bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectrophotometric, potentiometric, and density gradient ultracentrifugation studies of the binding of silver ion by DNA
Authors: Jensen Ronald H. , Davidson Norman 
Published: December 2004

AbstractThe equilibrium and the stoichiometry for the reversible complexing of silver ion by DNA have been studied by potentiometric titrations, proton release pH‐stat titrations, and by spectrophotometry. The complexing reactions involve primarily the purine and pyrimidine residues, not the phosphate groups. There are at least three types of binding (types I, II, and III), of which the first two have been intensively studied in this work. The sum of type I and type II binding saturates at one silver atom per two nucleotide residues. In the type I and type II reactions, zero and one proton, respectively, are displaced per silver ion bound. At pH 5.6, the reactions occur stepwise, type I being first, while at pH 8.0, they occur simultaneously. The silver ion binding curve is very sharp at pH 8, indicating a cooperative reaction. The strength of the binding increases with increasing GC content. Type I binding is more important for GC‐rich DNA's than for GC‐poor ones. Denatured DNA binds more strongly than does native DNA. The silver ion complexing reaction is chemically and biologically reversible. We propose that type II binding essentially involves the conversion of an \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm N} - {\rm H} \cdots {\rm N} $\end{document} hydrogen bond of a complementary base pair to an N—Ag—N bond. The nature of type I binding is less clear, but it may involve a π interaction with stacked bases. The buoyant density (ρ0) of DNA in a Cs2SO4 density gradient increases when the DNA reacts with silver ion. The buoyant density change is about 0.15 g./ml. for 0.5 silver bound per nucleotide. The large buoyant density changes and the selective nature of the complexing reaction make it possible to perform good separations between native and denatured DNA or between GC‐rich and GC‐poor native DNA's by density gradient centrifugation.
Further evidence of the protonation of the C‐terminal of the poly‐γ‐benzyl‐L‐glutamate helix by acids
Authors: Watanabe Hiroshi , Yoshioka Koshiro 
Published: December 2004

AbstractThe change of the specific Kerr constant upon the addition of several acids to poly‐γ‐benzyl‐L‐glutamate solution in ethylene dichloride has been measured by the rectangular pulse method. The addition of a small amount of strong acid (trifluoroacetic acid, trichloroacetic acid, monochloroacetic acid, or hydrogen chloride) caused a rapid decrease of the specific Kerr constant. On the other hand, the effect of weak acids (formic acid, acetic acid, and propionic acid) was small. These facts show that the apparent dipole moment of a helical poly‐γ‐benzyl‐L‐glutamate molecule is considerably diminished by the protonation of terminal peptide groups. The electric conductivity of poly‐γ‐benzyl‐L‐glutamate solution in ethylene dichloride–dichloroacetic acid mixtures has been measured. It was found that the specific conductivity per unit concentration of poly‐γ‐benzyl‐L‐glutamate increased considerably at small fractions of dichloroacetic acid. This shows that poly‐γ‐benzyl‐L‐glutamate can react as a base (proton acceptor) with dichloroacetic acid. This result also confirms the previous conclusion.
Polarographic studies of ion binding in solutions of pepsin. II. Binding of thallous ions
Authors: Lapanje Savo 
Published: December 2004

AbstractThe results of the application of a modified polarographic method to the study of binding of thallous ions in solutions of pepsin are reported. Isoionic solutions of pepsin were converted by using a cation exchange resin to solutions of thallous pepsin. The extent of ion binding was obtained as in the case of cadmium pepsin by assuming that only free, i.e., unbound, ions contribute to the diffusion and migration currents, respectively. However, the relations used previously for computing the degree of ion binding have been refined on the basis of experience acquired in a parallel study of solutions of thallous acrylate and polyacrylate, respectively.
Synthesis of poly‐L‐arginine
Authors: Ariely S. , Wilchek M. , Patchornik A. 
Published: December 2004

AbstractPoly‐L‐arginine was prepared by the guanidization of poly‐L‐ornithine with 1‐guanyl‐3,5‐dimethylpyrazole. The poly‐L‐ornithine was derived from poly‐δ,N‐trifluroacetyl‐L‐ornithine by removal of the blocking groups under mild basic conditions (1M piper‐idine).
Nuclear magnetic resonance investigation of the state of water in human hair
Authors: Clifford J. , Sheard B. 
Published: December 2004

