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At least 109 records · Page 6Linked to original sources
PubMed2001

Identification of a homopolymer of 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxy-D-glycero-D-talo-nonulosonic acid in the lipopolysaccharides of Legionella pneumophila Non-1 serogroups.

O-Specific polysaccharides (OPS) were isolated by mild acid hydrolysis of the lipopolysaccharides (LPS) of strains of Legionella pneumophila serogroups 2-14, as well as strains Lansing 3 and 16453-92 from newly proposed serogroups. The OPS were studied by (1)H- and (13)C-NMR spectroscopy, GLC/mass spectrometry, and chemical modifications (mild alkaline O-deacetylation and conversion of the N-acetimidoyl group into the N-acetyl group). All OPS were found to be a homopolymer of a 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxynonulosonic acid, which in some strains is 8-O-acetylated. In most strains studied, the monosaccharide has the D-glycero-D-talo configuration and is thus the C4 epimer of legionaminic acid (4-epilegionaminic acid), which has been previously identified as the monomer in the OPS of L. pneumophila serogroup 1. Poly(4-epilegionaminic acid) occurs as a minor polysaccharide in serogroups 5 (strain Dallas 1) and 13 and is absent in serogroups 1 and 7. The chemical basis for serological differentiation of L. pneumophila strains is discussed.

Acetylation↗
PubMed2003

Cytotoxicity study of homopolymers and copolymers of 2-hydroxyethyl methacrylate and some alkyl acrylates for potential use as temporary skin substitutes.

The cytotoxicities of both homopolymers and copolymers of 2-hydroxyethyl methacrylate (HEMA) and various alkyl acrylates (AA) were investigated using cell culture techniques. The particular alkyl acrylates used were methyl acrylate (MA), ethyl acrylate (EA) and butyl acrylate (BA). The AA contents of the polymers studied were in the range of 0-25% by weight. They were synthesized via bulk polymerization in the form of thin sheets of 0.5+/-0.1 mm thickness. After sterilization using ethylene oxide gas, cytotoxicity tests, including both direct and indirect contact tests, were performed using cell lines of L929 and normal human dermal fibroblasts. The results showed that P(HEMA-co-EA) with EA contents of 15-25% and P(HEMA-co-BA) with BA contents of 10-25% appeared to be non-cytotoxic and attractive for more specific cytocompatibility tests and in vivo studies with a view to their use as temporary skin substitutes.

Journal Article↗
PubMed2005

Experimental and theoretical study of the interaction of single-stranded DNA homopolymers and a monomethine cyanine dye: nature of specific binding.

The photophysical properties of an intercalating unsymmetrical monomethine cyanine dye and single-stranded DNA homopolymers show strong association for poly(dA) and poly(dG), but not for poly(dC) and poly(dT), as determined by several spectroscopic techniques and molecular dynamics calculations. While poly(dA) and poly(dG) appear to bind the dye as a monomer (with dramatic increase in fluorescence), poly(dC) and poly(dT) bind only very weakly, and seem to promote dye aggregation. Only in the case of poly(dA) there seems to be a unique, well defined form of intercalation, that molecular dynamics calculations suggest involve the quinoline ring between two bases, in an arrangement that should favor pi-stacking; consistently with this, the decay of the fluorescence shows a single exponential, the absorption spectrum shows a shift in the dye maximum, the fluorescence is strong, and the induced circular dichroism follows a simple pattern.

Carbocyanines↗
PubMed2002

Structures of two O-chain polysaccharides of Citrobacter gillenii O9a,9b lipopolysaccharide. A new homopolymer of 4-amino-4,6-dideoxy-D-mannose (perosamine).

