[Immunochemistry of polyribonucleotides. II. Complexes of different homopolymers].
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Adenine Nucleotides↗
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Effects of Neighboring DNA homopolymers on the biochemical and physical properties of the Escherichia coli lactose promoter. II. In vitro transcription analyses.
Transcription studies were conducted on the primary promoter (which initiates at +1) of lac wild type (wt) and UV5 that had insertions of poly(dA).poly(dT) or poly(dG).poly(dC) in their -60 region. This series of recombinant DNAs was designed to study systematically the effect of neighboring DNA sequences on the lac promoter. Investigations using linear templates showed that wild type expression was enhanced by the poly(dA).poly(dT) insertion, whereas UV5 activity was not affected by this polymer. Neither the wt nor the UV5 promoter was influenced by the presence of poly(dG).poly(dC). Quantitation of abortive transcripts from supercoiled templates showed that the influence of the polymers on promoter activity was small. Comparative studies of the primary promoter with a secondary promoter (which initiates near -22), activated by 25% glycerol, were performed.
Cloning, Molecular↗
Characterization of the homopolymer tailing reaction catalyzed by terminal deoxynucleotidyl transferase. Implications for the cloning of cDNA.
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Base Composition↗
Characterization of two crystalline polyurethane homopolymers as potential materials for biomedical applications.
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Animals↗
Thermal degradation products of homopolymer polystyrene in air.
Polystyrene without additional compounds was treated in a laboratory oven at elevated temperatures (200 degrees, 350 degrees, 500 degrees C) under slight air flow (0.7 l/min). The thermal degradation products appearing in different phases (gases, vapors, aerosols) were collected and analyzed by methods of chromatography. Thermogravimetric analysis showed the thermal degradation of the polymer to begin at 270 degrees C in air and stop at 425 degrees C. The main groups of vaporized compounds generated were monoalkyl-substituted aromatic hydrocarbons and their oxidized products, of which styrene monomer and benzaldehyde were the most abundant. Only trace amounts of carbon monoxide and aliphatic compounds (hydrocarbons, aldehydes, and acids) were produced. The aerosol produced, the amount of which increased as the temperature rose, contained mainly fragments of the polymer chain (e.g., dimers and trimers of styrene). The traces of styrene, cumene, and ethylbenzene that appeared at 200 degrees could represent residual compounds in the initial polymer and indicate the beginning of the thermal degradation. If proportional concentrations are kept as a criterion, the important products, from the point of view of industrial hygiene, were styrene, benzaldehyde, styrene oxide, acetophenone, and l-phenylethanol. The large amount of aerosol that appeared may also be of practical importance.
Acids↗
[Experimental effect of a lupinine-based homopolymer on blood coagulation in animals].
Effect of an active heparin antagonist, artificial polymer manufactured on the basis of alkaloid lupinin (poly-MAKL-C2H5J with a molecular weight of 20.000), on blood coagulation was studied to show that excessive doses of the compound exert an anticoagulant effect on the blood. Prolongation of blood coagulation is the result of the decreased activity of factor Y, contained by the prothrombin complex, as well as the decreased activity of factor VIII and transitional thrombocytopenia.
Alkaloids↗
[Adsorption of a homopolymer chain onto a homogeneous surface].
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Adsorption↗
Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans.
Homopolymeric nucleotide runs, also called mononucleotide microsatellites, are a ubiquitous, dominant, and mutagenic feature of eukaryotic genomes. A clear understanding of the forces that shape patterns of homopolymer evolution, however, is lacking. We provide a focused investigation of the abundance, chromosomal distribution, and mutation spectra of the four strand-specific homopolymer types (A, T, G, C) >or=8 bp in the genome of Caenorhabditis elegans. A and T homopolymers vastly outnumber G and C HPs, and the run-length distributions of A and T homopolymers differ significantly from G and C homopolymers. A scanning window analysis of homopolymer chromosomal distribution reveals distinct clusters of homopolymer density in autosome arms that are regions of high recombination in C. elegans. Dramatic biases are detected among closely spaced homopolymers; for instance, we observe 994 A homopolymers immediately followed by a T homopolymer (5' to 3') and only 8 instances of T homopolymers directly followed by an A homopolymer. Empirical homopolymer mutation assays in a set of C. elegans mutation-accumulation lines reveal an approximately 20-fold higher mutation rate for G and C homopolymers compared to A and T homopolymers. Nuclear A and T homopolymers are also found to mutate approximately 100-fold more slowly than mitochondrial A and T homopolymers. This integrative approach yields a total nuclear genome-wide homopolymer mutation rate estimate of approximately 1.6 mutations per genome per generation.
