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  • 1
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly-L-proline in the molecular weight range 50,000-90,000 has been synthesized from L-proline-N-carboxyanhydride. The molecular weight obtained is dependent on the initiator concentration. The rate constants for the polymerization have been determined by measuring the CO2 evolution. By observation of rotation during the polymerization, it is possible to deduce the conformation of the polymer in the polymerization solution. It is concluded that the immediate product of the polymerization is neither pure form I nor pure form II. The differences between form I and form II of poly-L-proline have been further characterized by measurements of their ultraviolet rotatory dispersion and their ultraviolet spectra.
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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 base-catalyzed hydrolysis rate of the cationic esters obtained by quaternization of N,N,N′,N′-tetramethylethylenediamine with phenylbromoacetate was studied in buffers and in solutions of partially neutralized polymeric acids. The polyanions were found to be powerful inhibitors of the reaction. This effect was interpreted as due to the association of the ester with the polyanion, from which the catalytically active hydroxyl groups are repelled. It is shown that kinetic data may be interpreted by a procedure similar to the Lineweaver-Burk plot to yield the reactivity of the bound ester and the dissociation constant of the polymer-ester complex.
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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: A series of high molecular weight copolypeptides of L-proline and sarcosine have been synthesized. Experimental evidence is presented which indicates that the products are true copolymers rather than mixtures of homopolymers. In contrast to poly-L-proline I, a copolymer of L-proline-sarcosine I containing approximately 50% sarcosine is soluble in water. Two molecular conformations of the copolymers, similar to those found for polyproline, have been characterized by means of infrared spectroscopy and optical rotatory dispersion. The residue rotation of L-proline has been obtained from the copolymers and is -250°.
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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 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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  • 5
    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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  • 6
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    New York : Wiley-Blackwell
    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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  • 7
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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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  • 8
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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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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 10
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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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  • 11
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    Biopolymers 23 (1984), S. 847-852 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 12
    ISSN: 0006-3525
    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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  • 13
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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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  • 14
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    Biopolymers 23 (1984) 
    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
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    Biopolymers 23 (1984), S. 191-194 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 16
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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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  • 17
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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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  • 18
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 19
    ISSN: 0006-3525
    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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  • 20
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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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  • 21
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    Biopolymers 23 (1984) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 22
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 23
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 24
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 25
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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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  • 26
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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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  • 27
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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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  • 28
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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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  • 30
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    Keywords: Chemistry ; Polymer and Materials Science
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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 
    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 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 
    ISSN: 0006-3525
    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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  • 35
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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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    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 
    ISSN: 0006-3525
    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 
    ISSN: 0006-3525
    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 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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  • 44
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    Topics: Chemistry and Pharmacology
    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 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    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
    Source: Wiley InterScience Backfile Collection 1832-2000
    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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    Keywords: Chemistry ; Chemistry
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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), S. 179-180 
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    Chemie in unserer Zeit 18 (1984), S. 60A 
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    Keywords: Chemistry ; Chemistry
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  • 61
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  • 62
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    Chemie in unserer Zeit 18 (1984), S. 211-212 
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    Keywords: Chemistry ; Chemistry
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  • 63
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    Keywords: Chemistry ; Chemistry
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  • 64
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    Biopolymers 1 (1963), S. 1-1 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 65
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    Biopolymers 1 (1963), S. 25-32 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The grand-partition-function theory of the preceding paper is used to derive expressions for the number of base pairs bonded in DNA with explicit consideration of the copolymeric nature of the DNA. The following features of the DNA molecule are taken into account: (1) the DNA's from different sources have different ratios of a-t and g-c pairs; (2) the a-t pair is weaker than the g-c pair; (3) the nearest-neighbor frequencies of the two kinds of base pairs are nonrandom; (4) the stacking energies (nearest-neighbor energies) of the various combinations of pairs may be different. An ensemble is constructed in which the features (1) through (4) are introduced by means of statistical weights on the various pairs and combinations of pairs, and an expression for the corresponding partition function is written. Expressions are derived for the number of bonded base pairs and the number of helical sequences.