Mild acid degradation of the lipopolysaccharide of Citro- bacter gillenii O9a,9b released a polysaccharide (PS), which was found to consist of a single monosaccharide, 4- acetamido-4,6-dideoxy-d-mannose (d-Rha4NAc, N-acetyl-d-perosamine). PS was studied by methylation analysis and (1)H-NMR and (13)C-NMR spectroscopy, using two-dimensional (1)H,(1)H COSY, TOCSY, NOESY, and H-detected (1)H,(13)C heteronuclear correlation experiments. It was found that PS includes two structurally different polysaccharides: an alpha1-->2-linked homopolymer of N-acetyl-d-perosamine [-->2)-alpha-d-Rhap4NAc-(1-->, PS2] and a polysaccharide composed of tetrasaccharide repeating units (PS1) with the following structure: -->3)-alpha-d-Rhap4NAc-(1-->2)-alpha-d-Rhap4NAc-(1-->2)-alpha-d-Rhap4NAc-(1-->3)-alpha-d-Rhap4 N Ac2Ac-(1--> where the degree of O-acetylation of a 3-substituted Rha4NAc residue at position 2 is approximately 70%. PS could be fractionated into PS1 and PS2 by gel-permeation chromatography on TSK HW-50S. Matrix-assisted laser desorption ionization MS data indicate sequential chain elongation of both PS1 and PS2 by a single sugar unit, with O-acetylation in PS1 beginning at a certain chain length. Anti-(C. gillenii O9a,9b) serum reacted with PS1 in double immunodiffusion and immunoblotting, whereas neither PS2 nor the lipopolysaccharide of Vibrio cholerae O1 with a structurally related O-chain polysaccharide were reactive.

Animals↗
PubMed2002

Ferritin from the spleen of the Antarctic teleost Trematomus bernacchii is an M-type homopolymer.

Ferritin from the spleen of the Antarctic teleost Trematomus bernacchii is composed of a single subunit that contains both the ferroxidase center residues, typical of mammalian H chains, and the carboxylate residues forming the micelle nucleation site, typical of mammalian L chains. Comparison of the amino-acid sequence with those available from lower vertebrates indicates that T. bernacchii ferritin can be classified as an M-type homopolymer. Interestingly, the T. bernacchii ferritin chain shows 85.7% identity with a cold-inducible ferritin chain of the rainbow trout Salmo gairdneri. The structural and functional properties indicate that cold acclimation and functional adaptation to low temperatures are achieved without significant modification of the protein stability. In fact, the stability of T. bernacchii ferritin to denaturation induced by acid or temperature closely resembles that of mesophilic mammalian ferritins. Moreover iron is taken up efficiently and the activation energy of the reaction is 74.9 kJ.mol(-1), a value slightly lower than that measured for the human recombinant H ferritin (80.8 kJ.mol(-1)).

Amino Acid Sequence↗
PubMed2004

The unphysical pinning of the domain growth during the separation of homopolymer blends near the spinodal.

We simulate model B of mesoscopic dynamic with the Flory-Huggins free energy for the homopolymer blend. We concentrate the study on the rescaling of the spatial coordinates in the model. We show that the commonly used rescaling of the spatial coordinates, by the function vanishing at the spinodal, leads to the unphysical freezing of the domains. We study the evolution of the system in two different processes: One is the growth process induced by the temperature quench to the metastable or unstable region of the phase diagram and the second is the quench-jump process in which we first allow the system to separate below the spinodal and next heat it up below or above the spinodal. The proper rescaling avoiding the unphysical pinning of the domain growth at the spinodal is proposed.

Journal Article↗
PubMed2004

Comparison of random-walk density functional theory to simulation for bead-spring homopolymer melts.

Density profiles for a homopolymer melt near a surface are calculated using a random-walk polymeric density functional theory, and compared to results from molecular dynamics simulations. All interactions are of a Lennard-Jones form, for both monomer-monomer interactions and surface-monomer interactions, rather than the hard core interactions which have been most investigated in the literature. For repulsive systems, the theory somewhat overpredicts the density oscillations near a surface. Nevertheless, near quantitative agreement with simulation can be obtained with an empirical scaling of the direct correlation function. Use of the random phase approximation to treat attractive interactions between polymer chains gives reasonable agreement with simulation of dense liquids near neutral and attractive surfaces.

Journal Article↗
PubMed2004

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study.

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.

Journal Article↗
PubMed2005

Scaling behavior of a brush-homopolymer interface in the limit of high grafting density.