Animals↗
A three centre study of the variability of ankle foot orthoses due to fabrication and grade of polypropylene.
This study investigates if fabrication techniques employed at different orthotic centres affect the characteristics of the manufactured plastic orthoses. Plaster models were formed from the same master mould. The thickness and bending stiffness of the supplied polypropylene sheets were measured prior to fabrication. An orthotic technician at each of the 3 orthotic centres manufactured 4 homopolymer and 4 copolymer polypropylene ankle-foot orthoses (AFOs), following each centre's fabrication practice. Another technician at one of the orthotic centres manufactured an additional 4 homopolymer and 4 copolymer AFOs. The thickness, the dorsiflexion stiffness and plantarflexion stiffness of the 32 fabricated AFOs were monitored and compared. Analysis of the results suggests: Copolymer polypropylene sheets are supplied marginally thicker than homopolymer polypropylene sheets. The difference between the thickness of the 16 copolymer and 16 homopolymer AFOs was not significant. The thickness of the AFOs manufactured in copolymer was less consistent than homopolymer. Dorsiflexion stiffness of the copolymer AFOs was less consistent than homopolymer AFOs. Although the bending stiffness of the copolymer and homopolymer sheets differed significantly, there was no significant difference between the dorsiflexion stiffness of the copolymer and homopolymer AFOs. Plantarflexion stiffness was consistent for both the copolymer and the homopolymer AFOs and there was no significant difference between the plantarflexion stiffness of the copolymer and homopolymer AFOs. The thickness and flexural stiffness of the AFOs manufactured by 2 technicians at the same centre did not differ. These results are useful benchmarks for the flexural stiffness of AFOs.
Ankle↗
Mutational analysis of the four alpha-helix bundle iron-loading channel of rat liver ferritin.
We previously reported that the heavy chain of ferritin was required for loading it with iron using ceruloplasmin as a ferroxidase [J.-H. Guo, M. Abedi, and S. D. Aust (1996) Arch. Biochem. Biophys. 335, 197-204]. Site-directed mutagenesis, K58E and G61H, on recombinant rat liver L chain ferritin (rL-Ft) was performed to construct a proposed iron-loading channel in the alpha-helix bundle similar to rat liver H chain ferritin (rH-Ft). Conversely, the channel in rH-Ft was closed by mutations E62K and H65G to form a K62 to E107 salt bridge, which is believed to exist in the L chain. Both variants were expressed in insect cells and were soluble and able to form multi-subunit homopolymers. The rH-Ft mutant homopolymer could not be loaded, whereas the rL-Ft mutant homopolymer could be loaded with iron by ceruloplasmin. However, we found that the initial rate of iron loading into the rL-Ft mutant homopolymer by ceruloplasmin was less than that into the rH-Ft homopolymer. When 500 atoms of iron per ferritin were used for loading, 98% was loaded into the rH-Ft homopolymer by ceruloplasmin in 15 min, but only 30% was loaded into the rL-Ft mutant homopolymer in the same time. Moreover, the ferroxidase activity of ceruloplasmin was enhanced in the presence of the rH-Ft and the rH-Ft mutant homopolymers, but not in the presence of the rL-Ft or the rL-Ft mutant homopolymers. These observations suggested that the four alpha-helix bundle channel of ferritin is required for iron loading, but an additional factor, i.e. , a site which stimulate the ferroxidase activity of ceruloplasmin, is also essential.
Animals↗
Nucleotide sequence-dependent opening of double-stranded DNA at an electrically charged surface.