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  • 66
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    Biopolymers 1 (1963) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 67
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    Topics: Chemistry and Pharmacology
    Notes: A method is described for formation of hydroxamic acids by direct coupling, in aqueous medium, of hydroxylamine hydrochloride and the sodium salt of a carboxylic acid. The reaction is mediated by a water-soluble carbodiimide, 1-cyclohexyl-3-[2-morpholinyl-(4)-ethyl]-carbodiimide metho-p-toluene sulfonate. Using model compounds, the production of α-, β- and γ-acyl hydroxamic acids was studied. Hydroxamic acid derivatives of α-polyglutamic and γ-polyglutamic acids were also prepared. Dinitro-phenylhydroxamate derivatives were prepared and subjected to Lossen rearrangement, and the reaction mixtures hydrolyzed. Analysis showed that α-polyglutamic acid yielded as many molecules of α,γ-diaminobutyric acid as there had been glutamic acid residues in the form of the dinitrophenylhydroxamate, and gave rise to no ammonia and succinic semialdehyde. In contrast, γ-polyglutamic acid yielded exactly twice the molar quantity of ammonia as there had been glutamic acid residues in the form of dinitrophenylhydroxamate, and also gave rise to significant quantity of succinic semi-aldehyde but no α,γ-diaminobutyric acid. Since production of the latter is characteristic of α-glutamyl hydroxamates and production of the former is associated with γ-glutamyl hydroxamates, the results indicated that the side-chain carboxyl groups of either polymer retained their identities during formation of the hydroxamic acid derivative, and no interchange had occurred between α- and γ-carboxyl groups. These methods were then used to establish that gelatin of ichthyocol contains (per 1000 total residues) at least 20 residues of glutamic acid in γ-peptide linkage. Due to the incomplete dinitrophenylation of the hydroxamic acid derivative of the protein, gelatin of calf skin collagen gave a lower figure of 10 such linkages per 1000 total amino acid residues-a value which must be considered a minimum value. These results show that γ-glutamyl peptide bonds exist in collagen.
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  • 68
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A statistical thermodynamic treatment of thermally induced helix-coil transitions is formulated with the matrix method for an (ensemble) of system(s) in which one strand of a double helix consists of a homopolymeric polynucleotide and the other strand comprises a number of complementary oligonucleotides. Each oligonucleotide is considered to be completely bound to the longer chain when in the helical configuration and completely free from it when in the randomly coiled configuration. The case of partial binding; i.e., “dangling,” is treated in a later paper. Taken into account in both cases are intrachain “stacking” interactions between nearest neighbor residues and interchain hydrogen bonding.An approximate treatment of the characteristic equation of the formulation indicates that the reciprocal of the transition temperature (1/T0) is a linear function of the reciprocal of the degree of polymerization (D.P.) of the oligonucleotides. In the same approximation, 1/T0 is also a linear function of the negative logarithm of the absolute activity of the oligonucleotides. Transition curves obtained by exact calculation on a computer are presented for various degrees of polymerization of both the oligo- and polynucleotides. These curves show a sharpening of the transition with increasing D.P. of the long chain and the aforementioned reciprocal D.P. dependence of 1/T0.
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  • 69
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    Biopolymers 1 (1963), S. 171-182 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric dispersion of polyglutamic acid (PGA) was studied in the pH range of 4-9.8. Three different dispersion curves were obtained. Above pH 6.0, where PGA has a random coil configuration, the dielectric dispersion is characterized by a large dielectric increment (ca. 450) and a relaxation time of 10-12.7 × 10-6 sec. Between pH 6.0 and 5.0, where PGA is in a transitional state with small viscosity, a dispersion curve with very small dielectric increment and also small relaxation time was observed. Below pH 5.0, where PGA has a helical configuration, the dispersion is characterized by a relaxation time of 10-12 × 10-6 sec. and a dielectric increment of about 120. The dipole moment of coil and helical forms of PGA were calculated by using Allgen's equation, and qualitative discussions of these dielectric properties are presented.
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  • 70
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    Biopolymers 1 (1963), S. 193-208 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultaviolet absorption spectra down to 185 mμ are presented for a number of nucleic acids and synthetic polynucleotides in the helical and random forms, and of their constituent mononucleotides, as well as the corresponding nucleosides and free bases. A short wavelength absorption band is in all cases observed with a maximum varying between about 187 and 201 mμ. These bands are more intense than those near 260 mμ. The helical polymers show a hypochromic effect in this region of a somewhat similar magnitude to that in the 260 mμ region. Other spectral phenomena accompanying denaturation and degradation are described.