AbstractMeasurements have been made of the nuclear magnetic relaxation times T1 and T2 of the protons of water in hair. These are interpreted as showing that water molecules in hair exist in a continuous range of environments with a wide spread of rates of molecular rotation. Even at high water contents most of the water molecules are much less mobile than molecules in bulk water. The term “mobility” is given a quantitative meaning.
The chain effect. Part III. Induction of secondary structure in copolymerizations
Authors: Bamford C. H. , Block H. , Imanishi Y. 
Published: December 2004

AbstractStudies of the properties of copolymers of N‐carboxy sarcosine anhydride with other N‐carboxy α‐amino acid anhydrides have shown that the secondary structure may be a function of the type of initiator used. In particular, when polysarcosine is the initiator, and the “chain effect” becomes possible, blocklike character appears in the copolymer. This is the result of selective and rapid polymerization of N‐unsubstituted N‐carboxy α‐amino acid anhydrides by the chain‐effect mechanism. In suitable circumstances, therefore, the latter may be used to induce order into copolymerizations of this type.
Effects of pressure on the helix–coil transitions of the poly A–poly U system
Authors: Hughes F. , Steiner R. F. 
Published: December 2004

AbstractStudies were made of the influence of hydrostatic pressure on the helix–coil transitions of poly (A + U) and poly (A + 2U). The results were analyzed by a thermodynamic treatment which emphasized the cooperative aspect of the transitions. The helix‐to‐coil volume changes were found to be small and negative indicating pressure stabilization of the coil form. The significance of the results with respect to other denaturation measurements was discussed.
Interaction of DNA with heavy metal ions and polybases: Cooperative phenomena
Authors: Miller I. R. , Bach D. 
Published: December 2004

AbstractThe polarographically determined binding constants of Cu++ and Cd++ to DNA were found to decrease with the degree of binding. The binding causes a reduction in the electrostatic potential ψ on the DNA molecule. The binding constant conforms to the relation K = K0 exp {‐zeψ/kT}. The binding constant at zero potential K0 depends on the nature of the competing counterfoils to the phosphate group of the DNA; it is apparently smaller when Na+ rather than the ethylpyridonium residue of polyvinylpyridine serves as the competing counterfoil. The specific interact ion between the ethylpyridonium residues of the polybase and the DNA is very weak, even though the polyelectrolytic interaction induced by the decrease of the electrostatic free energy is spectacular. The intereaction is reversible and equilibrium is maintained between the different interaction products. A reshuffling of the interacting partners can be effected by spontaneous or induced (by centrifugal forces) precipitation of the least soluble interaction products participating in the equilibrium.
Polypeptides. LVI. Effect of lithium bromide and of temperature on the conformation of a copolymer of glutamic acid and lysine
Authors: Morita Koichi , Simons Elizabeth R. , Blout Elkan R. 
Published: December 2004

AbstractBy using optical rotatory dispersion measurements, the helix content of poly Glu50Lys50 has been investigated and compared with that of poly Glu20Lys20Ala60 in aqueous solutions. Measurements were made at pH 3 and at pH 8 in various concentrations of lithium bromide. Various factors affecting helix stabilization are considered and their perturbation by lithium bromide is related to the shape of the observed transition curves. A residual helix content of 12% in 8M LiBr, based upon a b0 of +100 for a fully random conformation, was observed for poly Glu50Lys50 at pH 3 and 8. The loss of helix content of poly Glu50Lys50 as a function of temperature is also reported. ΔH is approximately −6.9 kcal./mole for the overall transition, compared to −6.5 kcal./mole for poly Glu20Lys20Ala60. The midpoint of the broad transition is near 40°C. at pH 3, but much lower, at −10 to 0°C., at pH 8. These results are discussed in terms of the stabilizing factors for the partial helix content of the polypeptides.
Effect of pressure on the helix and random coil forms of poly(D‐glutamic acid)
Authors: Suzuki Keizo , Taniguchi Yoshihiro 
Published: December 2004