It has been shown earlier that the DNA double helix is opened due to a prolonged contact of the DNA molecule with the surface of the mercury electrode. At neutral pH, the opening process is relatively slow (around 100 s), and it is limited to potentials close to -1.2 V (against SCE). The opening of the double helix has been explained by strains in the DNA molecule due to strong repulsion of the negatively charged phosphate residues from the electrode surface where the polynucleotide chain is anchored via hydrophobic bases. Interaction of the synthetic ds polynucleotides with alternating nucleotide sequences/poly(dA-dT).poly (dA-dT), poly (dA-dU).poly (dA-dU), poly (dG-dC).poly (dG-dC)/ and homopolymer pairs/poly (dA).poly (dT), poly (rA).poly (rU) and poly (dG).poly (dC)/ with the hanging mercury drop electrode has been studied. Changes in reducibility of the polynucleotides were exploited to indicate opening of the double helix. A marked difference in the behaviour was observed between polynucleotides with alternating nucleotide sequence and homopolymer pairs: opening of the double-helical structures of the former polynucleotides occurs at a very narrow potential range (less than 100 mV) (region U), while with the homopolymer pairs containing A X T or A X U pairs, the width of this region is comparable to that of natural DNA (greater than 200 mV). In contrast to natural DNA, the region U of homopolymer pairs is composed of two distinct phases. No region U was observed with poly (dG).poly (dC). In polynucleotides with alternating nucleotide sequence, the rate of opening of the double helix is strongly dependent on the electrode potential in region U, while in homopolymer pairs, this rate is less potential-dependent. It has been assumed that the difference in the behaviour between homopolymer pairs and polynucleotides with alternating nucleotide sequence is due to differences in absorbability of the two polynucleotide chains in the molecule of a homopolymer pair (resulting from different absorbability of purine and pyrimidine bases) in contrast to equal adsorbability of both chains in a polynucleotide molecule with alternating nucleotide sequence. It has been shown that the mercury electrode is a good model of biological surfaces (e.g. membranes), and that the nucleotide sequence-dependent opening (unwinding) of the DNA double helix at electrically charged surfaces may play an important role in many biological processes.
Adsorption↗
Temperature-dependent chaperone activity and structural properties of human alphaA- and alphaB-crystallins.
The chaperone activity and biophysical properties of recombinant human alphaA- and alphaB-crystallins were studied by light scattering and spectroscopic methods. While the chaperone function of alphaA-crystallin markedly improves with an increase in temperature, the activity of alphaB homopolymer appears to change very little upon heating. Compared with alphaB-crystallin, the alphaA-homopolymer is markedly less active at low temperatures, but becomes a more active species at high temperatures. At physiologically relevant temperatures, the alphaB homopolymer appears to be modestly (two times or less) more potent chaperone than alphaA homopolymer. In contrast to very similar thermotropic changes in the secondary structure of both homopolymers, alphaA- and alphaB-crystallins markedly differ with respect to the temperature-dependent surface hydrophobicity profiles. Upon heating, alphaA-crystallin undergoes a conformational transition resulting in the exposure of additional hydrophobic sites, whereas no such transition occurs for alphaB-crystallin. The correlation between temperature-dependent changes in the chaperone activity and hydrophobicity properties of the individual homopolymers supports the view that the chaperone activity of alpha-crystallin is dependent on the presence of surface-exposed hydrophobic patches. However, the present data also show that the surface hydrophobicity is not the sole determinant of the chaperone function of alpha-crystallin.
Cloning, Molecular↗
Temperature dependence of helical structures of poly(phenylacetylene) derivatives bearing an optically active substituent.
The temperature dependence of the helical conformations for the homopolymers of phenylacetylene derivatives bearing an optically active substituent, such as the (R)-((1-phenylethyl)carbamoyl)oxy and (R)-((1-(1-naphthyl)ethyl)carbamoyl)oxy groups at the phenyl group, and their copolymers with achiral phenylacetylenes were investigated in solution using circular dichroism (CD) and absorption spectroscopies. The magnitude of the induced CD (ICD) of the optically active homopolymers increased with decreasing temperature and was accompanied by a blueshift in their absorption maxima. On the other hand, the copolymers with achiral phenylacetylenes exhibited interesting ICD changes with temperature, depending on the bulkiness of the achiral comonomers. The copolymers with a less bulky phenylacetylene had a very intense ICD at low temperatures, the ICD pattern was almost opposite to those of the chiral homopolymers, while the copolymers with the most bulky phenylacetylene bearing a tert-butyldiphenylsiloxy group at the para position showed an ICD change similar to that of the optically active homopolymers. However, the copolymers with the phenylacetylene bearing a tert-butyldimethylsiloxy group with intermediate bulkiness at the para position showed no ICD change with temperature. These results indicate that the prevailing helix-sense of the chiral-achiral random copolymers of the phenylacetylenes is determined by a delicate interaction between the chiral and achiral side chains. The thermodynamic stability parameters for the helical conformations of the homopolymers and copolymers of the phenylacetylenes were estimated from the temperature dependence of the ICDs.
