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  • 1
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 1-8 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The results of electrophoresis experiments on aqueous solutions of native and thermally denatured DNA are reported. A significant decrease of the electrophoretic mobility has been observed following thermal denaturation, which under suitable conditions gives rise to a resolution into two peaks of 1 : 1 mixtures in the electrophoretic pattern. This result is entirely consistent with the previously reported increase of the activity coefficient of sodium counterions following thermal denaturation. The hypothesis that thermal denaturation of calf thymus DNA induces a large decrease of charge density on the macroion which has been ascribed to the population of more extended conformations of the chains in the disordered region of the molecule is therefore further confirmed.
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  • 2
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of the depolymerization of native dextran in dilute hydrochloric acid at different temperatures has been followed by measurements of M̄w, M̄n, [η], 〈ρ2〉1/2, and S. The data allow the correlation of the various parameters of the total hydrolyzate at various degrees of depolymerization. At a first approximation the results conform to a random splitting of a statistical, branched polymer.
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  • 3
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The γ-ethyl-L-glutamate NCA polymerization initiated by di-n-butyl and di-isopropyl amine was studied. The experimental kinetic curves show an autocatalytic portion with 25-30% conversion, followed by a pseudo first-order region which extends up to at least 85-90%. In this linear region, the reaction order appears to be 0.5 in initiator with both amines. High degrees of polymerization and high reaction rates were observed. These results are similar to those obtained in the γ-benzyl-L-glutamate NCA polymerization initiated by sodium methoxide.
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  • 4
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric constant and the electric birefringence of poly-γ-benzyl-L-glutamate in ethylene dichloride-dichloroacetic acid mixtures have been measured as functions of the solvent composition. These properties undergo a marked decrease with the addition of a small amount of dichloroacetic acid, as well as an abrupt change accompanying the helix-coil transition in the vicinity of 75 vol.-% dichloroacetic acid. The former is attributed to the apparent diminution of the dipole moment of helical poly-γ-benzyl-L-glutamate molecule, which may be due to the protonation of terminal amide groups.
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  • 5
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 6
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The polymerization of γ-benzyl-L-glutamate NCA initiated by n-hexylamine in DMF proceeds with two successive propagation rates whose ratio is about 1.5. The onset of the increase in rate of propagation occurred at a DPn of 7-14, which was independent of initiator to anhydride ratio and anhydride concentration and not a result of anhydride impurities. The increase in rate is likely a result of a conformational change in the polymer at a DPn of 7-14.
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  • 7
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 147-161 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The NCAs of the N-benzyl derivatives of β-alanine, β-DL-aminobutyric acid, and β-DL-aminoisobutyric acid (nonplanar six-membered rings) were prepared by reacting the corresponding N-chloroformyl derivatives, obtained on reaction of the N-benzyl amino acids with phosgene, with triethylamine. Contrary to the others, the NCA of N-benzyl-β-alanine polymerized readily on heating in vacuo or in solution, using n-hexylamine or methanolic sodium methoxide as initiators. With n-hexylamine the molecular weights of the polymers obtained in benzene, dioxan, and dimethylsulfoxide, were in accordance with DP = [NCA]/[Initiator], as was found with conventional five-membered ring NCAs of α-amino acids. With sodium methoxide initiation, DPs of the polymers obtained were smaller than the (NCA)/[Initiator] ratio, contrary to what was found previously with α-amino acid NCAs. The possibility that stereochemical factors are responsible for the differences in polymerization activity of various. N-alkyl β as well as α amino acid NCAs is discussed.
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  • 8
  • 9
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 231-236 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrophoretic mobility of DNA in the presence of tetramethylammonium and alkali metal ion chlorides has been studied as a function of ionic strength. Each cation exhibits a characteristic behavior in accord with the idea that the order of inter-action with DNA is Li+ 〉 Na+ 〉 K+ 〉 TMA+. The application of theories of the electrophoresis of polyelectrolytes is discussed, leading to an attempt to calculate the fractional charge per DNA phosphorus from the mobility data. Over the range 0.05-0.4M a constant and unique value of the DNA charge is obtained in the presence of each cation. Values of the zeta potential and of the friction factor per monomer unit are also calculated.
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  • 10
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 135-146 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple quantitative theory of inactivation of transforming DNA has been formulated. It is based on the idea that genetic recombination of the molecule of transforming DNA with the bacterial genome is possible only, from the point mutation of the gene up to the nearest hit or point of damage on the corresponding DNA molecule. Our data and the data of other authors on the kinetics of inactivation by HNO2 or U.V. light or both are consistent with these theoretical predictions. Theoretical predictions were made concerning the extent of reactivation by fusion mid annealing of damaged DNA with a diluting genetically inactive DNA. These estimates have been reasonably confirmed by our experimental results.
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  • 11
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    Biopolymers 2 (1964), S. 15-25 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to study the effect of glucose substitution on the sedimentation velocities of the T-even phage DNA's, T2 and T2*, and T6 and T6* bacteriophages were grown with H3and P32 labeling. Zone sedimentation of the DNA's isolated from these phagea showed that the glucosylated DNA's from both T2 and T6 sediment faster than the nonglucosylated molecules. Nonglucosylated DNA from TG and T2 phages sedimented with the same velocity, suggesting that the molecules of these phages are of the same length.
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  • 12
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    Biopolymers 2 (1964), S. 43-49 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report a simple method for measuring partial specific volumes, of polymers in dilute solutions with an accuracy of 3 parts per thousand. This method has been applied to 7 polypeptides in 4 organic solvents. The residue volumes deduced from these data are compared to those calculated by a differential method. The discrepancy is generally of the order of 1.5%.