AbstractThe absorption spectrum of the aqueous solution of acridine orange (AO)‐poly–(D‐glutamic acid) (PDGA) complex at pH 4.5 (helix form) did not show any wavelength shift, but at pH 7.5 (coil form) changed to the absorption curve of the helix form by compression up to 4500 atm. The ionization degree of PDGA estimated from the electric conductivity of the aqueous solution of PDGA at 4500 atm. was a value of about 5.3%. The entropy of the helix formation of PDGA from the titration data at 1 atm. and 30°C. was negative −2.98 e.u. It will be concluded in this report that the volume change for coil to helix could be positive for PDGA and negative for AO–PDGA complexes.
Kinetics of synthesis of polymeric dAT on oligomeric templates
Authors: Elson Elliot 
Published: December 2004

AbstractA model is developed to explain the following experimental observations: oligomers of the alternating DNA copolymer dAT serve as templates for the enzymatic synthesis of macromolecular dAT; the rate of polymer synthesis with a template oligomer of given length increases to a maximum and then decreases as the temperature increases; the temperature for the maximum rate of synthesis increases with the length of the template. These observations were interpreted in terms of the repeated “slipping” of the oligomer along the product strand to expose template sites. This communication extends this idea. We suppose that the rate‐limiting step in the polymerization is either the attachment of the substrate to the exposed template site or the synthesis of the phosphodiester bond. Then the rate of synthesis is proportional to the equilibrium concentration either of exposed template sites or of template sites occupied by substrate molecules. These concentrations are evaluated in terms of a simple theory of the helix–coil transition. The model qualitatively reproduces the dependence of the rate of synthesis on template length and temperature and predicts rates of synthesis in approximate agreement with experiment.
Molecular conformation of poly(S‐lactic acid)
Authors: De Santis P. , Kovacs A. J. 
Published: December 2004

AbstractThe predominant role of van der Waal interactions in determining the helical conformations of a simple synthetic linear polymer, as well as helical polypeptides, was pointed out in systematic studies by Liquori et al.1,2. In the case of homopolypeptides the conformational analysis carried out on the basis of a simple semiempirical function describing the van der Waal pairwise interactions between the non directly bonded atoms lead to the conclusion that only five helices are allowed (Rα, β, γ, δ, Lα).2,3In view of the close similarities with poly‐L‐alanine, we have investigated by x‐ray and conformational analysis the molecular conformation of poly(S‐lactic acid) which has recently been described by Kleine and Kleine4 and Schuls and Schwaab5 and studied in solution by Goodman and D'Alagni.6 In fact, this polymer may be related to the polypeptide by the interchange of a peptide bond with ester bond along the main chain. This operation is expected to involve only a relatively small change in the steric interaction within the possible helical conformation, but obviously rules out any possibility of hydrogen bonding.
Steric structure of L‐proline oligopeptides. I. Infrared absorption spectra of the oligopeptides and poly‐L‐proline
Authors: Isemura T. , Okabayashi H. , Sakakibara S. 
Published: December 2004

AbstractPoly‐L‐prolines I and II were differentiated by the characteristic bands in the far infrared region. Form I showed two broad bands at about 280 and 160 cm−1 and form II two bands at, 400 and 670 cm.−1. Furthermore, three broad bands at about 250, 200, and 100 cm.−1 were observed in the spectrum for form II. Infrared absorption bands of the pentamer, hexamer, and octamer of tert‐amyloxycarbonyl‐L‐proline were almost similar to those of poly‐L‐proline II in the 1800–75 cm.−1 region. In the far‐infrared region, especially, the absorption bands of these three oligopeptides were in good agreement with that of poly–L–proline II. Accordingly we concluded that the molecules of pentamer, hexamer, and octamer had a helical structure of a left‐handed threefold screw axis. The tetrapeptide of tert‐amyloxycarbonyl‐L‐proline might also have a left‐handed helix, probably one turn, since the tetramer clearly showed an absorption band at about 400 cm.−‐1 characteristic of poly–L–proline II.
Conformational studies of poly‐L‐alanine in water
Authors: Ingwall R. T. , Scheraga H. A. , Lotan N. , Berger A. , Katchalski E. 
Published: December 2004