The interface between a polymer brush and a chemically equivalent homopolymer is examined using self-consistent field theory (SCFT). Focusing on ultrahigh grafting densities, we extract how the properties scale with the brush thickness, L, and compare with predictions based on strong-stretching theory (SST). Although the scaling exponents are consistent, the overall agreement is poor. We attribute this to the inaccurate way the SST-based calculation treats chain fluctuations at the extremity of the brush. This accounts for a previous disagreement between SCFT and SST in regards to autophobic dewetting, and brings into question a number of other SST predictions. Our conclusion is that SST requires a more sophisticated treatment of finite-stretching corrections, along the lines of that proposed by Likhtman and Semenov [Europhys. Lett. 51, 307 (2000)].

Journal Article↗
PubMed2005

Studies on the behavior of nanoconfined homopolymers with cyclic chain architecture.

We have performed Monte Carlo simulations to study the effect of cyclic architecture on the behavior of homopolymer chains under several conditions of confinement. The collapse of the rings in two stages, a coil-to-globule and a liquidlike-to-solidlike transition, was observed even at extreme confinement. Both transitions were observed at lower temperatures than for linear chains of the same length, 2%-5% lower for unconfined systems, and 10%-15% lower for wall separations below three bond lengths due to the effect of confinement. When the plates separation approached the two-dimensional regime, the coil-to-globule transition shifted to lower temperatures. The inverse trend was observed when the chain length was increased. In the collapsed state, the average size and conformations of linear and cyclic molecules of same length were similar independently of confinement. At temperatures near the coil-to-globule transition, the radius of gyration of unconfined linear chains, [R(g)(2)](linear), became larger than for the cyclic chains, [R(g)(2)](cyclic), and this difference increased considerably with confinement. The radius of gyration ratio [R(g)(2)](linear)/[R(g)(2)](cyclic) in this region decreased rapidly. The decrease was more pronounced and occurred at lower temperatures for slit width confinements. At higher temperatures, in the coil state, the radius of gyration ratio became nearly constant for a given separation, and varied from 0.56 for unconfined systems to 0.47 when the chain was completely confined between the walls. This reduction was attributed to the higher increase in the average size of linear chains with confinement when compared with cyclic chains, due to architectural restrictions.

Algorithms↗
PubMed2005

Continuum formulation of the Scheutjens-Fleer lattice statistical theory for homopolymer adsorption from solution.

Homopolymer adsorption from a dilute solution on an interacting (attractive) surface under static equilibrium conditions is studied in the framework of a Hamiltonian model. The model makes use of the density of chain ends n(1,e) and utilizes the concept of the propagator G describing conformational probabilities to locally define the polymer segment density or volume fraction phi; both n(1,e) and phi enter into the expression for the system free energy. The propagator G obeys the Edwards diffusion equation for walks in a self-consistent potential field. The equilibrium distribution of chain ends and, consequently, of chain conformational probabilities is found by minimizing the system free energy. This results in a set of model equations that constitute the exact continuum-space analog of the Scheutjens-Fleer (SF) lattice statistical theory for the adsorption of interacting chains. Since for distances too close to the surface the continuum formulation breaks down, the continuum model is here employed to describe the probability of chain configurations only for distances z greater than 2l, where l denotes the segment length, from the surface; instead, for distances z < or = 2l, the SF lattice model is utilized. Through this novel formulation, the lattice solution at z = 2l provides the boundary condition for the continuum model. The resulting hybrid (lattice for distances z < or = 2l, continuum for distances z > 2l) model is solved numerically through an efficient implementation of the pseudospectral collocation method. Representative results obtained with the new model and a direct application of the SF lattice model are extensively compared with each other and, in all cases studied, are found to be practically identical.

Adsorption↗
PubMed2006

An off-lattice Wang-Landau study of the coil-globule and melting transitions of a flexible homopolymer.