Journal Article↗
The effect of phosphorylation on the structure of alpha-crystallin.
Homopolymers were constructed from the highly purified phosphorylated (A1 and B1) and non-phosphorylated (A2 and B2) polypeptides of alpha-crystallin. These were examined using electron microscopy, light scattering, fluorescence spectroscopy and sulphydryl probing to determine the effects of phosphorylation on the structure of alpha-crystallin. Each reconstituted aggregate consisted of uniform particles with circular cross-sections and diameters of 9.3-9.5 nm. Some of these were associated in chain-like structures. The molecular mass of the homopolymers varied from 360-507 kDa; for a single particle, it was estimated to be 216 +/- 10 kDa. Tryptophan residues in the alpha B2 homopolymers were more accessible to the solvent and to quenchers than those in alpha A2. Phosphorylation increased this accessibility in the alpha A homopolymer but decreased it in alpha B. This decrease could be attributed to phosphorylation of the serine adjacent to tryptophan 60 in the B chain. The kinetics of the reaction with DTNB indicated that the single cysteine in the A chain was buried in the alpha A2 homopolymer (k1' = 0.013 min-1) but more accessible in alpha A1 (k1' = 0.046 min-1). It was concluded that phosphorylation significantly alters the conformation of the alpha A subunits but probably has little effect on the B subunits. The alterations do not affect the ability of the subunits to associate into alpha-crystallin-like particles.
Animals↗
Control of the morphology of linear and cyclic PS-b-PI block copolymer micelles via PS addition.
We have studied the effect of polystyrene (PS) homopolymer addition on the morphology of self-assembled block copolymer micelles made from linear or cyclic poly(styrene-b-isoprene), PS-b-PI, in a selective solvent for the PI block (heptane). Both copolymers have the same composition: the degree of polymerization is 290 for the PS block, and 110 for the PI block, and we focused on the influence of the addition of small amounts of PS homopolymer on the micellar morphology. For the copolymer concentrations considered, the linear copolymer self-organizes into spherical micelles while the cyclic copolymer forms cylindrical micelles. PS and PI chains constitute the core and the corona of these micelles, respectively, due to the different affinity of the blocks for heptane. Consequently, the PS homopolymer added is "solubilized" into the micellar core. Dynamic light scattering (DLS) data combined with atomic force microscopy (AFM) results show that the addition of PS homopolymer induces a drastic change in the micellar organization. Indeed, a morphological transition, from spheres to cylinders for the linear copolymer, and from cylinders to vesicles for the cyclic copolymer, is observed. These results highlight the fact that a small incorporation of PS homopolymer is clearly sufficient to modify the morphology (size and shape) of the micelles. This approach could be a key parameter for the design/control of micelles for specific applications in nanotechnology.
Journal Article↗
Microemulsion efficiency boosting and the complementary effect. 1. Structural properties.
Amphiphilic diblock copolymers added to microemulsions proved to enhance the efficiency of surfactants dramatically. The complementary effect of homopolymers is considered in the current work. A possible application of the homopolymer addition could be the viscosity tuning of the microemulsion without changing the considered bicontinuous phase. Furthermore, (homo)polymers are added for many other reasons in technical applications. A theory by Eisenriegler predicts a decreased efficiency when homopolymers are added. In further experiments, the simultaneous addition of homopolymers and diblock copolymers probes whether the two opposite effects superpose and allow for a compensation. Then, efficiency and viscosity are adjustable independently. Experimentally, phase diagrams are investigated and the microscopic structure is measured by small-angle neutron scattering. Within the presented models, both experimental methods are compared and discussed on the basis of the surfactant membrane bending moduli. The homopolymer effect is about 7 times larger than that theoretically predicted, and the superposition of the two polymer effects allows for a compensation with an optionally tunable viscosity.
Emulsions↗
Parametric studies of interaction strengths in polymer/CO2 systems: discontinuous molecular dynamics simulations.