AbstractThe conformational properties of poly‐L‐alanine have been examined in aqueous solutions in order to investigate the influence of hydrophobic interactions on the helix–random coil transition. Since water is a poor solvent for poly‐L‐alanine, water‐soluble copolymers of the type (D, L‐lysine)m–(Lalanine)n‐(D, L‐lysine)m, having 10, 160, 450, and 1000 alanyl residues, respectively, in the central block, were synthezised. The optical rotatory dispersion of the samples was investigated in the range 190–500 mμ, and the rotation at 231 mμ was related to the α‐helix content, θH, of the alanine section. In salt‐free solutions, at neutral pH, the three large polymers show high θH values, which are greatly reduced when the temperature is increased from 5 to 80°C. No helicity was observed for the small (n = 10) polymer. By applying the Lifson‐Roig theory, the following parameters were obtained for the transition of a residue from a coil to a helical state: ν = 0.012; ΔH = −190 ± 40 cal./mole; ΔS = −0.55 ± 0.12 e.u. Since ΔH and ΔS differ from the values expected for a process involving only the formation of a hydrogen bond, and in a manner predicted by theories for the influence of hydrophobic bonding on helix stability, it is concluded that a hydrophobic interaction is also involved. In the presence of salt (0.2M NaCl), or when the ε‐amino groups of the lysyl residues are not protonated (pH = 12), the helical form of the two large polymers (n = 450 and n = 1000) is more stable than in water. Since the electrostatic repulsion between the lysine end blocks is greatly reduced under these conditions, the alanine helical sections fold back on themselves, and this conformation is stabilized by interchain hydrophobia bonds. This structure was predicted by the theory for the equilibrium between such interacting helices, non‐interacting helices, and the random coil.
Enthalpy of helix–coil transitions from heats of solution. I. Polyglutamates.
Authors: Giacometti Giovanni , Turolla Angelo , Boni Renzo 
Published: December 2004

AbstractThe heat of solution of a series of three polyglutamates as a function of solvent composition was measured. The abrupt increase in heat of solution at the solvent composition of the helix–coil transition (as evidenced by optical rotation data) allows the estimation of the transition enthalpy change. The difference of side chain in the three polyglutamates has no appreciable effect on the transition enthalpy, although it affects the helix stability, as judged from the solvent composition at the transition points. These facts are discussed on the basis of existing models of the transition.
Epitaxial crystallization of poly (γ‐benzyl L‐glutamate) on alkali halide single crystals
Authors: Carr S. H. , Walton A. G. , Baer Eric 
Published: December 2004

AbstractSingle crystals of poly(γ‐benzyl L‐glutamate) were formed by epitaxial crystallization from solution in mesitylene on NaCl, KI, and KCl (001) cleavage faces. From electron microscopy and diffraction studies, the structure of these overgrowths was determined to be that of lamellae containing chain‐folded α‐helical macromolecules. The usual type of crystal perfection, that of ordered helix axes and disordered side groups, was exhibited by this synthetic polypeptide. Unique orientation regimes were observed with each substrate.
Heats of the helix–coil transitions of the poly A–poly U complexes
Authors: Krakauer Henry , Sturtevant Julian M. 
Published: December 2004

AbstractThe heats of the conformational transitions of poly (A + U) and poly(A + 2U) were determined in a twin‐cell differential thermal analysis microcalorimeter capable of measuring heat effects of 25–35 meal, in reactions of this type, with a precision of about 3%. The dependence of these heats on the concentration of Na+ and K+ was studied and was found to be interpretable with fair success by a simple phenomenological argument which employs the concept of binding of counterions to polyelectrolytes.
Flow dichroism of deoxyribonucleic acid solutions
Authors: Lee Chong Sung , Davidson Norman 
Published: December 2004

AbstractThe flow dichroism of dilute DNA solutions (A260 ≈ 0.1) has been studied in a Couette‐type apparatus with the outer cylinder rotating and with the light path parallel to the cylinder axis. Shear gradients in the range of 5–160 sec.−1 were studied. The DNA samples were whole, “half,” and “quarter” molecules of T4 bacteriophage DNA, and linear and circular λb2b5c, DNA. For the linear molecules, the fractional flow dichroism is a linear function of molecular weight. The dichroism for linear λ DNA is about 1.8 that of the circular molecule. For a given DNA, the dichroism is an approximately linear function of shear gradient, but with a slight upward curvature at low values of G, and some trend toward saturation at larger values of G. The fractional dichroism increases as the supporting electrolyte concentration decreases.
Ion‐binding and conformation of poly‐L‐methionine S‐methylsulfonium salts in added salt systems
Authors: Makino Shio , Wakabayashi Katsuzo , Sugai Shintaro 
Published: December 2004

