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At least 73 records · Page 4Linked to original sources
PubMed1976

Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase.

Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with respect to initial rate tested with 2 single-stranded primer, is 5-6 fols higher than that observed with Mg+2 ion. In the presence of Co+2 ion, the primer specificity is altered so that all forms of duplex DNA molecules can be labeled at their unique 3' -ends regardless of whether such ends are staggered or even. Thus, using ribonucleotide incorporation, we have for the first time employed this reaction for sequence analysis of duplex DNA fragments generated by restriction endonuclease cleavages. Furthermore, by using Co+2 ion, it is possible to add a long homopolymer tract of deoxyribonucleotides to the 3'-terminus of double-stranded DNA. Therefore, without prior treatment with lambda exonuclease to expose the 3' terminus as single-stranded primer, this reaction now permits insertion of homopolymer tails at the 3'-ends of all types of DNA molecules for the purpose of in vitro construction of recombinant DNA.

Cobalt↗
PubMed1976

Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase.

Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of Co+2 ion with respect to initial rate tested with 2 single-stranded primer, is 5-6 fold higher than that observed with Mg+2 ion. In the presence of Co+2 ion, the primer specificity is altered so that all forms of duplex DNA molecules can be labeled at their unique 3'-ends regardless of whether such ends are staggered or even. Thus, using ribonucleotide incorporation, we have for the first time employed this reaction for sequence analysis of duplex DNA fragments generated by restriction endonuclease cleavages. Furthermore, by using Co+2 ion, it is possible to add a long homopolymer tract of deoxyribonucleotides to the 3'-terminus of double-stranded DNA. Therefore, without prior treatment with lambda exonuclease to expose the 3' terminus as single-stranded primer, this reaction now permits insertion of homopolymer tails at the 3'-ends of all types of DNA molecules for the purpose of in vitro construction of recombinant DNA.

Cobalt↗
PubMed2000

Early stages of homopolymer collapse

Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this paper, a phenomenological model is proposed for the kinetics of the early stages of homopolymer collapse following a quench from temperatures above to below the straight theta temperature. In the first stage, nascent droplets of the dense phase are formed, with little effect on the configurations of the bridges that join them. The droplets then grow by accreting monomers from the bridges, thus causing the bridges to stretch. During these two stages, the overall dimensions of the chain decrease only weakly. Further growth of the droplets is accomplished by the shortening of the bridges, which causes the shrinking of the overall dimensions of the chain. The characteristic times of the three stages scale as N0, N(1/5), and N(6/5), respectively, where N is the degree of polymerization of the chain.

Journal Article↗
PubMed2002

Local and segmental dynamics in homopolymer and triblock copolymers with one semicrystalline block.

Thermally stimulated depolarization currents, TSDC, experiments have been performed on a series of poly(styrene)-b-poly(butadiene)-b-poly(epsilon-caprolactone) triblock copolymers SBC with different proportions of the poly(epsilon-caprolactone) crystallizable block, PCL. The morphology of the segregated microphases varies with the PCL content and has been observed by transmission electron microscopy. The crystallinity of the PCL block is estimated by wide angle x-ray scattering, WAXS. The relaxation times distribution is extracted by a numerical decomposition of the TSDC spectra and it is shown that this distribution is not significantly changed on going from the homopolymer to the triblock copolymer with 16 wt % to 77 wt % of PCL in the original samples. Better segregation of the mesophase structure is reached when the samples are annealed at 413 K and important variations in the TSDC and WAXS spectra are observed as a result of the thermal treatment. For the S09B14C77 triblock copolymer the results obtained can be explained by postulating the existence of a rigid amorphous phase in the PCL block. Such rigid amorphous phase is located between the core-shell cylinders formed by the other blocks [with poly(styrene)(PS) as core and poly(butadiene)(PB) as shell] and is constrained by undulated lamellae of crystalline PCL material. In the case of S35B15C50 triblock copolymer, an important amount of diffuse PS-PCL interphase where the homopolymers are mixed must be present before annealing. The results for the material with the less abundant PCL block are explained as a result of the confinement in nanotubes of PCL surrounded by PB embedded in a vitreous PS matrix. Broadband dielectric experiments on these same materials confirm the results obtained by TSDC spectroscopy.

Journal Article↗
PubMed2004

Supersymmetry theory of microphase separation in homopolymer-oligomer mixtures.

