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PubMed1981

Resonant and localized breathing modes in terminal regions of the DNA double helix.

A Green's function approach is used in constructing a dynamic model of a semi-infinite length of the DNA homopolymer B poly(d) . poly(d). Considerable attention is focused on the hydrogen bond stretching close to the terminus. A melting (or breathing) coordinate (M) is defined as an average over the three linking hydrogen bond stretches in a unit cell. The thermal mean squared amplitude of (M) is enhanced at the chain end compared with the interior. Spectral branches at 69, 80 and 105 cm-1, as well as a local mode at 75 cm-1, are primary contributors to the enhancement. We suggest that this fact can affect the thermal melting of a DNA double helical homopolymer, enhancing the tendency to start from an end (if one is available). We show how certain infinite chain modes with small (M) amplitude can turn into breathing modes near the terminus, and suggest that the same phenomenon may occur near other specific base-pair sequences. There is also considerable attention paid to the low microwave region from approximately 0 to 1.75 cm-1. The thermally activated modes in this frequency region contribute approximately (0.02 A)2 to [M2(0)] at 40 K, approximately two orders of magnitude greater than for [M2(infinity)]. Most important however, is the existence of narrow resonant modes in this frequency region. Particularly pronounced resonances near 0.03 cm-1 and 0.08 cm-1 (approximately 0.9 and 2.4 GHz) amplify M2(0) at the terminus by about for orders of magnitude over the infinite chain value M2(infinity).

DNA↗
PubMed1994

Local modes in a DNA polymer with hydrogen bond defect.

Vibrations of a homopolymer DNA with localized hydrogen bond defects have been examined using the recently developed decaying mode theory for long-chain polymers with local structural defects. For a poly(dA)-poly(dT) homopolymer having perturbed hydrogen bonds in one base pair, a localized mode at 63.2 cm-1 has been found. This mode has a very nearly pure H-bond stretch or "breathing" character, although the backbones do not separate. This agrees in frequency with a similar result found by other authors using a different approach. We search the full microwave frequency range for other local modes for several models of weakened H bonds. Besides the local mode with breathing characteristics, local modes with other characteristic motions were found, but only for asymmetrically perturbed bonds. We find in general that local modes are not very robust, requiring quite specific, narrow ranges in parameter space. They are also not abundant, there being only three in our most prolific model.

Biophysical Phenomena↗
PubMed1981

Sialic acid polysaccharide antigens of Neisseria meningitidis and Escherichia coli: esterification between adjacent residues.

Colominic acid and meningococcal Group B polysaccharide, both (2 leads to 8)-alpha-linked homopolymers of sialic acid, are made water-insoluble either by reaction with a carbodiimide in aqueous solution at pH 4.75 or by treatment with 48% aqueous hydrofluoric acid at 0 degrees for 48 h. I.r. spectra of the products show a major band near 1750 cm-1, consistent with ester formation; this band virtually disappears after mild, alkali treatment. Esterification also occurs by incubating the native polysaccharides below pH 6.0, and their i.r. spectra show that the degree of esterification increases as the pH is lowered. The relatively low molecular weight of these partially esterified, water-soluble polymers is consistent with intra- rather than inter-molecular ester formation. Counter-current immunoelectrophoresis shows that esterification of approximately 9% is sufficient to abolish immunoprecipitation. 13C-N.m.r. spectroscopy of fully esterified colominic acid provides strong evidence for cross-linking between the carboxyl group of one residue and HO-9 of an adjoining residue. Meningococcal serogroup C polysaccharide, a (2 leads to 9)-alpha-linked homopolymer of sialic acid containing O-acetyl groups at C-7 and/or C-8, does not undergo intramolecular esterification after carbodiimide treatment. However, upon O-deacetylation of the polysaccharide, esterification occurs.

Escherichia coli↗
PubMed2000

Liquid adsorption chromatography of polyethers: experiments and simulation.