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  • 71
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    Biopolymers 1 (1963), S. 209-229 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The inactivation of sRNA by reaction with formaldehyde has been reported as it occurs under various conditions giving differing amounts of secondary structure. The theory of inactivation of an active macromolecule by a chemical reaction is developed. Results obtained with a partially melted out secondary structure show that formaldehyde inactivates sRNA by a single reaction at any one of about ten sites, while reaction at other sites does not affect the activity of the sRNA. In the presence of Mg++ at neutral pH, a large proportion of the active molecules are completely protected against inactivation. From the correlation between the amount of secondary structure and the difficulty of inactivation, it is shown that at least a portion of the secondary structure of sRNA is essential to its amino acid acceptor ability. A comparison of results of various workers shows that formaldehyde does not alter RNA as drastically as other reagents and thus enables more discrimination between sites of reaction which are essential and those which are not essential to biochemical activity.
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  • 72
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    Biopolymers 1 (1963), S. 295-295 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 73
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    Topics: Chemistry and Pharmacology
    Notes: Infrared absorption and x-ray diffraction measurements have been made of D,L-copoly-γ-benzylglutamate fibers (cast from dioxane solutions) with various D/L ratios and with various degrees of polymerization. It was found that each chain of these copolymers consists of a random coil portion and an α-helix portion and that the conformation of the latter is similar to the α-helix of pure poly-γ-benzyl-L-glutamate. It was also found that the fraction of the α-helix portion increases with the degree of polymerization of the copolymer. A simplified polymerization mechanism has been proposed for mixtures of D- and L-amino acid N-carboxyanhydrides. A model of the molecular conformation of the D,L-copolypeptide chains derived from this proposed polymerization mechanism is in good agreement with infrared, x-ray, and other measurements. Based on the results of these observations, we discuss the number of L- or D-residues linked in succession that is required for initiating the formation of an α-helix during the course of polymerization.
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  • 74
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    Topics: Chemistry and Pharmacology
    Notes: Poly-L-proline I and II, polyphydroxy-L-proline II, polysarcosine, and collagen, as well as two model amides have been examined by far ultraviolet spectrophotometry. Absorption spectral data are presented. Neither in solution nor in oriented films of poly-L-proline I and II is there any indication of excition resonance splitting of the peptide absorption band. In collagen there is some, in the poly-L-prolines only minimal, hypochromicity. These observations, at least in poly-L-proline II, run counter to theory. Optical rotatory dispersion measurements in the ultraviolet indicate simple dispersion in collagen and poly-L-proline II down to at least 232 mμ. The Cotton effect (trough at 233 mμ) observed in α-helical polypeptides and proteins is absent. The implications of these findings are discussed.
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  • 75
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    Notes: The helix - coil transition of poly-L-glutamic acid (PGA) in aqueous solutions was followed by volume changes, ΔV, and also differential refractive indices, Δn. The increase in ΔV or decrease in Δn upon mixing the sodium salt of PGA with dilute HCl gave three straight lines between pH 7 and 4, the two breaks corresponding to the transition zone observed by other physical methods. For the reaction: —COO- + H+ → —CO-OH, ΔV per mole of H+ bound was 11.4 and 11.1 ml. in 0.01 and 0.2M NaCl solutions, respectively. An additional conformational change of about 0.5-1 ml. per amino acid residue was observed for the reaction: coil → helix, after taking electrostatic interaction into consideration. This was probably due to the release of the water of hydration at the amide linkages when the polypeptide coil is converted into the α-helix, or even the occurrence of voids in the polypeptide chain as a result of imperfect packing of the atoms, although the origin of this volume change is still not fully understood at the present time. The volume changes as calculated from Δn by assuming a constant polarizability of the polymer was found to be higher for the association reaction than those mentioned above. On the other hand, the calculated ΔV for the transition was in fair agreement with those by direct measurements.
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  • 76
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    Topics: Chemistry and Pharmacology
    Notes: Dye-macromolecule complexes provide good models for the study of the effects of coupling between chromophores. In addition to modifications of the visible and UV absorption spectra of the dyes at small interchromophore distances, very efficient energy transfer has been demonstrated at longer distances. The probability of nonradiative transition increases with the number of excitation transfers so that an array of oscillators close to one another becomes nonfluorescent. The insertion of a dye molecule, acting as a trap for the excitation energy, in the highly ordered system of chromophores constituted by the purine and pyrimidine bases of native DNA has given results supporting the intercalation model of Lerman and providing an experimental approach to the problem of the path length of energy migration in the DNA molecule. The average excitation path length seems to be of the order of only ten base pairs, a result which can explain the lack of fluorescence of the DNA.