The mesoscopic structure of periodically alternating layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for systems with both strong (ionic) and weak (hydrogen) interactions. We focus on the consideration of the distribution of oligomers along the homopolymer chains that is described by the effective equation of motion with the segment number playing the role of imaginary time. The supersymmetry technique is developed to consider associative hydrogen bonding, self-action effects, inhomogeneity, and temperature fluctuations in the oligomer distribution. Making use of the self-consistent approach allows one to explain experimentally observed temperature dependence of the structure period and the order-disorder transition temperature and period as functions of the oligomeric fraction for systems with different bonding strengths. A whole set of parameters of the model used is found for strong, intermediate, and weak coupled systems being Poly (4-vinyl pyridine)-dodecyl benzene sulfonic acid [P4VP-(DBSA)(x)], P4VP-[Zn(DBS)(2)](x), and P4VP- 3-pentadecyl Phenol(x), respectively. A passage from the former two to the latter is shown to cause a crucial decrease in the magnitude of both parameters of hydrogen bonding and self-action, as well as the order-disorder transition temperature.

Journal Article↗
PubMed2004

Pseudoknots in a homopolymer.

After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the pseudoknot number (Npk) at different temperature regimes in two and three dimensions. We find that, although the total number of pseudoknots is extensive at all temperatures, the number of those forming between the two halves of the chain diverges logarithmically at (both dimensions) and below (two dimensions only) the theta temperature. We later introduce a simple model that emphasizes the role of pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched, and collapsed homopolymer phases with transitions between each pair.

Journal Article↗
PubMed2005

Orientational order transition of the striped microphase structure of a copolymer-homopolymer mixture under oscillatory particles.

Based on the three-order-parameter model, we investigate the orientational order transition of striped patterns in microphase structures of diblock copolymer-homopolymer mixtures in the presence of periodic oscillatory particles. Under suitable conditions, although the macrophase separation of a system is almost isotropic, the microphase separation of the system will be significantly perturbed by the oscillatory field, and composition fluctuations are suppressed anisotropically. The isotropy of the microphase will be broken up. By changing the oscillatory amplitude and frequency, we observe the orientational order transition of a striped microphase structure from the isotropic state to a state parallel to the oscillatory direction, and from the parallel state to a state perpendicular to the oscillatory direction. We examine, in detail, the microstructure and orientational order parameter as well as the domain size in the process of orientational order transition under the oscillatory field. We study also how the microphase structure changes with the composition ratio of homopolymers and copolymers in mixtures. The results suggest that our model system may provide a simple way to realize orientational order transition of soft materials.

Journal Article↗
PubMed2006

Hamiltonian dynamics of homopolymer chain models.

The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of observables numerically computed along dynamical trajectories are found to reproduce results given by the statistical mechanics of homopolymer models. The dynamical treatment, however, indicates a nontrivial transition between regimes of slow and fast phase space mixing. Such a transition is inaccessible to a statistical mechanical treatment and reflects a bimodality in the relaxation of time averages to corresponding ensemble averages. It is also found that a change in the energy dependence of the largest Lyapunov exponent indicates the Theta transition between filamentary and globular polymer configurations, clearly detecting the transition even for a finite number of particles.

Journal Article↗
PubMed2001

Attraction between nanoparticles induced by end-grafted homopolymers in good solvent.

The interactions between nanoparticles coated by end-grafted homopolymers of comparable size are studied using Edwards' self-consistent field (SCF) theory. The equilibrium monomer density distribution is obtained by solving the SCF equations in bispherical coordinates. It is shown that, because of the spherical geometry and redistribution of monomer density, end-grafted homopolymers in good solvent environment can induce attractive interactions. This result suggests that steric stabilization of nanoparticles requires new working principles and that the equilibrium distance between nanoparticles may be tuned by end-grafted polymers.

Journal Article↗
PubMed1990

The occurrence of alpha (1----2) linked N-acetylperosamine--homopolymer in lipopolysaccharides of non-O1 Vibrio cholerae possessing an antigenic factor in common with O1 V. cholerae.

Chemical analysis was carried out on lipopolysaccharides from Vibrio cholerae bio-serogroup Hakata 487-85. The O-specific chain of the phenol-soluble lipopolysaccharides was demonstrated by 13C-NMR spectroscopy and methylation analysis to contain a linear homopolymer of alpha(1----2) linked N-acetylperosamine (4-acetamido-4,6-dideoxy-D-mannopyranose), which was closely similar to but not identical to a linear alpha(1----2) linked N-3-deoxy-L-glycerotetronyl (S-2,4-dihydroxybutyryl) perosamine-homopolymer constituting that of O1 Vibrio cholerae lipopolysaccharides.

Amino Sugars↗
PubMed1989

Binding of globin mRNA, beta-globin mRNA segments and RNA homopolymers by immobilized protein of polysomal globin messenger ribonucleoprotein.

