bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions des ions métalliques avec le DNA. III. Stabilité et configuration des complexes Ag–DNA
Authors: Wilhelm F. X. , Daune M. 
Published: May 2005

AbstractThe thermal stabilization and the configurational changes of DNA were studied during the binding process of silver ion. Melting curves of silver–DNA complexes were analyzed according to the method of Felsenfeld. An increase of Tm occurred during the formation of the first complex with a preferential stabilization of G–C pairs. In the case of DNA from H. influenzae, the transforming power was maintained after heating in presence of silver at a temperature where AT pairs were dissociated but G‐C pairs were not. Shape modifications of the molecule were followed by light scattering, both with native and ultrasonic degraded DNA. In the case of native DNA, the binding of positive ions modified the electrostatic potential and increased the flexibility of the molecule. In the case of rod shaped fragments of DNA, the progressive formation of a kind of polyampholyte was accompanied by aggregation phenomena. The formation of the second complex, with proton release, induced changes of secondary structure and possibly a tilt of the plane of the base.
Interactions des ions métalliques avec le DNA. IV. Fixation de i'ion cuivrique sur le DNA
Authors: Schreiber J. P. , Daune M. 
Published: May 2005

AbstractThe binding of cupric ion (Cu++) to DNA was followed by spectrophotometry, melting profiles, and hydrodynamic techniques, in 0. 1M NaClO4 and at pH 5. 6. A small amount of Cu++ is bound specifically to bases (about 1 Cu++ per 20 nucleotides), in agreement with polarographic and EPR data. A preferential stabilization of G–C pairs and only a slight increase of the flexibility of the molecule were observed. In 5 × 10−3M NaClO4, a higher number of nonhomogeneous binding sites is found by spectrophotometry. It is concluded that at least two types of sites are available for Cu++. The first one, where Cu++ is chelating N7 of purines to phosphate, is observed only at low ionic strength and destabilizes the double helix. The second exists mainly at 0, 1M or higher ionic strength. All the sites are identical and could be attributed to two successive guanine residues in the same strand. Similar behavior was found for other divalent cations, e. g., Fe++, Mn++, and Co++.
Raman spectroscopy of poly‐L‐proline in aqueous solution
Authors: Smith M. , Walton A. G. , Koenig J. L. 
Published: May 2005

AbstractThe laser‐excited Raman spectra have been obtained of poly‐L‐proline in the solid and aqueous solution. In the solid state, the Raman spectra are of the form II which is the left‐handed helical form with the peptide bonds in the trans configuration. Dissolution of this form in water produced only minor changes in the Raman spectra. The differences in frequencies produced by dissolving the polymer are associated with vibrational modes of the pyrrolidine ring as indicated by comparison with the Raman spectrum of L‐proline. The similarity of the Raman spectra dictates that, the conformations of poly‐L‐proline chain are similar in the solid and aqueous solution.
Reversibility of thermal transitions in proteins: Racemization and aggregation as factors in the reversible denaturation of a soluble keratin derivative (SCMKA)
Authors: Harrap B. S. 
Published: May 2005

AbstractThe reversibility of the thermal denaturation of a low‐sulfur fraction of solubilized wool keratin (SCMKA) has been studied under a variety of conditions of time, protein concentration, and pH. Two types of irreversibility for the transition have been encountered. One of these is associated with an aggregation of the protein on denaturation to give a product which may contain elements of a β conformation. This type of irreversibility is favored by high protein concentration, and the original conformation may in fact be regained if the aggregated structure is broken down by a solvent such as 8M urea and the urea subsequently removed by dialysis. The other type of irreversibility appears to be due to racemization of the protein. It does not seem to be dependent on protein concentration and is apparent only at temperatures beyond the actual transition range (∼40–65°C) at pH values below 11, At pH 12, however, racemization appears to proceed slowly even at 4°C. The thermal transition at pH 9 and pH 10 has been shown to be multistage in nature. Over the pH range 9–12 there is a progressive decrease in thermal stability with increase of pH. Addition of NaCl at pH 10 leads to an increase in thermal stability of the molecule.
Studies of the optical properties of the proflavine–DNA complex
Authors: Li Hsueh Jei , Crothers Donald M. 
Published: May 2005