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  • 13
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    Biopolymers 2 (1964), S. 283-286 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 14
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 15
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that the formation of the three-strand poly (A + 2U) complex is accompanied by a decrease in optical absorbance at 280 mμ, while the format ion of poly (A + U) is not. This difference makes it possible to demonstrate that in dilute solutions (∼10-4 monomolar), a 1 : 1 mixture of poly A and poly U always forms poly (A + U) at room temperature. At higher temperatures in solutions containing more than about 0.2M sodium ion, poly (A + U) is converted to poly (A + 2U) and free poly A. These results are consistent with the observations reported by Miles and Frazier, using infrared absorption spectra, at much higher polymer concentrations. It is concluded that most of the physicochemical studies of 1 : 1 mixtures of poly A and poly U in dilute aqueous solution refer to the two-stranded species.A simple thermodynamic analysis is developed to explain the two- to three-strand conversion, and with the use of a “phase diagram” showing conditions of stability of the various poly A-poly U structures as a function of salt and temperature, it is possible to estimate the value of the enthalpy of formation of poly (A + 2U).
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  • 16
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    Biopolymers 2 (1964), S. 337-347 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using a chromatographic technique, the adsorption of the polyribonucleotides s-RNA and poly-A provided with tri-n-butylammonium ions from an aqueous solution on to the surface of polymeric hydrocarbon granules has been demonstrated. The aqueous solution from which adsorption takes place is the aqueous phase which results on agitating together n-butanol (100), water (130), tri-n-butylamine (10), n-butyl ether (10), and glacial acetic acid (2.5) (parts by volume). Microporous polyethylene granules, microporous fluorinated polyethylene granules, and solid grains of polyethylene powder have been employed as adsorbents. The adsorbed polyribonucleotides could be eluted by aqueous solutions of sodium chloride, urea, or triethylammonium acetate. s-RXA with tri-n-butylammonium counterions could also be adsorbed on polymethacrylic acid in tri-n-butylammonium form and eluted therefrom with aqueous urea solutions. It is considered that the adsorption from aqueous solution of polyribonucleotides with tri-n-butylammonium counterions on polymeric hydrocarbon surfaces is mediated by hydrophobic bond formation. Van der Waals forces may also contribute to the bonding. It is suggested that studies on the adsorption of polynucleotides provided with counterions: possessing nonpolar groups at an aqueous solution-polymeric hydrocarbon interlace may permit the elaboration of experimental systems to serve as models for the evaluation of the role of hydrophobic and van der Waals bonding forces in the interaction of polynucleotides with cell membrane surfaces.
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  • 17
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    New York : Wiley-Blackwell
    Biopolymers 2 (1964), S. 395-398 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 18
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    Biopolymers 2 (1964), S. 361-380 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Deoxyribonucleic acids (DNA's) extracted from several biological sources have been studied by means of the flow dichroism method, using the transparent coaxial cylinder apparatus. This study has two purposes: (1) to make clear the hydrodynamic behavior of the DNA chain, and the regularity in the orientation of purine and phrimidine bases about the molecular axis; and (2) to develop this particular flow dichroism method as an established device for the study of chain regularity of DNA and other chain polymers. The velocity gradient dependence of dichroism agrees well, to a first approximation, with the behavior of a model of a hydrodynamically equivalent ellipsoid in revolution. Differences between theoretical and empirical curves have been tentatively ascribed to the flexibility of the chain under consideration. Two kinds of data, 1 lie rotary diffusion coefficient and internal dichroism, have been evaluated by a graphical device in which the double logarithmic plots of reduced dichroism and velocity gradient of flow are compared with the theoretical curve. The data obtained have shown good reproducibility for DNA samples prepared by the same method from the same biological source. However, a remarkable difference in internal dichroism and rotary diffusion constant has been observed between DNA groups of different biological origin. The difference may be caused by fragmentation of DNA during the deproteinization procedure, bill the possibility that some of these differences originate in the biological source of the DNA cannot be denied. Orientation of purine and phrimidine bases in aqueous solution is found to be quite regular in direction, as predicted by the Watson-Crick model. Dichroic spectra have shown that the direction of the oscillator dipole corresponding to the 260 mμ absorption band has a different angular relationship to the helical axis than the oscillator dipole for the 220 mμ band.
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  • 19
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    Biopolymers 2 (1964), S. 381-393 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A study of the super helical structure of synthetic polypeptides, such as poly-γ-benzyl-D (or L)-glutamate (PBDG or PBLG) was carried out. The PEG was dissolved in dimethylformamide (DMF). The solution was either allowed to remain at room temperature for a long time or poured into some fatty acid, such as formic acid, acetic acid, propionic acid, or caprylic acid. Whether the polymer precipitated slowly or rapidly depended upon the aging of the solution or the nature of the acid used. The precipitated gels revealed the coiled coil fibrils, but the feature and degree of coiling varied, depending upon the length of aging or the nature of the acid used for precipitation. After a short aging of the solution, there was no helical structure in the gels. After long aging, very fine-coiled coil macrofibrils or small spindle-like fibrils were obtained. The macrofibrils consisted of the spindle-like fibrils which in turn consisted of microfibrils (diam. 60-70A.). When using the fatty acid precipitation very fine to medium fine super helices were obtained. Extremely fine super helices were obtained in propionic acid. In these gels the PBG chains have an α-helical conformation. When PMLG-DCA solution was stored for a long time, another type of precipitation was obtained, one giving evidence of so-called cross-β crystallization and no coiled coil fibrils. The precipitation of cross-β fibrils was obtained when the concentration of the solution was above 8%.