The binding of rabbit globin mRNA, in-vitro-generated beta-globin mRNA segments, and RNA homopolymers by proteins of rabbit reticulocyte polysomal messenger ribonucleoproteins (mRNP) after SDS gel electrophoresis and electroblotting was examined. The polysomal mRNP proteins have a higher affinity for mRNA than for rRNA and tRNA while having a higher affinity for polypurine than polypyrimidine homopolymers. Binding experiments with synthetic poly(A) and with segments of beta-globin mRNA transcribed from a cDNA in vitro revealed a set of polysomal mRNP proteins which preferentially bind the poly(A)-free beta-globin mRNA. A protein of Mr 90,000 binds specifically the 3'-nontranslated trailer of the poly(A)-free beta-globin mRNA and not the poly(A)-containing globin mRNA. Another set of proteins preferentially binds poly(A). The latter group of proteins contains a prominent species of Mr 72,000, which is most likely the rabbit poly(A)-binding protein. Three polysomal mRNP proteins which bound rabbit globin mRNA did not bind preferentially any of the other RNA probes used.

Animals↗
PubMed1995

Peripherin assembles into homopolymers in SW13 cells.

The properties of full-length and mutant peripherins were studied in intermediate filament-less SW13 cells to define regions of peripherin that are essential for initiation of filament assembly. A full-length rat peripherin gene transfected into SW13 cells resulted in filament formation, consistent with the close structural relationship of peripherin to other type III intermediate filament proteins that readily form homopolymers. Translation of full-length rat peripherin is initiated predominantly at the second of two inframe AUGs. Deletions within the amino terminus of wild-type peripherin abolished its ability to form filaments in SW13 cells. In contrast, deletion of the entire carboxyl-terminal tail of peripherin did not affect its ability to form filamentous arrays in transfected SW13 cells. These results indicate that, of the intermediate filament proteins that are expressed in mature neurons, only peripherin and alpha-internexin are capable of making homopolymer intermediate filaments. In addition, mutations of the carboxyl tail of peripherin generally do not interfere with filament network formation.

Animals↗
PubMed2005

Determination of the percentage of homopolymer component in Ziegler/Natta catalyst linear low-density polyethylene resins using high-temperature cell Fourier transform infrared and partial least squares quantitative analysis technique.

A new method for the determination of the percentage of homopolymer component, using high-temperature cell Fourier transform infrared (FT-IR) by partial least squares (PLS) quantitative analysis technique, was developed and applied to Ziegler Natta linear low-density polyethylene (LLDPE). The method is based on the IR spectrum changes between the 730 cm(-1) band and 720 cm(-1) band at the temperature of 110 degrees C, which is near the melting point of the polyethylene. The HD % (the percentage of high-density component, i.e., the percentage of homopolymer component) results obtained by CTREF (CRYSTAF in TREF mode) technique are used as the input data together with the respective FT-IR spectra for PLS analyses to establish a calibration curve. The PLS quality is characterized by a correlation coefficient of 0.997 (cross-validation) using four factors and a root mean square error of calibration (RMSEC) of 0.772. The HD% of the unknown can then be predicted by the PLS software from the unknown FT-IR spectrum. A control resin was tested seven times by CTREF and FT-IR. The HD% of the control resin was 28.59+/-0.88% by CTREF and 29.05+/-2.37% by FT-IR. It was found that the method was applicable for the same comonomer type of LLDPE within a melt index range and density.

Algorithms↗
PubMed1996

Sequencing homopolymer tracts and repetitive elements.

We investigated the use of Taq dye primer and Taq terminator sequencing chemistry to optimize the quality of sequence data obtained from templates containing homopolymer tracts and repetitive elements. In direct side-by-side comparisons using the Applied Biosystems Model 373A Fluorescent Sequencer, the Taq terminator sequencing chemistry gave much cleaner and more consistent results on long homopolymer tracts and dinucleotide repeats. We also investigated various thermal cycling conditions and determined that higher annealing temperatures and longer denaturation times improved the ability to sequence through these problem templates.

Base Sequence↗
PubMed1982

Effects of neighboring DNA homopolymers on the biochemical and physical properties of the Escherichia coli lactose promoter. I. Cloning and characterization studies.

