Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

(2R,3R,4aS,6S,7S,8aS)-4a-Fluoro-8a-hydroxyperhydronaphthalene-2,3,6,7-te trayl tetraacetate

The title compound, C18H25FO9, exhibits a similar unit cell and packing to the alpha polymorph of axial 4a,8a-dihydroxyperhydronaphthalene-2,3,6,7-tetrayl tetraacetate. The carbonyl O atoms of two of the four acetate groups in the molecule are disordered over two sites with occupancy ratios of 0.59 (4):0.41 (4) and 0.57 (6):0.43 (6). Crystal packing is effected via intermolecular O-H center dot center dot center dot O hydrogen bonds, which link the tetraacetate molecules into tapes along the c axis.

Effect of fenvalerate, a pyrethroid insecticide on membrane fluidity

Fenvalerate is a commonly used pyrethroid insecticide, used to control a wide range of pests. We have studied its interaction with the membrane using fluorescence polarization and differential scanning calorimetry (DSC) techniques. Fenvalerate was found to decrease the DPH fluorescence polarization value of synaptosomal and microsomal membrane, implicating that it makes the membrane more fluid. At different concentrations of fenvalerate, the activation energy of the probe molecule in the membrane also changes revealed from the change in slope of the Arrhenius plot. At higher concentrations the insecticide slowly saturates the membrane. The effects of fenvalerate on model membrane were also studied with liposomes reconstituted with dipalmitoylphosphatidylcholine (DPPC). Fenvalerate decreased the phase transition temperature (Tm) of DPPC by 1.5 °C at 40 μM concentration, but there was no effect on the cooperativity of the transition as interpreted from the DSC thermogram. From the change in the thermogram profile with fenvalerate it has been interpreted that it localizes in the acyl chain region of the lipid, possibly between C10 and C16 region and weakens the acyl chain packing. Fenvalerate was also found to interact with DPPC liposomes containing cholesterol to fluidize it.

Supermacroporous Polymer-Based Cryogel Bioreactor for Monoclonal Antibody Production in Continuous Culture Using Hybridoma Cells

Cryogel matrices composed of different polymeric blends were synthesized, yielding a unique combination of hydrophilicity and hydrophobicity with the presence or absence of charged surface. Four such cryogel matrices composed of polyacrylamide-chitosan (PAAC), poly(N-isopropylacrylamide)-chitosan, polyacrylonitrile (PAN), and poly(N-isopropylacrylamide) were tested for growth of different hybridoma cell lines and production of antibody in static culture. All the matrices were capable for the adherence of hybridoma cell lines 6A4D7, B7B10, and H9E10 to the polymeric surfaces as well as for the efficient monoclonal antibody (mAb) production. PAAC proved to be relatively better in terms of both mAb production and cell growth. Further, PAAC cryogel was designed into three different formats, monolith, disks, and beads, and used as packing material for packed-bed bioreactor. Longterm cultivation of 6A4D7 cell line on PAAC cryogel scaffold in all the three formats could be successfully done for a period of 6 weeks under static conditions. Continuous packed-bed bioreactor was setup using 6A4D7 hybridoma cell line in the three reactor formats. The reactors ran continuously for a period of 60 days during which mAb production and metabolism of cells in the bioreactors were monitored periodically. The monolith bioreactor performed most efficiently over a period of 60 days and produced a total of 57.5 mg of antibody in the first 30 days (in 500 mL) with a highest concentration of 115 mu g mL(-1), which is fourfold higher than t-flask culture. The results demonstrate that appropriate chemistry and geometry of the bioreactor matrix for cell growth and immobilization can enhance the reactor productivity. (C) 2010 American Institute of Chemical Engineers Biotechnol. Prog., 27: 170-180, 2011

Vesicle and Stable Monolayer Formation from Simple ``Click'' Chemistry Adducts in Water