AbstractWe report studies of the optical properties of the proflavine–DNA complex, using absorbance and circular dichroism spectroscopy. From comparison of the absorption spectra of proflavine complexed with calf thymus and T2 DNA, we conclude that stacking of the dyes external to the double helix is comparatively much weaker with T2 DXA, probably because of its glucosylation. Several sources are found for the circular dichroism induced in proflavine when it is complexed with DNA. There is a relatively weak circular dichroism induced when the dye is infinitely dilute on the DNA lattice; this presumably arises from the environmental asymmetry of the binding site. Stronger circular dichroism effects are induced by interaction of intercalated and stacked dyes; studies with T2 DNA, for which stacking seems to be blocked, permit a tentative resolution of effects due to the two modes of binding. One recurring theme of these studies is the observation that the optical properties are quite dependent on environment. The most dramatic example is a strong variation with salt concentration of the amplitude of the circular dichroism induced in the isolated (intercalated) monomer by the surrounding DNA. This suggests that the structure of the intercalated complex is quite sensitive to external conditions.
Studies on the helical conformational of amylose and possible interconversions
Authors: Sundararajan P. R. , Rao V. S. R. 
Published: May 2005

AbstractThe nonbonded energy (van der Waals) was computed for isolated helical amylose chains as a function of the dihedral angles (ϕ,ψ), i.e., the relative orientations of the glucose residues in the polysaccharide chain. In conformity with x‐ray data, different helical conformations have been proposed for different crystalline modifications of amylose. Right‐handed helical conformations were preferred for 71.13, 61.33, and 42.65‐type helices from minimum energy considerations. The hydrogen bond search reveals the possibility of formation of strong OH ⃛O type hydrogen bonds between contiguous residues in the polymer chain for 61.33 and 71.13 helices. Smooth transition from a 71.13 to a 61.13 helix is possible with small changes in the values of (ϕ,ψ) and without the loss of intramolecular hydrogen bonds, whereas all the intramolecular hydrogen bonds will be broken during the conversion from 61.33 to 42.65 helix.
Configurational statistics of polysaccharide chains. Part I. Amylose
Authors: Rao V. S. R. , Yathindra N. , Sundararajan P. R. 
Published: May 2005

AbstractThe conformational energy of amylose molecule was computed as a function of rotations ϕ and ψ about interunit glycosidic bonds. The characteristic ratio 〈r2〉0/Nl of the mean‐square end‐to‐end distance of the unperturbed chain to the product of n, the number of glucose residues in the chain and the square of the virtual bond length lV = 4.2 Å calculated for amylose chain is about 6.9, which is in good agreement with the experimental value (6.6 ± 0.2). The value of this ratio calculated for free rotation about the inter unit glycosidic bond is 1.1. The conformational map reveals that the rotations of pyranose units about the interunit glycosidic bonds are highly restricted; this tends to lock these units in a preferred orientation. From the probability of occurrence of the glucose residue conformations it is concluded that amylose exists as a random coil with short helical sequences in neutral aqueous solutions.
Circular dichroism of the “random” polypeptide chain
Authors: Tiffany M. Lois , Krimm S. 
Published: May 2005

AbstractThe circular dichroism (CD) spectrum of an unordered polypeptide chain does not correspond, as has been assumed heretofore, to that of a charged chain such as poly‐L‐glutamic acid or poly‐L‐lysine. The latter have been shown to have locally ordered structures with characteristic CD spectra. We have now obtained CD spectra of the unordered forms of the above synthetic, polypeptides, as well as of two fibrous proteins (collagen and feather keratin) and a globular protein (myoglobin). These spectra are all similar to that of unordered polyproline, having a negative band in the vicinity of 2000 mμ and no additional bands at longer wavelengths. The lack of structural uniqueness of the unordered polypeptide chain is emphasized by these studies.
Polynucléotides protonés. VII. Transitions thermiques entre differents complexes de l'acide polyinosinique et de l'acide polycytidylique en milieu acide
Authors: Thiele Danielle , Guschlbauer Wilhelm 
Published: May 2005