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  • 20
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    Biopolymers 2 (1964) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 21
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    Biopolymers 2 (1964), S. 399-413 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Titration studies of the 1 : 1 helical polynucleotide complex of polyinosinic acid and polycytidylic acid reveal that these two polymers form a complex when the polycytidylic acid is protonated near pH 3. Sedimentation studies show that the protonated complex also has a 1 : 1 stoichiometry. However, the protonated complex is more stable than the unprotonated neutral complex as judged by its thermal stability. The molecular structure of the protonated complex is not the same as the neutral form. Study of the kinetics of the reaction of the protonated complex with formaldehyde suggests that the amino group of cytosine is involved in hydrogen bonds which hold the polynucleotide strands together.
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  • 22
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    Biopolymers 2 (1964), S. 415-444 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The protein sequences now known have been reconstructed as a kind of intriguing logical-mathematical puzzle using information about fragments of the molecules. We wish to show that the reconstruction can be done systematically by repeating a series of elementary operations on these same data governed by a set of well-defined rules. The completely automatic reconstruction of polymer sequences by a high speed digital computer using these operations and rules is demonstrated.
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  • 23
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The mechanism of the renaturation of DNA molecules is examined on the basis of the bimolecular interaction of Gaussian chain polymers. In the nucleus formation by hydrogen bonding in segment-segment interaction, two types of interchain interaction, that is, one between complementary chains and one between noncomplementary chains, and one noncomplementary intrachain interaction are considered to be, in competition. Several previously observed characteristics of the renaturation process are displayed by this simple model. In particular it accounts for the dependence of the extent of renaturation on the heterogeneity, molecular weight, and radius of gyration of DNA, and of the ratios of the reaction rates between complementary and noncomplementary segments. Among these variables the ratio of reaction rates has shown to have a quite specific value, as high as the order of 104, which favors the complementary-strand interaction. This very great bias in favor of complementary strand interaction emphasizes that the renaturation phenomena displays the same character of biological specificity that is associated with enzyme-substrate interaction or antigen-antibody interaction. Moreover, since DNA is a good example of a one-dimensional system, it seems to provide a suitable clue for pursuing the analysis of pattern recognition at the macromolecular level.
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  • 24
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    Biopolymers 2 (1964), S. 463-481 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The polymerization of DL-β-Phenylalanine N-carboxy anhydride adsorbed on polysarcosine dimethylamide has been studied further. This unusual reaction, which is analogous kinetically to reactions catalyzed by enzymes, was called the “chain-effect.” For polymerization of N-carboxy anhydrides by this mechanism it is necessary that the initiating polymer should possess an adsorption site and a terminal base group. The effect is shown to occur with simple compounds such as amino acid dimethylamides but not with poly-L-proline due to the inability of this polymer to adsorb the anhydride. From a study of the reaction of block copolymers of L-proline and sarcosine with DL-β-phenylalanine it is concluded that the relative positions of the adsorption site and terminal base group do not greatly influence the reaction rate, but the accessibility of the adsorption sites is an important factor determining the reactivity of polysarcosine dimethylamides of various degrees of polymerization (n). At high values of n the polymer exists in a coiled form and only those sites close to the terminal base group participate in the reaction. Initial rate studies give a detailed description of the early stage of the chain-effect polymerization. With these data and by use of analog computer techniques the complete reaction has been studied. It is concluded that the poly-DL-β-phenylalanine block produced is not permanently attached to the polysarcosine chain by hydrogen bonds during its formation but that an equilibrium exists between the polysarcosine and the poly-DL-phenylalanine blocks.
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  • 25
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Del Re's method for the study of saturated compounds has been adapted so as to deal with the σ-framework of conjugated molecules. This modified procedure is used in evaluating the σ-contribution to the dipole moments of the nucleic bases and of the A-T and G-C base pairs and also to the free energy change in the tautomeric, equilibria of the bases. Associated with an appropriate Hückel method for evaluating the π-contribution, the results obtained predict a small resultant moment for A-T versus a large moment for G-C. The energy calculations predict the keto and amino forms of the bases to be the most stable forms and cytosine to be the most easily involved in tautomeric shift to the rare form.
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  • 26
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    Biopolymers 2 (1964) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 27
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Temperature jump measurements employing optical rotation to follow transients show an upper limit of 10μsec. on the half time of the helix-random coil relaxation in poly-α, L-glutamic acid. No relaxations are observed under conditions where the polymer exists in completely helical or completely random coil form. Assuming that the helix-coil transition can be described kinetically as a pure growth process, expressions for the relaxation time are derived for three special cases. A comparison is made between the rate of the helix-coil transition and the rate of imide proton exchange.
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  • 28
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    Biopolymers 2 (1964), S. 501-501 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 29
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    Biopolymers 2 (1964), S. 561-574 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Numerical calculations have been done on the exciton spectrum of a schematic model of a linear polymer. The model consists of a random sequence of two kinds of subunit whose energy levels and transition moments are almost, but not quite, the same. The orders of magnitude of parameters are taken from DNA, but the full helical geometry has not been considered. Results are given for the density of energy levels, the dipole transition strength per unit energy, and the distribution of excitation energy along the polymer in individual states. A number of localized exciton states were found.