AbstractIn order to study the type of ion binding and the conformation of several salts of poly‐L‐methionine S‐methylsulfonium hydroxide, the viscosity, conductance, counterion activity, and optical rotatory dispersion of the polysalts were measured in systems with a small amount of added salt. It was shown that the ion binding of chloride and bromide salts was of a diffuse binding type due only to the electrostatic potential of the polyion, and that both polysalts underwent no conformational transition by the addition of a simple salt, NaCl for chloride salt and NaBr for bromide salt, and retained a random coil conformation. Iodide and thiocyanate salts showed a conformational change, probably from the random coil into the β form, with increasing concentrations of NaI and NaSCN, respectively. On the other hand, perchlorate salt existed in the α‐helix conformation in part even in pure aqueous solution, and the fraction of α‐helix increased on the addition of NaClO4. On considering several possible situations, it is suggested that there is a specific and strong interaction between the polyion and the small counterion in iodide, thiocyanate, and perchlorate salts.
Breakage by hydrodynamic shear of the bonds between cohered ends of λ‐DNA molecules
Authors: Yew Foch Fu Hsie , Davidson Norman 
Published: December 2004

AbstractThe rate of breakage by hydrodynamic shear of the cohered ends of λ‐DNA molecules has been observed for the circular monomers, joined half molecules, and joined quarter molecules, in a capillary apparatus with known flow parameters. The rate constant for breakage has been measured as a function of shear stress, temperature, ionic strength, and molecular length. There is a large temperature coefficient, with an activation energy of 120 ± 20 kcal./mole. The values of d ln k/dG, where k is the rate constant for breaking and G is shear gradient, in aqueous solution at 25°C. are about 3.8 ± 0.3 × 10−4 see. The shear stresses needed for breakage of joined quarter molecules and of circular monomers, respectively, are about equal, and about half that needed for breakage of joined half molecules. The rate of breakage at a given shear stress increases with decreasing ionic strength, approximately as [Na+]−1.6. Self‐protection effects are not observed for opening of circular monomers at a DNA concentration of 5 μg./ml. but are observed for breakage of joined half molecules at concentrations down to 0.5 μg./ml. The large temperature coefficient which is approximately equal to that of the thermal dissociation of the cohered ends is interpreted to mean that shear breakage is a mechanically assisted thermal reaction in which the thermal fluctuations provide most of the free energy of activation for breakage. A detailed model for this interpretation is presented. The self‐protection effect implies that those molecules which break are not average molecules but exceptional ones which, due to some fluctuation, are more fully extended in the flow field.
Denaturation and renaturation of DNA. II. Possible use of synthetic periodic copolymers to establish model and parameters
Authors: Goel Narendra S. , Montroll Elliott W. 
Published: December 2004

AbstractA detailed comparison of the various models used in the literature to calculate the melting curve of DNA molecules is made. It is shown that basically all the models are identical. The form developed earlier by the authors has been extended to include the dependence of the correlation parameter on the type and the orientation of the nearest neighbor bonds. A rather exhaustive theoretical study of the metling curves for the synthetic polydeoxyribose copolymers is made. A comparison of these results with the suggested experimental results obtained will enable us to decide on a reliable model which could be used to determine the melting curve if the sequence of the bonds is given. A preliminary discussion of a very general model which we will call a “bubble model” is given.
Rheology of hyaluronic acid
Authors: Gibbs D. A. , Merrill E. W. , Smith K. A. , Balazs E. A. 
Published: December 2004

AbstractThe dynamic viscoelastic properties of hyaluronic acid solutions have been measured over the frequency range 0.02–1.67 cps. The effects of varying temperature, hyaluronic acid concentration, pH, and ionic strength on the dynamic shear moduli were studied. The solutions exhibited a sharp transition from viscous to elastic behavior as the strain frequency increased. No entanglement coupling of the hyaluronic acid molecules was evident over the concentration range 2.0–4.0 mg./ml. Solutions at pH 2.5 showed a pronounced elastic behavior relative to both higher and lower pH's. This effect was attributed to a stiffening of the hyaluronic acid molecule at this pH.