Click chemistry has been successfully extended into the field of molecular design of novel amphiphatic adducts. After their syntheses and characterizations, we have studied their aggregation properties in aqueous medium. Each of these adducts forms stable suspensions in water. These suspensions have been characterized by dynamic light scattering (DLS) studies and transmission electron microscopy (TEM). The presence of inner aqueous compartments in such aggregates has been demonstrated using dye (methylene blue) entrapment studies. These aggregates have been further characterized using X-ray diffraction (XRD), which indicates the existence of bilayer structures in them. Therefore, the resulting aggregates could be described as vesicles. The temperature-induced order-to-disorder transitions of the vesicular aggregates and the accompanying changes in their packing and hydration have been examined using high-sensitivity differential scanning calorimetry, fluorescence anisotropy, and generalized polarization measurements using appropriate membrane-soluble probe, 1,6-diphenylhexatriene, and Paldan, respectively. The findings of these studies are consistent with each other in terms of the apparent phase transition temperatures. Langmuir monolayer studies confirmed that these click adducts also form stable monolayers on buffered aqueous subphase at the air-water interface.

Crystallography of solid-liquid interface and evolution of texture during directional solidification of Tb0.3Dy0.7Fe1.95 alloy

The effect of growth texture on the magnetostriction of ternary Tb0.3Dy0.7Fe1.95 was studied by conducting unidirectional solidification experiments using a zoning set-up. Detailed texture evolutions were studied using X-ray diffraction on samples obtained by varying growth rates from 18 to 72 cm/h, under a temperature gradient of 100 degrees C/cm. The estimated texture co-efficient and pole figures of the samples indicate that during the onset of the solidification, < 110 > and < 331 >/'rotated < 110 >' texture components nucleate and grow in all the samples. However, as the solidification progresses, < 112 > texture component becomes dominant at higher growth rate. This results in an improvement of magnetostriction from 1000 to 1300 microstrains for samples grown at growth rates of 18 and 72 cm/h respectively. The transition of preferred growth direction occurs through intermediate orientations < 123 >. An attempt has been made in this paper to explain the occurrence of different growth texture by considering the stability of growing interface, its planar packing fraction and atomic stacking sequence of several low index planes. (C) 2010 Elsevier Ltd. All rights reserved.

Crystal structures of fluorinated aryl biscarbonates and a biscarbamate: a counterpoise between weak intermolecular interactions and molecular symmetry

Conformational features and supramolecular structural organization in three aryl biscarbonates and an aryl biscarbamate with rigid acetylenic unit providing variable spacer lengths have been probed to gain insights into the packing features associated with molecular symmetry and the intermolecular interactions involving `organic' fluorine. Four structures but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 1; but-2-yne-1,4-diyl bis(4-fluorophenylcarbonate), 2; but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbamate), 3 and hexa-2,4-diyne-1,6-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 4 have been analyzed in this context. Compound 1 adopts a non-centrosymmetric ``twisted'' (syn) conformation, whereas 2, 3 and 4 acquire a centrosymmetric ``extended'' (anti) conformation. Weak intermolecular interactions and in particular those involving fluorine are found to dictate this conformational variation in the crystal structure of 1. A single-crystal neutron diffraction study at 90 K was performed on 1 to obtain further insights into these interactions involving `organic' fluorine.

Composition Driven Monolayer to Bilayer Transformation in a Surfactant Intercalated Mg-Al Layered Double Hydroxide

The structure and organization of dodecyl sulfate (DDS) surfactant chains intercalated in an Mg-Al layered double hydroxide (LDH), Mg(1-x)Alx(OH)(2), with differing Al/Mg ratios has been investigated. The Mg-Al LDHs can be prepared over a range of compositions with x varying from 0.167 to 0.37 and therefore provides a simple system to study how the organization of the alkyl chains of the intercalated DDS anions change with packing density; the Al/Mg ratio or x providing a convenient handle to do so. Powder X-ray diffraction measurements showed that at high packing densities (x >= 0.3) the alkyl chains of the intercalated dodecyl sulfate ions are anchored on opposing LDH sheets and arranged as bilayers with an interlayer spacing of similar to 27 angstrom. At lower packing densities (x < 0.2) the surfactant chains form a monolayer with the alkyl chains oriented flat in the galleries with an interlayer spacing of similar to 8 angstrom. For the in between compositions, 0.2 <= x < 0.3, the material is biphasic. MD simulations were performed to understand how the anchoring density of the intercalated surfactant chains in the Mg-Al LDH-DDS affects the organization of the chains and the interlayer spacing. The simulations are able to reproduce the composition driven monolayer to bilayer transformation in the arrangement of the intercalated surfactant chains and in addition provide insights into the factors that decide the arrangement of the surfactant chains in the two situations. In the bilayer arrangement, it is the dispersive van der Waals interactions between chains in opposing layers of the anchored bilayer that is responsible for the cohesive energy of the solid whereas at lower packing densities, where a monolayer arrangement is favored, Coulomb interactions between the positively charged Mg-Al LDH sheets and the negatively charged headgroup of the DDS anion dominate.

Diacetylenic lipid tubules:experimental evidence for a chiral molecular architecture

Molecular self-assembly is of key importance for the rational design of advanced materials. To investigate the causal relation between molecular structure and the consequent self-assembled microstructure, self-assembled tubules of diacetylenic lipids were studied. Circular-dichroism studies give experimental evidence that the formation of tubules is driven by chiral molecular packing, in agreement with recent theories of tubules. On the basis of these results, a molecular mechanism for the formation of tubules is proposed.

Dynamic structure factors of a dense mixture

We compute the dynamic structure factors of a dense binary liquid mixture. These describe dynamics on molecular length scales, where structural relaxation is important. We find that the presence of a few large particles in a dense fluid of small particles slows down the dynamics considerably. We also observe a deep narrowing of the spectrum for a disordered mixture composed of a nearly equal packing of the two species. In contrast, a few small particles diffuse easily in the background of a dense fluid of large particles. We expect our results to describe neutron scattering from a dense mixture.

Photobehavior of crystalline 4-styrylcoumarin dimorphs: structure-reactivity correlations

4-Styrylcoumarin crystallizes from chloroform and hexane mixture in two morphologically different modifications. The monoclinic form (needles, P2(1)/c) undergoes stereospecific photodimerization producing anti head-to-tail dimer across pyrone double bond, whereas the triclinic modification (prisms, P ($) over bar 1) dimerizes yielding photodimer of the same configuration, but across styrenic double bond. Single crystal X-ray analyses of the dimorphs reveal the packing differences permitting rationalization of the regio- and stereochemistry of the photoproducts. The significantly low dimer yield from the prismatic crystals is rationalized.

Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

Role of organic fluorine in crystal engineering

The design of compounds with novel and improved physico-chemical properties as advanced functional materials with a specific application spectrum requires the knowledge about possible supramolecular packing motifs and their experimental control in crystalline lattice. Besides the structure of the individual molecule, non-covalent interactions play a significant role in the determination of molecular conformation, along with the formation of three-dimensional supramolecular architecture in a crystal as a requirement for molecular recognition processes, and the related bioactivity. Involvement of functional groups will contribute to the formation of a predefined packing motif due to their well-defined interactions. The strength and directionality of these interactions create characteristic packing motifs, which can be used for the design of supramolecular arrangements by the development of appropriate strategies for the precise control of their topology. Most relevant of these non-covalent interactions are stacking interactions and hydrogen bonds, which have been subjects of extensive study in the last two decades. In recent literature, substantial efforts have been put in by various researchers towards the understanding of interactions involving organic fluorine and the role they play in generating different packing motifs which guides assembling of molecules in the crystal lattice.

Scanning tunneling microscopy and spectroscopy of C70 thin films

Scanning tunneling microscopy of C-70 films deposited on HOPG and gold substrates has been carried but to investigate the 2D packing, defects and disorder. Besides providing direct evidence for orientational disorder, high resolution; images showing the carbon skeleton as well as the molecular arrangement in a solid solution of C-70 and C-60 are presented. Tunneling conductance measurements Indicate a small gap in the C-70 film deposited on HOPG substrate.

Studies in crystal engineering: structure�reactivity correlations of substituted styrylcoumarins and related systems

The solid state photochemical behaviour of 7-hydroxy-4-styrylcoumarin 1 and several of its derivatives and analogues has been investigated. All the compounds with the exception of 7-methoxy-4-styrylcoumarin 2 are photolabile and yield anti-HT dimers. It has been observed that chloro substitution in the systems studied does not lead to the expected beta-packing mode. The photobehaviour of 1 and 2 has been correlated with their crystal structures. Reasons for alpha-packing have been examined. The systematics in the arrangement of the carbonyl group and phenyl group of the close neighbours in the crystals of 1, 2 and a few other cases are presented.