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  • 30
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The DNA-ligand interactions of a series of phenanthridinium compounds with various combinations of amino, azido, and hydrogen functions at R3 and R8 were examined to determine the contribution of these particular substituents to ligand binding. Spectrophometric titrations using calf-thymus DNA emphasized the importance of amino substituents in conferring a strong interaction and also stabilizing the interaction against reversal by high ionic strength. Although azido groups were not as effective as amino groups, they were more effective than hydrogen functions in enhancing the interaction. Furthermore, an amino substitution at R8 was consistently, though only slightly, more effective than an amino substituent at R3. The results from superhelical titrations using plasmid pBR322 DNA demonstrated that analogs with amino and/or azido functions at both R3 and R8 produced the greatest unwinding, and compounds with an amino or an azido function at R8 proved more effective than those with the corresponding amino or azido substituent at R3.
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  • 31
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic shielding constant of the 31P nucleus of the dimethylphosphate anion is calculated by an ab initio method for different values of the torsion angles about the PO ester bond and different orientations of the methyl groups. The results obtained tend to show that both types of conformational parameters contribute to the value of σ31P. The largest shielding is obtained when the methyl groups are staggered with respect to the PO bond; the smallest, for the eclipsed arrangement. Measurements carried out on the 16 deoxyribodinucleoside monophosphates show that in the majority of cases σ31P is shifted toward lower field for the dimers having large values of 3JPH3′ and 3JPH5′(5″). The theoretical results are discussed in relation to experimental data for polynucleotides and nucleic acids.
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  • 32
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    Biopolymers 23 (1984), S. 471-491 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The optical modes of DNA that displace one strand against the other are modeled by the motion of an oscillator in an asymmetric quartic double-well potential whose minima represent the A- and B-conformations. Assuming that the variation of the polarizability during vibration derives mainly from the tilting of the base rings relative to the helix axis, the total polarizability tensor is shown to possess approximately ellipsoidal symmetry and to depend nonlinearly on the instantaneous displacement of the two strands. The Raman spectrum of a collection of randomly oriented molecules is calculated. It consists of one or more peaks with characteristic shape. The depolarization ratio is 3/4, independent of molecular conformation and frequency. The results are discussed in the light of existing experimental and theoretical information.
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  • 33
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    Biopolymers 23 (1984), S. 511-536 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using the semiempirical potential functions, conformational energies of the model compounds DMP-, d(pCp), d(pGp), and d(pCpGpCp) are calculated, and the B → Z transition is discussed along the pseudorotational path of the sugar ring. For dimethylmonophosphate anion, DMP-, the energy contour map is presented and the stabilities of the phosphodiester conformations discussed. For the sugar ring without the base attached, the minimum energies for each sugar-puckering form are calculated along the pseudorotational path. The energy barrier of the interconversion between the C(3′)-endo form and the C(2′)-endo form is calculated to be about 2.0 kcal/mol. From the conformational energy calculations of the interconversions of mononucleoside diphosphates, d(pCp) and d(pGp), between the C(2′)-endo conformer and the C(3′)-endo conformer, the purine sugar segment is known to be more convertible than the pyrimidine sugar segment. The results also support the finding that the pseudorotational transition occurred with the O(1′)-endo form more easily than with the O(1′)-exo form. Based on the results of conformational studies of DMP-, d(pCp), and d(pGp), a topological transition of the handedness of the model compound, d(pCpGpCp), is studied. The left-handed Z-form is found to be less stable by about 8.5 kcal/mol than is the right-handed B-form. The energy barrier of the Z → B transition is calculated to be about 17.4 kcal/mol. The contributions of the electrostatic and nonbonded energies to the energy barrier are discussed in connection with the conformation changes of the model compound, d(pCpGpCp).
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    Biopolymers 23 (1984), S. 593-599 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of aqueous solutions of DNA were measured at frequencies ranging from 0.1 to 12 GHz. The results are analyzed using the Maxwell mixture theory and yield a value for the hydration of the DNA of about 0.4 g/g, which is in the range observed in other investigations. No evidence was found for an additional absorption effect at microwave frequencies, which has been predicted to occur in certain DNA analogs due to the vibrational excitation of the double helix by the applied microwave field.
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    Topics: Chemistry and Pharmacology
    Notes: Self-association of substance P and its C-terminal partial peptide sequences was studied by CD, quasi-electric light scattering, and sedimentation experiments. CD spectra of these peptides are strongly influenced by self-association. They exhibit strong characteristic negative ellipticities, suggesting the formation of a presumably B-type ordered structure. The tendency to form multimers depends on chain length and constitution and has its maximum at the octapeptide (SP 8). The peptide multimers have a broad distribution of sizes in the range of 30- and 800-nm diameter. Subdivision of this distribution into two size classes gives mean diameters of 60-100 nm (predominating)/200-800 nm for substance P and 30-50 nm/200-800 nm for SP 8 multimers.
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    Biopolymers 23 (1984), S. 819-829 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr chemical shifts of backbone carbonyl and side-chain β-carbons in polypeptides provide structural information. Recent utilization of substituent effects on 13C-nmr chemical shifts (principally γ-effects) has permitted the rationalization of their sequence and conformation dependence when observed in linear, flexible polypeptides. In this report, we apply the γ-effect method to study the 13C-nmr chemical shifts observed in solution and in the solid state for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides, which are usually cyclic. As found previously for flexible, linear polypetides, the relative 13C-nmr chemical shifts observed for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides are predictable from knowledge of their peptide residue sequence (primary structure) and conformation (secondary structure) via the γ-effect method.