Discontinuous molecular dynamics simulations are performed on homopolymer/solvent and surfactant/solvent systems. The homopolymer and surfactant molecules are modeled as freely jointed square-well chains. Solvent molecules are modeled as both hard spheres and square-well spheres. We explore how the various interaction parameters affect the types of phase behavior and micellization observed in the homopolymer/solvent and surfactant/solvent systems. Increasing the packing fraction of homopolymers in both hard-sphere solvents and square-well solvents increases the solvent's ability to dissolve homopolymers only when the segment-solvent interaction strength exceeds a critical value. Although only upper critical solution temperature (UCST) behavior is observed for homopolymers in hard-sphere solvents, both UCST and lower critical solution temperature (LCST) behavior are observed for homopolymers in square-well solvents, depending upon the interaction strengths and chain length. This indicates that it is necessary to account for the solvent-solvent attraction to model LCST behavior in supercritical CO2. Our simulation results on surfactants in hard-sphere solvents show that it is necessary to account for the interactions experienced by both the head and tail blocks in order to capture the essential features of surfactant/supercritical CO2 systems.
Journal Article↗
Enthalpy-entropy compensations in drug-DNA binding studies.
We present a comparative study of calorimetrically derived thermodynamic profiles for the binding of a series of drugs with selected DNA host duplexes. We use these data to demonstrate that comparisons between complete thermodynamic profiles (delta G zero, delta H zero, delta S zero, delta Cp) are required before drug binding can be used as a probe of DNA conformation, since enthalpy-entropy compensations can cause two drug-DNA binding events to exhibit similar binding free energies (delta G zero) despite being driven by entirely different thermodynamic forces (delta H zero, delta S zero). In this work, we employ a combination of spectroscopic and calorimetric techniques to characterize thermodynamically the DNA binding of netropsin and distamycin (two minor groove-directed ligands), ethidium (an intercalator), and daunomycin (a combined intercalator/groove binder). Our free energy data (delta G zero) show that each drug exhibits similar binding affinities at 25 degrees C for the alternating copolymer duplex poly[d(A-T)].poly[d(A-T)] and for the homopolymer duplex poly(dA).poly(dT). However, our calorimetric measurements reveal that the nature of the thermodynamic forces (delta H zero, delta S zero) that drive drug binding to these two host duplexes at 25 degrees C are entirely different, despite similar binding free energies (delta G zero) and similar salt dependencies (lnK/ln[Na+]). Specifically, the 25 degrees C binding of all four drugs to the alternating copolymer poly[d(A-T)].poly[d(A-T)] is overwhelmingly enthalpy driven, whereas the corresponding binding of each drug to the homopolymer duplex poly(dA).poly(dT) is overwhelmingly entropy driven. Thus, the similar binding free energies (delta G zero) we measure for complexation of each drug with poly[d(A-T)].poly[d(A-T)] and poly(dA).poly(dT) result from compensating changes in the enthalpy and entropy terms. Comparison with the thermodynamic profiles for the complexation of these drug molecules to other DNA host duplexes at 25 degrees C reveals that the binding of each is strongly enthalpy driven, except when the poly(dA).poly(dT) homopolymer serves as the host duplex. This comparison allows us to conclude that poly[d(A-T)].poly[d(A-T)] behaves thermodynamically as the more "normal" host duplex toward drug binding, whereas the entropy-driven binding to the poly(dA).poly(dT) duplex represents "aberrant" behavior. Furthermore, since each of the four drugs exhibits different modes of DNA binding, we conclude that the observed entropy-driven behavior for binding to poly(dA).poly(dT) reflects an intrinsic property of the homopolymer duplex that is perturbed in a common manner upon ligation rather than a common property of all four binding ligands. To rationalize the large positive entropy changes that drive drug complexation with poly(dA).poly(dT) duplex, we propose a model that emphasizes binding-induced perturbations of the more highly hydrated, altered B conformation of the homopolymer. Our results suggest that an aberrant thermodynamic binding profile may reflect an unusual DNA conformation in the host duplex. However, before such a conclusion can be reached, complete thermodynamic binding profiles must be examined, since enthalpy-entropy compensations can cause two binding events to exhibit similar binding constants even when they are driven by very different thermodynamic forces.
Calorimetry↗