The adsorption behavior of poly(ethylene glycol) (PEG) in reversed-phase chromatography is studied both experimentally and theoretically and a computer simulation of chromatograms is performed on the basis of these studies. The experimental conditions were: different reversed-phase adsorbents and a solvent methanol-water system as the mobile phase. At varying mobile phase compositions highly resolved chromatograms of PEG samples were obtained, in which all peaks could be identified, and the dependencies of the distribution coefficient on the degree of polymerization for PEG molecules were evaluated by processing these chromatograms. The data were interpreted by using a theory of homopolymers based on a continuum Gaussian chain model of flexible macromolecules and a slit-like model of pores of stationary phase. The theory proved to describe well the experimental data in the whole range of studied molecular masses, and the thermodynamic parameters characterizing interactions of ethylene oxide repeating units in PEG molecules with the adsorbent pore walls have been determined from the comparison of the theory with the experimental data. The dispersion of chromatographic peaks corresponding to individual oligomer molecules is also estimated. In the system studied the peak width occurred to be proportional to the distribution coefficient of corresponding macromolecule. The theory is used to develop a computer-assisted procedure for simulation of chromatograms for samples of linear homopolymers. Using the obtained data on the thermodynamic parameters and the estimates of peak dispersion, chromatograms are simulated for PEG samples at two different chromatographic conditions. These simulated chromatograms were in good quantitative agreement with the real chromatograms.

Adsorption↗
PubMed2003

Application of the reversed-phase liquid chromatographic model to describe the retention behaviour of polydisperse macromolecules in gradient and isocratic liquid chromatography.

This paper illustrates how conventional models of chromatographic behaviour can be used to predict the separation behaviour of polydisperse macromolecules. Using polystyrene and polymethylmethacrylate homo- and co-polymeric standards, the models were validated by comparing experimental retention behaviour with that predicted by the chromatographic model. The experimental retention time of each of the samples was entered into a spreadsheet application, which calculated the parameters that best described retention (for a given model). When a correlation between the relevant parameters and molecular mass was established, that correlation was used to predict the change in retention behaviour over the molecular-mass range. An expression introduced in a previous paper, to calculate the critical mobile-phase composition of a homopolymer was validated using polystyrene homopolymers. A second expression, which can predict the elution behaviour of copolymers, was also validated. This expression can predict the retention of a copolymer, based solely onthe retention of the homopolymeric units that make up the copolymer.

Calibration↗
PubMed2003

The adsorption of cationic and amphoteric copolymers on glass surfaces: zeta potential measurements, adsorption isotherm determination, and FT Raman characterization.

The adsorption of cationic and amphoteric copolymers onto controlled pore glass (CPG) powders has been studied by measurement of the powder particle zeta (zeta) potential, by determination of the adsorption isotherm, and by FT Raman measurements of the polymer-coated powder. The cationic polymers consisted chiefly of homopolymers of dimethyldiallylammonium chloride (DMDAAC) or copolymers of DMDAAC and acrylamide. The amphoteric polymers studied included copolymers of DMDAAC and acrylic acid. The comonomer ratio was varied to explore the dependence of cationic charge density on the extent and effect of adsorption. Both types of polymers adsorb onto the anionic glass surface via an ion-exchange mechanism. Consequently, a correspondingly higher mass of a low-charge-density copolymer adsorbs than of a cationic homopolymer. The presence of the anionic portion in the amphoteric polymers does not significantly alter this picture. The zeta potential, however, reflects the overall nature of the polymer. Cationic polymers effectively neutralize the glass surface, while amphoteric polymers leave the zeta potential net negative. Adsorption isotherms, determined via the depletion technique using colloidal titration, were used to "calibrate" a FT Raman method. The latter was used to determined the amount of adsorbed polymer under solution conditions in which colloidal titration could not be performed.

Journal Article↗
PubMed2003

Synthesis, characterization and evaluation of urethane derivatives of Bis-GMA.