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    Biopolymers 23 (1984), S. 847-852 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 38
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The CD spectra of the peptides Boc-X-(Aib-X)n-OMe (n = 1, 2, 3) and Boc-(Aib-X)5-OMe, where X = L-Ala or L-Val have been examined in several solvents. The X = Ala and Val peptides behave similarly in all solvents, suggesting that the Aib residues dominate the folding preferences of these peptides. The decapeptides adopt helical conformations in methanol and trifluoroethanol, with characteristic negative CD bands at 222 and 205 nm. In the heptapeptides, similar spectra with reduced intensities are observed. Comparison with nmr studies suggest that estimates of helical content in oligopeptides by CD methods may lead to erroneous conclusions. The pentapeptides yield solvent-dependent spectra indicative of conformational perturbations. Peptide association in dioxane results in an unusual spectrum with a single negative band at 210 nm for the decapeptides. Disaggregation is induced by the addition of methanol or water to dioxane solutions. Aggregation of the heptapeptides is less pronounced in dioxane, suggesting that a critical helix length may be necessary to promote association stabilized by helix dipole-dipole interactions.
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    Biopolymers 23 (1984), S. 831-841 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of poly-5-bromouridylic acid [poly(BU)] with adenosine and 9-methyladenine was studied by equilibrium dialysis, optical melting, and microcalorimetry. The stacking free energy, ω, was estimated as -17.6 kJ/mol for adenosine·2poly(BU) and -18.8 kJ/mol for 9-methyladenine·2poly(BU) from the binding isotherms constructed from equilibrium dialysis results. The binding isotherms constructed from a series of melting curves also gave ω values for adenosine·2poly(BU). The thermal stability of the complex depends on monomer concentration, and the partial molar enthalpies of the complex formation at the midpoint of the transition were evaluated from the Tm coefficients as a function of free monomer concentration. The values of -92.0 and -90.4 kJ/mol were obtained for adenosine·2poly(BU) and 9-methyladenine·2poly(BU) in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0), respectively. Microcalorimetric measurements provided lower integral heats of reaction values for these complexes, i.e., -73.2 kJ/mol for adenosine·2poly(BU) and -71.5 kJ/mol for 9-methyladenine·2poly(BU). A comparison with a polyribouridylic acid system provided a quantitative understanding of a stabilization by bromination in terms of thermodynamic parameters.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 23 (1984), S. 191-194 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 23 (1984), S. 257-270 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular-dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A- or B-DNA helix with one Na+ counterion per nucleotide. Four Na+ ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ ions were assumed to be Lennard-Jones spheres that also carried charges. Stillinger four-point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B-DNA and 20, 32, and 46 in A-DNA fragments. The arrangements of the Na+ ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of DNA molecules.
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    Biopolymers 23 (1984), S. 313-323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ethylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in vitro. Intact and enzyme-digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme-digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin-digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C-terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C-terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and growth in vitro.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 45
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report the crystal-structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl-3′,5′-adenosine (CpA) and uridylyl-3′,5′-guanosine (UpG). The planar drug molecule is intercalated between C⃛G and U⃛A Watson-Crick base pairs, in a double-helical fragmentlike arrangement. Sugar conformations at the 3′-ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence-dependent effects of the drug binding.
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    Biopolymers 23 (1984), S. 1057-1066 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Helical hydrophobic moment ratios, 〈h2〉/〈H2〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by 〈h2〉, and 〈H2〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h2〉/〈H2〉 tend to be substantially larger than values of the analogous ratio formulated for the mean-square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h2〉/〈H2〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ-hemolysins. It is also large for two other surface-active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h2〉/〈H2〉 is found for melittins. If melittins is to form helices with large 〈h2〉/〈H2〉, the configurational statistics must be governed by effects in addition to those short-range interactions that occur when water is the solvent.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 48
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy computations have been carried out for the N-acetyl-N′-methylamides of the Pro-Pro, Pro-Gly, and Gly-Pro dipeptides and of the Pro-Pro-Gly-Pro tetrapeptide, serving as models for the conformational analysis of single-stranded poly(Gly-Pro-Pro). The probability of β-bend formation for the Pro-Gly sequence is very high, viz., 0.72 for the terminally blocked Pro-Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β-bend conformations of the Pro-Gly sequence are of low energy in single-chain poly(Gly-Pro-Pro) as well. The β-bend structure had been postulated earlier to be a requirement for post-translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β-bend structure is energetically favorable and hence can be accommodated easily in single-stranded poly(Gly-Pro-Pro).
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  • 49
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The interaction of Cu(II) with the protamine scylliorhinine Z3 was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5-6.5, the results suggest the formation of a five-membered chelate ring through the coordination of two nitrogen atoms, the N-terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2 group of Arg; at pH 6.5-8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)-Z3 solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge-transfer dichroic band transitions. At Cu(II):Z3 molar ratios ≥ 2 and at pH 〉 8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in metal-ion complexation.
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Studies of the optical birefringence of solutions of acid-soluble collagen from rat-tail tendon at 22°C in the pH range 1.0-6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt-soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the magnetic field.
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    Biopolymers 23 (1984), S. 1295-1306 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyamines are ubiquitous cellular components that interacts strongly with nucleic acids. Although many of the interactions of oligocations with DNA can be rationalized with polyelectrolyte theories that treat counterions as point charges, some structural effects are evident. We have explored the effects of polyamine structure on one important aspect of DNA behavior, its thermal melting transition, by using a series of spermidine analogs NH3(CH2)3NH2(CH2)nNH33+, where n varies from 2 to 8 [Jorstad et al. (1980) J. Bacteriol. 141, 456-463]. For spermidine itself, n = 4. Tm for calf-thymus DNA in the presence of each of these analogs, and the other naturally occurring polyamines putrescine2+ and spermine4+, was measured over a wide range of NaCl concentrations and polyamine:DNA phosphate ratios. There are modest, but significant structural effects. particularly with the shorter n = 2 and 3 derivatives, whose geometry my not allow full electrostatic interaction with DNA. Longer analogs, on the other hand, are not much different than spermidine in their effects on Tm, though a moderate maximum occurs at n = 5. Since polyamines are important in the cellular condensation and packaging of DNA, we have also delineated the critical polyamine and salt concentrations that are required to cause DNA aggregation. Here again, there are significant structural effects, which are not easily rationalized by any simple considerations.