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  • 77
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    Biopolymers 1 (1963), S. 473-495 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sedimentation, diffusion, and osmotic behavior of poly-L-lysine hydrochloride is examined over a wide range of ionic strengths and in solutions which range in relative composition from a swamping excess of added salt (suppression of charge effect) to salt-free solutions (maximum effect). The charge effect is found to essentially obey the theoretical treatment proposed in Part I of this work. The frictional coefficient of the macroion in salt-free solutions is comparable to that of the fully stretched chain. In excess of salt the friction is appreciably smaller, its magnitude not varying greatly with ionic strength. The molecular weight is determined osmotically and also from diffusion-sedimentation, with the charge effect suppressed by addition of salt or eliminated through the use of non-ionized forms of the polymer; a reasonable agreement is obtained between the methods. The influence of small ions on sedimentation is also examined. The secondary salt effect is found to be much smaller than that predicted theoretically; on the other hand, the substitution of different counterions in the absence of secondary salt effect gives rise to changes of the expected magnitude.
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    Biopolymers 1 (1963), S. 500-502 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 79
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    Notes: Poly-β-hydroxybutyric acid has been isolated from two bacterial sources by two different procedures. Molecular weight and intrinsic viscosity for the two samples were vastly different. This was blamed on degradation occurring during polymer isolation. An optical rotatory dispersion curve for the high molecular weight sample showed a sharp increase in specific rotation at wavelengths less than 450mμ. From this fact and the reported optical activity of the monomer it is concluded that the polymer is stereo-regular. X-ray examination of the “native” and “regenerated” polymer yielded the same crystalline pattern. Electron diffraction and x-ray data on single crystals of the polymer indicate a fiber repeat of 5.9 A. The value can only be reconciled with some kind of helical conformation in the solid state.
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  • 80
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    Topics: Chemistry and Pharmacology
    Notes: It has been suggested previously that water is a nearly indifferent solvent for amylose on the basis that the exponent a of the Mark-Houwink equation is very nearly 0.50 and the second virial coefficient A2 is extremely small. It is shown that such solutions do not show the expected precipitation on cooling and the temperature coefficient of the intrinsic viscosity is small and negative. It is suggested that water is both an indifferent and a nearly athermal solvent for this polymer. Various lines of evidence suggest the polymer to exist as a very stiff coil in this and in other solvents. Variations in the intrinsic viscosity and radius of gyration in various solvents show the importance of skeletal effects in addition to the usual osmotic effects. Application of the Porod-Kratky wormlike coil model leads to unreasonably short persistence lengths if the contour length is based on a fully extended conformation but large and reasonable values of the order 40-70 A. if it is assumed that the basic conformation is the helical one observed in various amylose complexes in the crystalline state. As was previously known, the specific optical rotation decreases sharply in aqueous solutions above approximately pH 12. Accompanying this change in rotation there is first a decrease, then an increase in intrinsic viscosity. This later behavior is strikingly reminiscent of the known behavior of polyglutamic acid in the pH-dependent transition from helix to coil. It is concluded that the conformation is that of a stiff coil with essentially helical backbone contour in neutral solution, and the decrease in rotation and in intrinsic viscosity at high pH results from a partial breakdown of the helical structure with a concomitant increase in backbone flexibility. The increase in viscosity and radius of gyration in extreme alkaline solution is probably due to a polyelectrolyte expansion of the polymer coil. Some other miscellaneous observations which are in accord with this model are also pointed out.
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  • 81
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    Biopolymers 1 (1963) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 82
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    Biopolymers 1 (1963), S. 419-429 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Lifson-Roig theory for the helix-random coil transition in polyglycine has been modified to take side-chain interactions into account. The modified theory is developed specifically for poly-L-alanine which probably contains a β1-α4 hydrophobic bond. A conditional probability, expressing the strength of such a hydrophobic bond, is evaluated from the Nemethy-Scheraga data for the free energy of formation of the bond. This, together with the conditional probabilities for the states of the backbone chain, permit an evaluation of the partition function and properties of the helix-random coil transition. It is seen that the hydrophobic bond renders the poly-L-alanine helix much more stable than the corresponding polyglycine one, in agreement with data obtained by Gratzer and Doty.