The Wang-Landau Monte Carlo approach is applied to the coil-globule and melting transitions of off-lattice flexible homopolymers. The solid-liquid melting point and coil-globule transition temperatures are identified by their respective peaks in the heat capacity as a function of temperature. The melting and theta points are well separated, indicating that the coil-globule transition occurs separately from melting even in the thermodynamic limit. We also observe a feature in the heat capacity between the coil-globule and melting transitions which we attribute to a transformation from a low-density liquid globule to a high-density liquid globule.

Journal Article↗
PubMed2006

Mapping a homopolymer onto a model fluid.

We describe a linear homopolymer using a grand canonical ensemble formalism, a statistical representation that is very convenient for formal manipulations. We investigate the properties of a system where only next neighbor interactions and an external, confining, field are present and then show how a general pair interaction can be introduced perturbatively, making use of a Mayer expansion. Through a diagrammatic analysis, we shall show how constitutive equations derived for the polymeric system are equivalent to the Ornstein-Zernike and Percus-Yevick equations for a simple fluid and find the implications of such a mapping for the simple situation of Van der Waals mean field model for the fluid.

Journal Article↗
PubMed1970

Role of adrenal cortical function in toxicity of polyriboinosinic-polyribocytidylic acid and its component homopolymers.

Adrenalectomized rats are 1000 times more sensitive to lethal effects of the double-stranded complex polyriboinosinic.polyribocytidylic acid than intact rats. They are protected from such lethal effects by corticosterone. The complex can rapidly induce diffuse, severe necrosis of villous epithelium in small intestine without damage in crypts. Injection of the individual homopolymers, polyriboinosinic acid and polyribocytidylic acid, separately but in rapid succession is at least as lethal as injection of the complex.

Adrenal Glands↗
PubMed1984

A linear biopolymer in the vicinity of the triple point. The homopolymer case.

This is a theoretical study of a situation where each residue of a linear biopolymer may adopt one of three conformational states. Such a situation exists in the case of DNA, since it may be in helical A, B, . . ., Z forms as well as the melted state. In the vicinity of the triple point in the phrase diagram three states, e.g. the A form, the B form and the denatured state, co-exist within a given molecule. We present an exact analytical solution of the simplest homopolymer model. Theory predicts that the presence of two helical states in one molecule should affect the helix-coil transition in two ways. The melting temperature experiences an upward shift and the melting range width is increased, by a factor of square root of two as a maximum.

Alcohols↗
PubMed1993

Characteristics of the large (dA).(dT) homopolymer tracts in D. discoideum gene flanking and intron sequences.

D. discoideum, the slime mold, is one of the most AT rich eukaryotic genomes known. In this paper we examine this organism's database for overlapping N-tuples of high frequency and find A and T tracts possess among the highest frequencies in flanking sequences but not in coding sequences. We examined both overlapping and non-overlapping frequencies of the A, T, G and C homopolymer tracts of 2 < N < 6. Overlapping (dG).(dC) and (dA).(dT) tracts occur at greater frequencies than expected, based on random occurrence. Long (dA).(dT) tracts of N > 10 occur at well above expected frequencies in flanking and intron regions, while (dG).(dC) tracts above N = 5 are rarely found. Some of the implications of these findings for tract origins in slip-strand replication and for chromatin structure are discussed.

Animals↗
PubMed1994

Alignment of (dA).(dT) homopolymer tracts in gene flanking sequences suggests nucleosomal periodicity in D. discoideum DNA.

It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A and T tracts (N > 10) in long flanking sequences by scored alignments of those tracts (N > 10) with the nucleosomal repeat. A tract spacing was found at 185-190 bp that corresponds to a maximum alignment score. This is exactly the average spacing of D. discoideum nucleosomes determined experimentally. A majority of A and T tracts in flanking sequences are often spaced by short DNA stretches and the total length of adjacent A and T tracts plus the interrupting short DNA stretch corresponds closely to the average experimentally measured nucleosomal linker DNA size in D. discoideum-42 bp. These data suggest a model which has A and T runs of N > 10 bp in flanking DNA of D. discoideum organized in a regular phase with nonhomopolymer sequences along the DNA. This model has functional implications for A and T tracts, suggesting that they are found in nucleosomal linker DNA regions of chromatin during some necessary portion(s) of the life of the cell.

Animals↗