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    Biopolymers 23 (1984), S. 1315-1323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The observed difference between the CD spectrum of B-DNA mononucleosomes and that of free DNA has been attributed to the tertiary structure of the core DNA. This conjecture is tested here. The tertiary structure is modeled as an optical system consisting of two identical, planar, linear retarders rotated with respect to each other. The retarders have the same linear birefringence and linear dichroism as oriented B-DNA. Such an optical system is circularly dichroic. The predicted wavelength dependence and magnitude of the CD are in reasonably close agreement with the experimental results.
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    Biopolymers 23 (1984), S. 1367-1377 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The absorption and CD spectra of the complexes of poly(L-arginine) (PLA) and azo dyes have been measured in aqueous solution. On complexation, Blue-shifted additional absorption bands were observed. In the wide pH 4-11 range, induced CD was observed at the visible wavelengths corresponding to the blue-shifted absorption bands. The induced CD arose from the dimeric dye molecules bound to PLA in the α-helical structure. When a modified analysis of induced CE is made by the excition chirality method, the origin of the induced CD can be assigned to the dipole coupling. The PLA-dye complexes showed the counterlockwise (negative, S) chirality of the transition dipole moments of dyes.
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    Biopolymers 23 (1984), S. 1347-1365 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ionization properties of the tyrosyl groups of bovine plasma albumin in various conformational states - the native state (N), the two acid states (F and E), and the state (B) stable at slightly alkaline pH - were studied by means of a stopped-flow-pH-jump technique. The technique allows us to obtain the tyrosyl titration curve in a conformational state that is unstable in the pH region of the titration. The pH jumps from the N and B states to various alkaline pH's, where the tyrosines ionize to bring about a time-dependent increase in absorption at 296 nm, indicating that a number of the tyrosines buried initially become susceptible to ionization as a result of the alkaline transition occurring above pH 10.8. Extrapolation of the observed absorption change to zero time gives a spectrophotometric titration curve in the initial conformational state. Only 30-401% of the 19 tyrosines of the protein can ionize both in the N and the B state at pH 12. The pH jumps from the F and E states, on the other hand, give a decrease in absorption between pH 9 and 11.7, indicating that the tyrosyl groups initially exposed are remarked by refolding after the pH jumps, and the zero-time titration curves show that essentially all the tyrosyl groups ionize normally in these acid states. The results are discussed in relation to the known results of the tyrosyl exposure of the protein measured by other techniques, and the consistency among them demonstrates the effectiveness of the pH-jump titration method. Hydrogen bonding between the abnormal tyrosyl and carboxylate groups as a mechanism to stabilize native albumin is suggested from characteristics of the alkaline transition, which also involves the exposure of the tyrosyl groups, and from the tyrosyl titration curves in the native and acid states.
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    Biopolymers 23 (1984), S. 1137-1139 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Topics: Chemistry and Pharmacology
    Notes: Two series of peptides with hydrophobic side chains, Nps-(L-Leu-L-Leu-L-Ala)n-OEt and Nps-(L-Met-L-Met-LLeu)n-OEt (n = 1-6), were synthesized by the fragment condensation method using dicyclohexylcarbodiimide in the presence of N-hydroxysuccinimide. The tripeptide fragments were prepared stepwise by dicyclohexylcarbodiimide-mediated reaction of Nps-amino acids, which were synthesized by an improved rapid procedure.
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    Biopolymers 23 (1984), S. 1457-1463 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of sonicated calf-thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix-to-coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.
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    Biopolymers 23 (1984), S. 1465-1479 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The oxidation of L-adrenaline (epinephrine) in the presence of [Fe(tetpy)(OH)2]+ ions bound to poly(L-glutamate) or to poly(D-glutamate) has been studied at pH 7 (tetpy = 2,2′:6′,2″:6″,2‴-tetrapyridyl). Electron transfer from the substrate to the central metal ion, which is rate-determining, proceeds stereoselectively only when extensive and possibly specific interactions between adrenaline and the peptidic residues of the ordered polymer in the close environment of the active sites occur. This ensures different steric constraints for the two diastereomeric precursor complexes, which are thought to affect the separation and orientation of the redox centers differently, leading to the observed phenomena. Some data on the catalytic oxidation of L-dopa(3,4-dihydroxyphenylalanine) are also presented, showing stereoselective effects similar to those observed with L-adrenaline, despite the diverse distance of the chiral center from the reacting OH groups. A mechanistic interpretation of the results is discussed in the light of a few general considerations concerning the structural features of the catalytic systems. Possible explanations for the finding that stereoselectivity occurs at the expense of the efficiency of catalysis are also considered.
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    Biopolymers 23 (1984), S. 1917-1930 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solution-phase Raman spectra of diastereomeric alanyl dipeptides, D-Ala-L-Ala and L-Ala-L-Ala, and various mono- and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled-oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.