OBJECTIVES: The aims of the study were to synthesize derivatives of Bis-GMA having pendant n-alkyl urethane substituents and to characterize and evaluate their physicochemical properties. METHODS: Stoichiometric amounts of Bis-GMA and n-alkyl isocyanates were reacted in dichloromethane with dibutyltin dilaurate as a catalyst. Volumetric shrinkage, water uptake, degree of vinyl conversion, refractive index and viscosity of resulting urethane monomers and those of Bis-GMA were measured. The flexural strengths of their corresponding homopolymers and that of Bis-GMA were also measured. RESULTS: These types of urethane derivatives of Bis-GMA exhibited lower viscosities and were more hydrophobic than Bis-GMA. Generally, the viscosity of these experimental monomers decreased with increasing chain length of the alkyl urethane substituent. Photopolymerization of the new monomers gave high degrees of vinyl conversion compared to Bis-GMA. The experimental monomers also yielded polymers with lower polymerization shrinkages at equivalent degrees of vinyl conversion, than Bis-GMA. The refractive indices of these urethane derivatives were similar to Bis-GMA, but the flexural strengths of their polymers were lower than that of the Bis-GMA homopolymer, decreasing with increasing chain length of the alkyl urethane substituent. SIGNIFICANCE: Because of their excellent overall properties, these new derivatives of Bis-GMA have potential as dental monomers that can improve many properties of resin based dental materials that utilize methacrylate monomer systems.

Bisphenol A-Glycidyl Methacrylate↗
PubMed2002

Synthesis and characterization of injectable, water-soluble copolymers of tertiary amine methacrylates and poly(ethylene glycol) containing methacrylates.

Several homopolymers and copolymers of 2-(diethylamino)ethyl methacrylate (DEAEM) and poly(ethylene glycol) methyl ether methacrylate (PEGMEM) were synthesized using anionic polymerization initiated by potassium t-butoxide. The polymers were characterized by average molecular weight, polydispersity and monomeric unit composition. A very narrow molecular weight distribution was achieved with a well-controlled composition. The glass transition temperatures and compositions of the copolymers followed a Gordon-Taylor relationship. The water solubility and biocompatibility of the copolymers was compared to their parent homopolymers to determine if the addition of a poly(ethylene glycol) group was sufficient to solubilize the polymers in aqueous buffer solutions and to increase the biocompatibility of the polymers. These water-soluble, injectable cationic copolymers have potential applications in gene delivery as well as other biomaterial applications.

Amines↗
PubMed2000

Transfection efficiency increases by incorporating hydrophobic monomer units into polymeric gene carriers.

The water soluble terpolymer, poly(N-isopropylacrylamide (IPAAm)-co-2-(dimethylamino)ethyl methacrylate (DMAEMA)-co-butylmethacrylate (BMA)) was synthesized, and its efficiency in in vitro gene transfection was evaluated. Copolymers with different compositions were synthesized by radical polymerization. For a series of copolymers containing 60 mol% of DMAEMA, the plasmid bands were retained within the gel loading slot, independent of polymer/plasmid weight ratios or BMA monomer content. In contrast, for a series of copolymers containing 20 mol% DMAEMA, plasmid bands of complexes were retarded with increasing weight ratios. For the copolymer with 10 mol% BMA content, the plasmid was completely retained within the gel loading slot. The transfection efficiency of polymer/plasmid complexes was evaluated in COS-1 cells using a pCMV-lacZ plasmid, encoding for beta-galactosidase as a reporter gene. Transfection efficiency of a series of copolymers containing 20 mol% of DMAEMA varied with BMA content. The transfection efficiency of the copolymers with 0, 2, and 5 mol% of BMA was low. The transfection efficiency of the copolymers with 10 mol% of BMA was about 2-fold higher than that of the PDMAEMA control homopolymer. The transfected cells were observed at a very wide range of polymer/plasmid weight ratios. The transfection efficiency of all copolymers containing 60 mol% of DMAEMA was lower than that of the PDMAEMA homopolymer.

Animals↗
PubMed2002

pH-induced solubility transition of sulfonamide-based polymers.

As an approach to designing new pH-sensitive polymers for bio-related application, we have modified selected sulfonamides, with various pK(a), to polymerizable monomers. The pK(a) of the monomers, homopolymers, and copolymers with N,N-dimethylacrylamide were examined, and pH-induced phase transition behavior, particularly in solubility, was investigated. The pK(a) of sulfonamide monomers and polymers at 25 degrees C was slightly higher than those of corresponding sulfonamides but the enthalpy of the ionization was influenced due to interfering resonance structures that are present in the mother compounds. The solubility transition of each homopolymer in aqueous solutions occurred at a degree of ionization of 85-90%. For the copolymers, the solubility transition observed by light transmittance completed in a narrow pH range (0.2-0.3 pH units) and this transition pH shifted to a higher pH region with the increasing sulfonamide unit in the copolymer, though the pK(a) was not considerably changed. This polymer precipitation occurs because of the relative balance of overall hydrophilicity/hydrophobicity along the polymer chain. Because the unionized form of sulfonamide units is considered to be hydrophobic, the copolymer with higher content of sulfonamide unit requires a higher degree of ionization for solubilization and thus solubility transition occurred at higher pH.