AbstractThe interaction between poly (I) and poly (C) in acid medium has been studied by potentiometric titration, mixing curves and thermal denaturation. Phase diagramms as a function of ionic strength, pH, and temperature have been established. From these data it is shown that the acid titration of the complex poly (I) · poly (C) passes through a triple‐stranded intermediate poly (I) · poly (C) · poly (C+) to yield finally the protonated double‐helical complex poly (I) · poly (C+). The mixing curves indicate the sole presence of the three‐stranded complex in the intermediate zone. On the basis of the pK's the coexistence between the three‐stranded complex with the neighboring double‐stranded structure is demonstrated in a narrow rang of pH and ionic strength. The geometry of the base arrangements, their conformation and the sense of the strands are discussed in the light of the data presented. A Hoogsteen‐type pairing between the bases for poly (I) · poly (C+) is favored, although the reverse Hoogsteen pair cannot be excluded.
Hydrodynamic relaxation times of DNA from decay of flow dichroism measurements
Authors: Callis Patrik R. , Davidson Norman 
Published: May 2005

AbstractThe relaxation of the flow dichorism signal of native DNA molecules after rapid (∼0.004 sec) stoppage of the flow has been studied in the narrow‐channel flow dichroism apparatus previously described. The flow dichroism signal decays with a spectrum of relaxation times. The slowest relaxation time accounts for about 0.40 of the total signal for shear gradients in the range of 100–300 sec−1 and for about 0.25 of the total signal for shear gradients in the range of 5,000– 20,000 sec−1. This longest relaxation time in dilute aqueous salt solution at 25°C for T4‐DNA molecules is measured as 0.45 sec; in the molecular weight range from 125 × 106 to 12 × 106, the relaxation time varies as. M(1.6±0.1). The relaxation time is proportional to η/T for large (sixfold) changes in solvent viscosity and for temperature changes between 25 and 0°C, showing that the molecular relaxation is hydrodynamically limited. An accurate analysis of the data at short times to determine the shorter relaxation times was not possible. A theoretical prediction based on the Zimm‐Rouse theory of polymer dynamics for the longest relaxation time is in good agreement with the observed value, but the theory predicts that 87%, of the total signal should decay with this relaxation time, whereas experimentally only a smaller fraction of the total signal does so. This discrepancy occurs because the theory is applicable to low hydrodynamic shear stress flows and the experiments were made at higher shear stresses.
Helix‐coil transition of poly(L‐glutamic acid) in N‐methylacetamide
Authors: Harry John B. , Franzen James S. 
Published: May 2005

AbstractThe folding of randomly coiled poly(L‐glutamic acid) to the helical state has been studied in N‐methylacetamide by titration methods. Since this solvent would be expected to form amide‐peptide group hydrogen bonds with the unfolded form of the polymer, to a first approximation no helix stabilization could come from intrapolymer hydrogen bonds. The titration data, collected from 30 to 70°C yield the following values per residue for the thermodynamic parameters governing the coil‐helix reaction for the uncharged polymer: ΔG30°C°, −1. 9 ± 0.1 kcal; Δ H°, 0 ± 0.1 kcal; ΔS30°C°, 6.3 ± 0.6 eu. In N‐methyl acetamide, the helix is an order of magnitude more stable than in water, and this stabilization appears to be entirely the result of the entropy gained by solvent molecules which are released from the polymer upon folding.
Electron microscopy of poly (O‐acetyl hydroxy‐L‐proline) crystals
Authors: Andries J. C. , Walton A. G. 
Published: May 2005

AbstractSingle crystals of POAHP II were grown from acetic anhydride, a solvent in which POAHP I is thought to be stable. The single crystals gave an electron diffraction pattern which specified a hexagonal unit cell and the lateral spacing between molecular chains (11.4 Å). There is reasonable indication that molecular chain folding occurs in the POAHP single crystals. Epitaxial crystallization of POAHP II has been observed in the [100] and [320] directions on NaCl, [110] direction on KCl, and [100] direction on KI. Evidence indicates that the molecular axis is normal to the long axis of the POAHP needles and parallel to the substrate surface.
Stereochemistry of nucleic acids and polynucleotides. V. Conformational energy of a ribose‐phosphale unit
Authors: Lakshminarayanan A. V. , Sasisekharan V. 
Published: May 2005