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    Biopolymers 23 (1984), S. 1951-1960 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational equilibria of five β-cellobiose conformers have been studied theoretically in 10 solvents. The stability of the conformers in dilute solution has been compared by using the method that has already been tested for 2-methoxytetrahydropyran, β-maltose, and D-glucose. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from the properties of the solute calculated by the PCILO quantum-chemical method and physicochemical properties of the solvents. The calculated abundance of conformers depends on the solvent (e.g., in dioxane C1:C2:C3:C4:C5 = 60.0:34.1:2.9:2.0:1.0; in dimethylsulfoxide, 75.5:22.1:1.8:0.5:0.2; and in water, 82.2:16.2:1.3:0.2:0.1). The results obtained indicate that the preponderant conformer in the aqueous solution is similar to the one adopted by β-cellobiose in the crystalline form. The role of individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and nmr parameters have been calculated and compared with observable properties. The marked differences observed between solvent-induced conformational changes for β-cellobiose and β-maltose have been discussed from the viewpoint of the solubility of the cellulose.
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    Topics: Chemistry and Pharmacology
    Notes: With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu-, and Asp-) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G-X 〉 C-X 〉 A-X U-X or T-X, and G · C-X 〉 A · T(U)-X, where X is one of these amino acid residues. It has been shown that Glu- and Asp- can recognize guanine in single-stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double-stranded structures.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 23 (1984), S. 2195-2210 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of histone H1 on the conformation and stability of control and acetylated HeLa high-molecular-weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
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  • 64
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    Topics: Chemistry and Pharmacology
    Notes: Human fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ-γ ligation was determined from the former. The latter provided the size distribution of ligated end-to-end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p-nitrophenyl-p′-guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end-to-end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ-γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ-γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end-to-end sequences agreed with a theory based on random ligation of ligatable junctions.
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    Biopolymers 23 (1984), S. 201-212 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A mean-square helical hydrophobic moment, 〈h2〉, is defined for polypeptides in analogy to the mean-square dipole moment, 〈μ2〉, for polymer chains. For a freely jointed polymer chain, 〈μ2〉 is given by Σmi2, where mi denotes the dipole moment associated with bond i. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣHi2, where Hi denotes the hydrophobicity of residue i. The tendency for correlations in orientations of residue hydrophobic moments in helices therefore dictates the size of 〈h2〉/〈H2〉, where 〈H2〉 denotes the average value of ΣHi2 for all helices. The value of 〈h2〉/〈H2〉 will be greater than one in amphiphilic helices. A necessary prerequisite for this diagnostic usage of 〈h2〉/〈H2〉 is that the residue hydrophobic moment be oriented prependicular to the principal axis of the helix. Matrix-generation schemes are formulated that permit rapid evaluation of 〈h2〉 and 〈H2〉. The behavior of 〈h2〉/〈H2〉 is illustrated by calculations performed for model sequential copolypeptides.
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    Biopolymers 23 (1984), S. 271-285 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: We report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson-Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson-Boltzmann equation when only the species with 1-Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson-Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter- and co-ions, but particularly co-ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surface of the polyion.
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    Biopolymers 23 (1984), S. 337-351 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Brillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high-humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799-2815] with the variations of the sonic velocity with water content.
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    Biopolymers 23 (1984), S. 353-361 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Optical rotation, viscosity, and density studies are reported on solutions of α-gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
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    Biopolymers 23 (1984) 
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    Notes: We have recorded high-resolution 13C-nmr spectra of collagen fibrils in the solid state by the cross-polarization-magic-angle-spinning(CP-MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31-helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (Ala—Gly—Gly)nII], and the triple-helical polypeptides [(Pro—Gly—Pro)n and (Pro—Ala—Gly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31-helical (Ala—Gly—Gly)n and triple-helical (Pro—Ala—Gly)n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31-helix, reflecting further conformational change from the 31-helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C = O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1-5.1 ppm), with respect to those of the 31-helical polypeptides. These displacements are interpreted by that Gly C = O of the former is not involved in NH … O = C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
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    Biopolymers 23 (1984), S. 2349-2360 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Dermorphin (Tyr—D-Ala—Phe—Gly—Tyr—Pro—Ser—NH2), a potent natural peptide opioid, its synthetic L-Ala2 analog, and all the N fragments from the tripeptide (Tyr—D-Ala—Phe—NH2) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N-terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.
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    Biopolymers 23 (1984), S. 2715-2724 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′-diphosphate reveals that, for each species, the uv-absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
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    Biopolymers 23 (1984), S. 2963-2966 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 23 (1984), S. 719-734 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The aggregation of poly(γ-benzyl-α,L-glutamate) and its enantiomer in toluene has been investigated by following the viscosity as a function of temperature, concentration, molecular weight, molecular-weight distribution, helix chirality, and shear rate. The temperature and concentration data for a 138,000-molecular-weight sample was fitted to an open, reversible end-to-end aggregation model. The aggregation numbers resulting from this fit were consistent with the sudden onset in non-Newtonian flow resulting from only a 0.2-wt% increase in concentration. The association equilibrium constant was then used to predict viscosity for comparison with other data, in particular, the effect of molecular weight and molecular-weight distribution. A mixture of right-and left-handed helices showed the aggregation was not chiral selective. The stiffness of end-to-end aggregated (hydrogen-bonded) molecules differed little from their covalent counterparts, at least below a molecular weight of ∼106. We conclude that polybenzylglutamate aggregation in toluene can be described by an open end-to-end aggregation model.