Anti-Infective Agents↗
PubMed1998

2-(Dimethylamino)ethyl methacrylate based (co)polymers as gene transfer agents.

Poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) is a water-soluble cationic polymer, which is able to bind to DNA by electrostatic interactions. At a polymer/plasmid ratio above 2 (w/w) positively charged complexes were formed with a size around 0.2 microm. The transfection efficiency of polymer/plasmid complexes was evaluated in cell culture (COS-7 and OVCAR-3 cells) using a pCMV-lacZ plasmid, encoding for beta-galactosidase, as a reporter gene. The optimal transfection efficiency was found at a PDMAEMA/plasmid ratio of 3-5 (w/w). Under these conditions 3-6% of the cells were actually transfected. Like other cationic polymers, PDMAEMA is slightly cytotoxic. This activity was partially masked by complexing the polymer with DNA. A pronounced effect of the molecular weight of the polymer on the transfection efficiency was observed. An increasing molecular weight resulted in an increasing number of transfected cells. Dynamic light scattering experiments showed that high molecular weight polymers (Mw>300 kDa) were able to condense DNA effectively (particle size 0.15-0.20 microm). In contrast, when plasmid was incubated with low molecular weight PDMAEMA, large complexes were formed (size 0.5-1.0 microm). Copolymers of DMAEMA with methyl methacrylate (MMA), ethoxytriethylene glycol methacrylate (triEGMA) or N-vinyl-pyrrolidone (NVP) also acted as transfection agents. A copolymer with 20 mol % of MMA showed a reduced transfection efficiency and a substantial increased cytotoxicity compared with a homopolymer of the same molecular weight. A copolymer with triEGMA (48 mol %) showed both a reduced transfection efficiency and a reduced cytotoxicity, whereas a copolymer with NVP (54 mol %) showed an increased transfection efficiency and a decreased cytotoxicity as compared to a DMAEMA homopolymer.

Animals↗
PubMed2003

Use of ADME studies to confirm the safety of epsilon-polylysine as a preservative in food.

Epsilon-polylysine is a homopolymer of L-lysine, containing approximately 30 L-lysine subunits, as synthesized in aerobic bacterial fermentation by Streptomyces albulus. epsilon -Polylysine is approved for food use in Japan as an antimicrobial preservative. A series of pharmacokinetic and metabolic profile studies on epsilon -polylysine have been conducted in rats in order to provide a better understanding of the reason for its lack of toxicological effects in subchronic and chronic feeding bioassays using relatively high concentrations in the diet up to 50000 ppm. As reported in this article, epsilon -polylysine was practically non-toxic in an acute oral toxicity study in rats, with no mortality up to 5 g/kg and was not mutagenic in bacterial reversion assays. Absorption, distribution, metabolism and excretion (ADME) studies on 14C-radiolabeled epsilon -polylysine, given in a single dose to fasted male rats at 100mg/kg, revealed low absorption from the gastrointestinal tract. All but trace amounts of the dosed radioactivity was eliminated by excretion within 168 h and over 97% was accounted for in urine (1.2%), feces (92.9%), or expired air (3%) by 48 h. The sum of the cumulative excretion with routes associated with absorption in urine, expired air and carcass was 6.4% of total recovered radioactivity; approximately 94% of the dose of epsilon -polylysine passed unabsorbed through the gastrointestinal tract in the feces. Whole body autoradiography did not show concentration of absorbed epsilon -polylysine in any tissue or organ. Excretion half-lives of epsilon -polylysine equivalents in blood and plasma were 20 and 3.9 days, likely prolonged by the incorporation into protein of cleaved L-lysine. Metabolic profiles by HPLC analysis of plasma samples suggest that L-lysine is the predominant early metabolic by-product, likely from protease activity in the upper GI tract; only 0.2% of the administered parent compound was found in plasma. At 8-72 h, HPLC profiles show diminishing levels of epsilon -polylysine and L-lysine in plasma, accompanied by a shift to larger peaks of homopolymer fragments of varying subunit length, presumably from microbial degradation of epsilon -polylysine in the lower gut. HPLC profiles of urine and feces collected from 0 to 24 h post-dosing revealed three distinct peaks in urine, the first peak likely to be epsilon -polylysine and epsilon -polylysine less a few amino acid subunits, and the second, L-lysine and the third, a metabolite of L-lysine. Radiolabeled L-lysine was reduced from 67.2% of the radioactivity in plasma at 30 min to 7.5% at 4 h, indicating that L-lysine is readily removed from plasma from essential amino acid incorporation into protein. Based on the findings of the ADME studies and lack of toxicity in safety studies, the proposed use of epsilon -polylysine as a preservative in foods is considered to be safe.