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  • 83
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    Topics: Chemistry and Pharmacology
    Notes: Optical, hydrodynamic, and titration properties of polyribouridylic acid (poly U) were investigated in 0.2M Na+, pH 6. Above 15°C., poly U was shown to be a randomly coiled single chain, devoid of secondary structure. There is no shear rate dependence of viscosity; molecular weight is independent of ionic strength; there is virtually no conformationally dependent hypochromicity; no anomalous optical rotatory dispersion; and no anomalous titration behavior. The dependence of the sedimentation constant and intrinsic viscosity on molecular weight was determined. Poly U was shown to be the most highly expanded of all synthetic and naturally occurring randomly coiled polynucleotides.
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    Biopolymers 1 (1963) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 85
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    Topics: Chemistry and Pharmacology
    Notes: Free poly-L-lysine base has been synthesized from ∊,N-trifluoroacetyl-α,N-carboxy-L-lysine anhydride via poly-∊,N-trifluoroacetyl-L-lysine (IV). No racemization occurred during the removal of trifluoroacetyl groups from IV with 1M piperidine. Measurements of optical rotatory dispersion suggest that IV exists in methanol in a helical form. The synthesis of poly-L-lysyl rabbit serum albumin is also described.
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    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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  • 87
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    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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    Biopolymers 23 (1984), S. 213-233 
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    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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    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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    Biopolymers 23 (1984), S. 435-470 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A-RNA, A-DNA, and B-DNA, when coordinates derived from x-ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum-uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long-wavelength absorption band. Using alternative conformations for DNA in low-salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B-form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z-DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329-1332], is in contrast with the current identification of Z-DNA with the high-salt form of poly(dGC·dGC). Finally, the optical properties of single-stranded polyribonucleotides appear to be better explained when alternative structures [91-helix for poly(rA) and 61-helix for poly(rC)] are introduced instead of the A-RNA form.
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    Biopolymers 23 (1984), S. 607-608 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 92
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 93
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    Biopolymers 23 (1984), S. 675-694 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The diffusion-collision model of protein folding has been solved exactly for a three-microdomain protein subunit. Numerical analysis shows that the exact kinetics may be excellently approximated in all cases studied by a standard chemical kinetics approach with the forward rate constants calculated from the mean folding time formula found previously.
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    Biopolymers 23 (1984), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10-14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10-14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X-100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk-shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
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  • 95
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    Biopolymers 23 (1984), S. 617-621 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 23 (1984), S. 23-38 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single- and double-stranded model helices having idealized bond lengths and angles, and any arbitrary, user-specified, pitch and number of residues per turn. The variation of inter- and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β-helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation-bound gramicidin A.
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    Biopolymers 23 (1984), S. 71-81 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low-temperature conformation appears to have a more regular ribose-phosphate backbone and a more effective G base-stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G-C base pairs in tRNAAsp.
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  • 98
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    Biopolymers 23 (1984), S. 493-509 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9-substituted adenine and 2-aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well-resolved bands in the range of 210-350 nm. Other adenine derivative-poly(BU) complexes also afford similar CD spectra, while 2-aminoadenine derivative-poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative-poly(BU) complexes are nearly identical in structure except for the ribose-phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9-methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer-poly(U) system was found to be about 20°C in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0). Further, it was noted that the monomer-poly(BU) complexes are formed even when the Tm is lower than that of self-folded poly(BU).
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    Biopolymers 23 (1984), S. 575-592 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The assignments of 31P resonances of eight short oligonucleotides have been achieved through specific heterodecoupling techniques reported previously from our laboratory [Cheng et al. (1982) Biopolymers 21, 697-701]. The temperature dependence of the assigned 31P chemical shifts of these oligomers was studied and compared to the constitutive dimeric units. This comparison gives some insight to the chemical-shift values of the phosphorus resonances of oligonucleotides. (1) The 3′-end terminal phosphorus resonance in an oligomer tends to locate at a spectral position relatively close to its constitutive dimeric unit. (2) On chain elongation (from 5′-toward 3′-end), the phosphorus resonance in the oligomer will be shifted upfield by 0.2-0.3 ppm, as compared to its constitutive dimeric unit. (3) The relative positions of phosphorus resonances in an oligomer tend to remain in the same order as their constitutive dimeric units. The above obsrvations lead to the development of a new procedure to assign the 31P resonance of a single-stranded oligonucleotide.
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    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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