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    Biopolymers 23 (1984), S. 797-808 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Quasielastic light-scattering (QELS) studies were performed on a monodisperse preparation of dinucleosomal-sized DNA having an average of 375 base pairs. The QELS data were obtained at several time intervals at each angle examined over the range 30° 〈 θ 〈 60° for the ionic strength solvents 500, 50, 10, and 1 mM in KCl. What results from this study is that two relaxation domains persist over the entire ionic strength range where the “splitting” between these two domains increases as the ionic strength is lowered. The ordinate intercept of Dapp vs Cp/2Cs, where Cp is the polyion concentration and Cs is the added salt concentration, is shown to give the “true” hydrodynamic value for the diffusion coefficient. The “splitting phenomenon” is interpreted in terms of two models currently in vogue: small ion-polyion coupled modes and translational-rotational coupled modes for rigid rods in congested solutions. Although neither model is in perfect agreement with the experimental results, the small ion-polyion coupled mode theory appears to provide a better quantitative description of the observations.
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    Biopolymers 23 (1984) 
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    Chemie in unserer Zeit 18 (1984) 
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    Chemie in unserer Zeit 18 (1984), S. A4 
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    Chemie in unserer Zeit 18 (1984), S. 55-61 
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    Keywords: Chemistry ; Chemistry
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    Chemie in unserer Zeit 18 (1984), S. 62-67 
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    Chemie in unserer Zeit 18 (1984), S. 68-69 
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    Chemie in unserer Zeit 18 (1984), S. 109-119 
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    Chemie in unserer Zeit 18 (1984) 
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    Chemie in unserer Zeit 18 (1984), S. 179-180 
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    Chemie in unserer Zeit 18 (1984), S. 60A 
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    Chemie in unserer Zeit 18 (1984), S. 211-212 
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    Biopolymers 2 (1964) 
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    Biopolymers 2 (1964), S. 9-14 
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    Topics: Chemistry and Pharmacology
    Notes: A calculation based upon Gorin's equation for the electrophoresis of a rigid cylinder is used to compare the available results of electrophoresis and membrane equilibrium experiments on DNA. The distribution of chloride ions across a membrane impermeable to DXA is considered. For a reasonable choice of parameters, agreement within about 2% is obtained between the values calculated from electrophoresis and the results of membrane equilibrium studies over a twenty-fold range of NaCl concentration.
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    Notes: Light-scattering, sedimentation, viscosity, and reducing power measurements have been carried out on a sample of native dextran from Leuconostoc mesenteriodes B-512. The results are discussed in relation to the structure, polydispersity, and branching of the polysaccharide. The effect of different solvents on the behavior of native dextran has been studied. The molecular weight of the dextran remains unchanged in all the solvents used, while the radius of gyration shows a significant increase in some of them (concentrated salts, urea, and glucose solutions); in water-methanol solutions the radius of gyration slightly decreases.
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    Biopolymers 2 (1964), S. 65-68 
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    Topics: Chemistry and Pharmacology
    Notes: The statistical mechanical theory of the helix-coil transition of DNA has been recently discussed by one of the authors, who considered an assembly of DNA molecules with a Markoff distribution of nucleotide sequences. The present communication improves upon the above mentioned theory by introducing approximate normalization factors for the unnormalized statistical weights of finding a given molecule of the assembly in a given microscopic state.
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    Biopolymers 2 (1964), S. 103-103 
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    Biopolymers 2 (1964), S. 79-89 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The effect of small quantities of metal ions on the electrophoretic mobility of calf thymus DNA in solutions maintained at 0.2 ionic strength with weakly interacting (CH3)4N+ ions yields information about interactions occurring in a region very close to the polymer chain. By means of this technique, it is demonstrated that the binding order to DNA is Li+ 〉 Na+ 〉 K+ for the alkali metal ions and Mn++ 〉 Mg ++ 〉 Ca++ for the divalent ions studied. The quantitative details are compared to earlier work on the long-chain polyphosphates. Close agreement between the two systems is obtained indicating that an intrinsic property of individual phosphate groups is being observed and that minor discrepancies probably arise from secondary factors. Three types of stability constants representing the binding of alkali metal ions to DNA are calculated and although differing in absolute magnitude, they all satisfactorily represent the result that the order of interaction is Li+ 〉 Na+ 〉 K+ with respective relative strengths of 1.5 : 1 : 0.8.
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    Biopolymers 2 (1964), S. 113-121 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Birefringence relaxation times on removing the electric field characterize the rigidity of a flexible linear macromolecule structure. Electrical birefringence investigation of DNA solutions supports this view. This principal regularities displayed by relaxation times of electric birefringence decay curves in solutions of chain macromolecules are considered.
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  • 97
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 139-158 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, -0.4), (II, -0.4), and (III, -1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base-pair and base-sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base-pair, and base-sequence resulting from the DNA site and the DNA-drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo-5′-monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space-filling model with steric contours illustrate the results.
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  • 98
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small-angle x-ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
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  • 99
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 213-233 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo-oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest-neighbor exclusion. For the ribo-oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo-oligonucleotide showed all sites equivalent and no cooperativity. For the ribo-oligonucleotides the enthalpy for ethidium binding is -14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M-1 for the two strong sites (4 × 103M-1 for the weak site) or K = 2.5 × 105M-1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo-oligonucleotide the enthalpy of binding is -9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M-1).
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  • 100
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 287-312 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye-Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear-charge-density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye-Hückel theory. Therefore, we turn to the analytical solution of the Poisson-Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we call RM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration; RM varies as κ-1/2, where κ is the Debye-Hückel screening parameter. The Manning fraction, 1 - 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ-1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson-Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson-Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given polyion radius and charge density.
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