To assess the role of neighboring DNA sequences in gene regulation, poly(dA).poly(dT) and poly(dG).poly(dC) were cloned adjacent to promoters of the lactose control region. Recombinant plasmids were constructed which were suitable for large scale purification of restriction fragments containing these promoters, 95-base pair (bp) AluI fragments containing the lack operator and promoter for the lac wild type and for the catabolite gene activating the protein-independent mutant, lac UV5, were cloned into pBR322. Homopolymers of varying lengths were inserted into the -60 region of these promoters using recombinant DNA techniques. Six of the recombinant plasmids were chosen for detailed analysis: wild type (wt); wt-AT, containing 70 bp of poly(dA).poly(dT); wt-GC, containing 23 bp of poly(dG).poly(dC); UV5; UV5-AT, containing 70 bp of poly(dA).poly(dT) and finally UV5-GC, containing 43 bp of poly(dG).poly(dC). These plasmids were characterized by restriction mapping and DNA sequencing. The effects of the DNA homopolymers on the interaction of the Escherichia coli RNA polymerase with the promoters were studied using nitrocellulose filter binding. The results show that poly(dA).poly(dT) increases the level of RNA polymerase binding, whereas poly(dG).poly(dC) has no detectable effect.

Base Sequence↗
PubMed1982

Effects of neighboring DNA homopolymers on the biochemical and physical properties of the Escherichia coli lactose promoter. III. High resolution thermal denaturation and circular dichroism studies.

High resolution thermal denaturation and circular dichroism studies were performed on a series of six recombinant DNA restriction fragments. The fragments varied in size from 132 to 193 bp and contained Escherichia coli wild type and UV5 lactose promoters both with and without homopolymer insertions of poly(dA).poly(dT) and poly(dG).poly(dC). A differential thermal destabilization of the wild type promoter region, as compared to the UV5 promoter, was observed when dA70.dT70 was inserted into the -60 region or both DNAs. This effect may depend, in part, on the differences in the base composition between adjoining cooperative units in the fragments. The relatively larger effect of the AT sequence on the wild type promoter region may be correlated with the increased levels of in vitro transcription activity described in the preceding paper (Klein, R. D., and Wells, R. D. (1982) J. Biol. Chem. 257, 12962-12969). Stretches of homopolymeric GC base pairs stabilized the wild type and UV5 promoter regions by over 2.5 degrees C. CD studies could not detect conformational differences between DNAs containing the wild type or UV5 promoter. The presence of homopolymers had a marked effect on the CD spectra of the fragments.

Circular Dichroism↗
PubMed1975

Isolation of bacterial and phage proteins by homopolymer RNA-cellulose chromatography.

Nucleic acid-free extracts of Escherichia coli have been analyzed by chromatography on columns of cellulose, to which poly(A), poly(U), or poly(C) have been attached by ultraviolet irradiation. Proteins are released from the columns by stepwise elution with increasingly higher concentrations of salt, followed by washing with urea to remove very tightly bound molecules. The pattern of protein elution is reproducibly different for each of the homopolymer RNA-cellulose columns used: some proteins bind very tightly to one column, but poorly to others. Analysis by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis, by immunological cross-reactivity in double diffusion tests, and by enzymological assays, has allowed the identification of a number of these proteins. The RNA polymerase core enzyme binds to poly(C)- and to poly(U)-cellulose columns, and can be purified to 20 to 30 percent homogeneity in a single step. Ribosomal protein S1 and the termination factor rho bind very tightly to poly(C)-cellulose, and both can be purified to homogeneity rapidly, in much higher yields than previously reported. Poly(A)-cellulose chromatography allows the isolation of large amounts of an 80,000 molecular weight protein having an as yet unassigned cellular function. The host factor required for RNA phage Qbeta RNA replication in vitro can also be obtained from poly(A)-cellulose, and chromatography of extracts of phage Qbeta-infected E. coli on RNA-cellulose columns results in very rapid isolation of the Qbeta replicase enzyme. Homopolymer RNA-cellulose chromatography thus appears to be a simple, general technique, useful for the efficient isolation of a variety of RNA-binding proteins.

Bacterial Proteins↗
PubMed1998

A monte carlo simulation of the depolymerization of linear homopolymers by endo-enzymes exhibiting random-attack probability and single-attack mechanism: application to the (1-->3), (1-->4)-beta-D-glucan/endo-(1-->3),(1-->4)-beta-D-glucanase system

A Monte Carlo simulation of the depolymerization of linear homopolymers by specific endo-enzymes exhibiting random-attack probability and a single-attack mechanism has been developed. The program simulates the "real" depolymerization versus time of a polydisperse sample of substrate by a specific endo-enzyme. Given the initial mass distribution and concentration of the substrate, the initial concentration of the enzyme, and its Michaelis-Menten constant, the program simulates the evolution of the mass distribution of the substrate with the depolymerization time. When tested against experimental data from the depolymerization of barley (1-->3),(1-->4)-beta-D-glucan by malt endo-(1-->3), (1-->4)-beta-D-glucanase, monitored using the Calcofluor-FIA method with fluorescent detection, excellent results were obtained. Copyright 1998 John Wiley & Sons, Inc.

Journal Article↗