Absorption↗
PubMed2001

Classification of CD and absorption spectra in the Soret band of H(2)TMPyP bound to various synthetic polynucleotides.

The binding mode of porphyrins, namely meso-tetrakis(N-methyl pyridinium-4-yl)porphyrin (H(2)TMPyP), was classified in this work by absorption and circular dichroism(CD) spectroscopy. The three binding modes of intercalation, minor groove binding and external stacking exhibit their own characteristic absorption and CD spectra. Intercalation occurs for this porphyrin when bound to GC-rich polynucleotides at a low mixing ratio, as expected. This binding mode produces hypochromism and a red shift in the absorption band and a negative CD band in the Soret absorption region. When it is complexed with AT-rich polynucleotides at a low mixing ratio, hypochromism and a red shift in the absorption band and a positive CD peak is apparent, and this species can easily be assigned to the minor groove-binding mode. For both AT- and GC-rich polynucleotides at a high binding ratio, an excitonic CD was apparent. The sign of excitonic CD depends on the order of the DNA bases; the CD spectra of H(2)TMPyP complexed with non-alternating homopolymer (disregarding the nature of base pairs, i.e. AT or GC) are characterized by a positive band at short wavelengths followed by a negative band at long wavelengths. In contrast, those complexed with alternating polynucleotide were opposite to those of non-alternating homopolymers.

Chemical Phenomena↗
PubMed1997

Solid-state NMR characterization of copolymers of nylon 11 and nylon 12.

Solid-state 13C and 15N NMR spectroscopy, in conjunction with differential scanning calorimetry, wide-angle X-ray diffraction and infrared spectroscopy, were used to characterize a series of nylon 11 and 12 copolymers with mole percentages of nylon 12 monomer of 0, 15, 35, 50, 65, 85, and 100%. Monotonic melting point (Tm) and heat of fusion depressions were observed for the copolymer series with the 65 mol% nylon 12 copolymer having the lowest apparent crystallinity and Tm at 148 degrees C. Solid-state 15N NMR spectra showed a smooth shift of the main peak position for the as-prepared copolymers from 84 ppm for the alpha-form of pure nylon 11 to 89 ppm for the gamma-form of pure nylon 12. Similar behavior was seen for FTIR amide V and VI modes which are also sensitive to the alpha- and gamma-crystal forms. 13C NMR T1 measurements showed that the overall most mobile sample was the 65:35 copolymer. The amide group of the 1:1 copolymer was labelled using 15N-labelled amino acids available through the Gabriel synthesis; an annealed, solution-cast film of this sample showed a T1N value of 349 s, similar to values seen for annealed nylon 11 and nylon 12 homopolymers. The WAXS pattern for the 65 mol% nylon 12 sample showed a sharp peak at 2 theta = 21.3, overlapping a broad peak centered at 2 theta = 21.0. These are consistent with the values seen for gamma-form nylon 12. The 1:1 copolymer (15N labelled) was shown to be polymorphic, like the homopolymers after specific treatments, with a gamma-like phase formed upon solvent casting, and an alpha-like phase dominating for as-polymerized material and precipitated flakes.

Calorimetry, Differential Scanning↗
PubMed2002

Monitoring ibuprofen enantiomers released from polymeric systems.

Two methacrylic derivatives of ibuprofen (N-[4-[2-(4-isobutylphenyl)propionyloxy]phenyl] methacrylamide (MAI) and 2-[(4-isobutylphenyl)propionyloxy]ethyl methacrylate (MEI)) were used together with 2-hydroxyethyl methacrylate (HEMA) to synthesize four polymeric materials: two hydrophobic homopolymers, PMAI and PMEI, and two hydrophilic copolymers containing 70% (w/w) HEMA, MAI-HEMA 30 and MEI-HEMA 30. The enantiomeric determination of R- and S-IBU released from these four systems has been carried out by capillary electrophoresis. Release of R- and S-IBU was monitored during in vitro assays done at 37 degrees C at pH 7.4 and 10 in buffered solutions and rat plasma. There is a hydrolytical activation in plasma and at pH 10 compared to pH 7.4; moreover, the release rate from the copolymers is much higher than from the homopolymers as a consequence of the greater hydrophilic character. A slight excess of the S-enantiomer of IBU is observed in all the experiments, being more relevant at higher release rates, i.e. copolymers at pH 10.

Animals↗
PubMed1993

Static secondary ion mass spectrometric investigation of the surface chemistry of organic plasma-deposited films created from oxygen-containing precursors. 3. Multivariate statistical modeling.

Partial least squares (PLS) multivariate statistical models were developed to predict the surface composition and chemistry of a set of model homopolymers based on their static SIMS fragmentation patterns. In the calibration or model-building step, the positive and negative ion static SIMS spectra of different classes of model homopolymers were related to specific chemical attributes of the polymers. The models were then used to examine the surface chemistry of oxygen-containing plasma-deposited films prepared from a variety of precursors. PLS models were developed to predict the surface oxygen concentration and H/C ratios. The results obtained from the PLS models were compared with experimental results.

Analysis of Variance↗
PubMed2002

Oligonucleotide mixture analysis via electrospray and ion/ion reactions in a quadrupole ion trap.

Electrospray ionization combined with ion/ion reactions in a quadrupole ion trap can be used for the direct analysis of oligonucleotide mixtures. Elements to the success of this approach include factors related to ionization, ion/ion reactions, and mass analysis. This paper deals with issues regarding the ion polarity combination, viz., positive oligonucleotides/negative charge-transfer agent versus negative oligonucleotides/positive charge-transfer agent. Anions derived from perfluorocarbons appear to be directly applicable to mixtures of positive ions derived from electrospray of oligonucleotides, in direct analogy with positive protein ions. Conditions for forming positive oligonucleotide ions devoid of adducts were more difficult to establish than for forming relatively clean negative oligonucleotide ions. A new approach for manipulating negative ion charge states in the ion trap is described and is based on use of the electric field of the positive charge-transfer agent for storage of high-mass negative ions formed during the ion/ion reaction period. Oxygen cations are shown to be acceptable for charge-state manipulation of mixed-base oligomers but induce fragmentation in polyadenylate homopolymers. Protonated isobutylene (C4H9+), on the other hand, is shown to induce significantly less fragmentation of polyadenylate homopolymers.

Anions↗
PubMed2005

Strategies for constructing polymeric micelles and hollow spheres in solution via specific intermolecular interactions.

We succeeded recently in developing a series of new pathways to polymeric micelles and hollow spheres via intermolecular specific interactions. A new micellization mechanism of block copolymers was realized by using the specific interaction between a low molecular weight compound and one of the blocks in low-polarity solvents. Many more successes have been achieved by our "block copolymer-free" strategies. We are now able to use homopolymers, random copolymers, oligomers, etc. as building blocks to construct noncovalently connected micelles (NCCM), in which the core and shell are connected by hydrogen bonding. Some of such NCCMs are readily converted further into hollow spheres by cross-linking the shell and then switching the medium to one that dissolves the core. Rigid polymer chains and their complementary homopolymers can directly assemble into large hollow spheres thanks to the propensity to parallel packing of the rigid chains. In addition, some of the NCCMs show perfect stimuli-responsive properties. pH-dependent micellization and pH-dependent micelle-hollow-sphere transition are realized in water-soluble graft copolymers driven by complexation and decomplexation between the main chain and grafts.

Journal Article↗