mu M among the leukemic cells studied, while it was more than 200 A mu M when morpho-PTQ was used. Cell cycle analysis shows an increase in sub-G1 phase, without any particular cell cycle arrest. Annexin V staining in conjunction with comet assay and DNA fragmentation suggest that MPTQ induces cytotoxicity by activating apoptosis. Thus the observed low IC(50) value of MPTQ makes it a promising cancer chemotherapeutic agent.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Design and Characterization of Stabilized Derivatives of Human CD4D12 and CD4D1

CD4 is present on the surface of T-lymphocytes and is the primary cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. A construct consisting of the first two domains of CD4 (CD4D12) is folded and binds gp120 with similar affinity as soluble 4-domain CD4 (sCD4). However, the first domain alone (CD4D1) was previously shown to be largely unfolded and had 3-fold weaker affinity for gp120 when compared to sCD4 [Sharma, D.; et al. (2005) Biochemistry 44, 16192-16202]. We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L511/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregation of CD4D1 upon removal of the second domain. Two mutations, G6A and V86L in CD4D12 increased the stability and yield of the protein relative to the wild-type protein. The mutant CD4D1 (CD4D1a) with the 4 mutations was folded and more stable compared to the original CD4D1, but both bound gp120 with comparable affinity. In in vitro neutralization assays, both CD4D1a and G6A-CD4D12 were able to neutralize diverse HIV-1 viruses with similar IC(50)s as 4-domain CD4. These stabilized derivatives of human CD4 can be useful starting points for the design of other more complex viral entry inhibitors.

Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange

The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN), HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair.