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.

Behaviour of the curve of critical exponents near and away from a double critical point

To investigate the nature of the curve of critical exponents (as a function of the distance from a double critical point), we have combined our measurements of the osmotic compressibility with all published data for quasibinary liquid mixtures. This curve has a parabolic shape. An explanation of this result is advanced in terms of the geometry of the coexistence dome, which is contained in a triangular prism.

Stereoelectronic control of Cope rearrangement energetics through remote double bonds in novel, rigid polycyclic frames

The presence and orientation of remote double bonds are shown to completely alter the shapes of Cope rearrangement energy profiles in a heptacyclic system.

Tuning the electronic effective mass in double-doped SrTiO3

We elucidate the relationship between effective mass and carrier concentration in an oxide semiconductor controlled by a double-doping mechanism. In this model oxide system, Sr1-xLaxTiO3-delta, we can tune the effective mass ranging from 6 to 20m(e) as a function of filling (carrier concentration) and the scattering mechanism, which are dependent on the chosen lanthanum-and oxygen-vacancy concentrations. The effective mass values were calculated from the Boltzmann transport equation using the measured transport properties of thin films of Sr1-xLaxTiO3-delta. We show that the effective mass decreases with carrier concentration in this large-band-gap, low-mobility oxide, and this behavior is contrary to the traditional high-mobility, small-effective-mass semiconductors.

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

A novel double friedel-crafts reaction: A new entry into bicyclo[3.2.2]nonane system

A novel synthesis of dibenzobicyclo[3.2.2]nonane systems is described through a double Friedel-Crafts reaction.

Augmentation of murine natural killer cell and antibody dependent cellular cytotoxicity activities by phyllanthus emblica, a new immunomodulator

When administered orally, Phyllanthus emblica, an excellent source of vitamin C (ascorbate), has been found to enhance natural killer (NK) cell activity and antibody dependent cellular cytotoxicity (ADCC) in syngeneic BALB/c mice, bearing Dalton's lymphoma ascites (DLA) tumor. P. emblica elicited a 2-fold increase in splenic NK cell activity on day 3 post tumor inoculation. Enhanced activity was highly significant on days 3, 5, 7 and 9 after tumor inoculation with respect to the untreated tumor bearing control. A significant enhancement in ADCC was documented on days 3, 7, 9, 11 and 13 in drug treated mice as compared to the control. An increase in life span (ILS) of 35% was recorded in tumor bearing mice treated with P. emblica. This increased survival was completely abrogated when NK cell and killer (K) cell activities were depleted either by cyclophosphamide or anti-asialo-GM, antibody treatment. These results indicate: (a) an absolute requirement for a functional NK cell or K cell population in order that P. emblica can exert its effect on tumor bearing animals, and (b) the antitumor activity of P. emblica is mediated primarily through the ability of the drug to augment natural cell mediated cytotoxicity.

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.

Double Aromaticity in the 3,5-Dehydrophenyl Cation and in Cyclo[6]carbon

The presence of two (4n+2)-electron conjugated systems in perpendicular planes results in considerable aromatic stabilization. Despite having two fewer hydrogens, the 6 pi e-2 sigma e 3,5-dehydrophenyl cation (C6H3+, 1) is 32.7 (CCSD(T)/6-31G**) and 35.2 kcal/mol (RMP4sdtq/6-3iG*//RMP2(fu)/6-31G*) more stable than the phenyl cation (evaluated by an isodesmic reaction involving benzene and m-dehydrobenzene (4)). Cation 1, the global C6H3+ minimum, is 11.7,24.2, 11.8, and 30.4 kcal/mol lower in energy than the 2,6- (11) and 3,4-dehydrophenyl (12) cations as well as the open-chain isomers 13 and 14 (RMP4sdtq/6-31G*//RMP2(fu)/6-31G* + ZPE(RMP2(fu)/6-31G*)). The stability of 1 is increased hyperconjugatively by 2,4,6-trisilyl substitution. The double aromaticity of 1 is indicated by the computed magnetic susceptibility exaltations (IGLO/II//RMP2(fu)/6-31G*) of -5.2, -6.8, -15, and -23.2 relative to 11, 12, 13, and 14, respectively. Thus, 1 fulfills the geometric, energetic, and magnetic criteria of aromaticity. The double aromaticity of the D-6h cyclo[6]carbon is apparent from the same criteria

Excision of uracil from the ends of double stranded DNA by uracil DNA glycosylase and its use in high efficiency cloning of PCR products

We show that uracil DNA glycosylase from E. coli excises uracil residues from the ends of double stranded oligos. This information has allowed us to develop an efficient method of cloning PCR amplified DNA. In this report, we describe use of this method in cloning of E. coli genes for lysyl- and methionyl-tRNA synthetases. Efficiency of cloning by this method was found to be the same as that of subcloning of DNA restriction fragments from one vector to the other vector. Possibilities of using other DNA glycosylases for such applications are discussed.

Inhibition of nuclear protein import by a monoclonal antibody against a novel class of nuclear pore proteins

Nuclear import of proteins is mediated by the nuclear pore complexes in the nuclear envelope and requires the presence of a nuclear localization signal (NLS) on the karyophilic protein. In this paper, we describe studies with a monoclonal antibody, Mab E2, which recognizes a class of nuclear pore proteins of 60-76 kDa with a common phosphorylated epitope on rat nuclear envelopes. The Mab Ea-reactive proteins fractionated with the relatively insoluble pore complex-containing component of the envelope and gave a finely punctate pattern of nuclear staining in immunofluorescence assays. The antibody did not bind to any cytosolic proteins. Mab E2 inhibited the interaction of a simian virus 40 large T antigen NLS peptide with a specific 60-kDa NLS-binding protein from rat nuclear envelopes in photoaffinity labeling experiments. The antibody blocked the nuclear import of NLS-albumin conjugates in an in vitro nuclear transport assay with digitonin-permeabilized cells, but did not affect passive diffusion of a small nonnuclear protein, lysozyme, across the pore. Mab E2 may inhibit protein transport by directly interacting with the 60-kDa NLS-binding protein, thereby blocking signal-mediated nuclear import across the nuclear pore complex. (C) 1994 Academic Press, Inc.

High-rate, Double-Symbol-Decodable STBCs from Clifford Algebras

For the number of transmit antennas N = 2(a) the maximum rate (in complex symbols per channel use) of all the Quasi-Orthogonal Designs (QODs) reported in the literature is a/2(a)-1. In this paper, we report double-symbol-decodable Space-Time Block Codes with rate a-1/2(a)-2 for N = 2(a) transmit antennas. In particular, our code for 8 and 16 transmit antennas offer rates 1 and 3/4 respectively, the known QODs offer only 3/4 and 1/2 respectively. Our construction is based on the representations of Clifford algebras and applicable for any number of transmit antennas. We study the diversity sum and diversity product of our codes. We show that our diversity sum is larger than that of all known QODs and hence our codes perform better than the comparable QODs at low SNRs for identical spectral efficiency. We provide simulation results for various spectral efficiencies.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

Antibodies raised against guanosine bind to double-stranded DNA

Antibodies elicited against guanosine have been reported to bind to single-stranded DNA. Using an avidin-biotin microELISA, we report that these antibodies also bind to double-stranded DNA. The binding is specific and is completely inhibited by the homologous hapten. The cross-reactivity of double-stranded DNA binding antibodies to single-stranded DNA is low. The antibodies are shown to bind to the topoisomers of plasmid DNA as assessed by a gel retardation assay.