AbstractThe potential energy calculations on the sugar‐phosphate unit for different puckerings of the sugar are reported in this paper. The results obtained here essentially confirm our earlier predictions made by using criteria of contact distances (hard‐sphere potential) and are also supported by observed conformation in crystal structures. The minimum energy conformations of the sugar phosphate unit, along with the preferred orientations of the base with respect to the sugar given in the previous paper, determine the probable conformations of the monomer unit of a polynucleotide (or nucleic acid) chain.
Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate
Authors: Sasisekharan V. , Lakshminarayanan A. V. 
Published: May 2005

AbstractAs part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles ϕ and ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche–gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.
Chain conformation of copoly(γ‐methyl D, L‐glutamate)
Authors: Musuda Yukio , Miyazawa Tatsuo , Goodman Murray 
Published: May 2005

AbstractCopolymers of γ‐methyl D‐ and L‐glutamates with various D/L ratios were prepared. Infrared absorption spectra of solid films were measured and sums of right‐ and left‐handed helix contents were determined from intensities of amide V bands. Farultraviolet absorption spectra and optical rotatory dispersion of these copolymers in solutions are used to ascertain their helical character. Chain conformations of DL‐copolypeptides are discussed.
Theoretical model for the equilibrium behavior of DNA superhelices
Authors: Laiken Nora 
Published: May 2005

AbstractA statistical‐mechanical model for superhelical DNA is presented. The partition function for a DNA superhelix is written by using a combinatorial approach in order to allow for the known relation between the number of superhelical twists and the states of the base pairs in the double helix. While the theory allows any factors which might contribute to the free energy of superhelical twisting to be included in the statistical weights of the superhelical twists, only the reduction in configurational entropy is considered in this paper. Similarities between an imperfectly matched DNA double helix and a DNA superhelix are used in the derivation of expressions for the entropy of superhelical DNA. Although the partition function is presented in a general form, permitting many equilibrium properties of DNA superhelices to be treated, the application considered in this paper is the calculation of helix–coil transition curves. Several experimentally observed features of such transitions are predicted. For example, the curves are bimodal, with an early and a late transition relative to that of a nicked molecule. The results are very sensitive to the volume within which two parts of the double helix must meet when forming a superhelical twist. The free energy of superhelix formation is calculated, and the results are compared with those obtained from the data of Bauer and Vinograd for ethidium bromide intercalation. In the present model, the free energy increases less sharply with an increase in the number of superhelical twists than observed experimentally, indicating that factors other than configurational entropy probably make important contributions to the free energy of superhelix formation.
Flexibility of tropocollagen from sedimentation and viscosity
Authors: Utiyama Hiroyasu , Sakato Kuniaki , Ikehara Kenji , Setsuiye Takashi , Kurata Michio 
Published: May 2005

AbstractSedimentation constant and intrinsic viscosity were measured on purified tropocollagens extracted from earthworm‐cuticle and lathyritic ratskin. A cartesian diver viscometer was used to make viscosity measurements at small shear stress and to avoid the effects of surface forces. By comparing the experimental data with the hydrodynamic theories of wormlike‐coil of Ullman a value of 1300 Å has been assigned for the persistence length of these tropocollagens. Other factors which may affect the estimate are discussed.
Study of dielectric behavior of DNA in shear gradient
Authors: Takashima Shiro 
Published: May 2005

AbstractThe dielectric behavior of the DNA molecule is investigated in the presence of mechanical force as well as the electrical field. In the present experiment, the direction of the electrical field is perpendicular to that of the mechanical force. The dipole moment of polar molecules manifest itself as dielectric increment at low frequencies or as the conductance increment at high frequencies. These two quantities are closely related to each other by Eq. (1) in the text. Because of the difficulty due to electrode polarization at low frequencies, no useful information was obtained by investigating the dielectric increment in the present system. Therefore, the effect of shear gradient was studied by measuring the conductance increment at high frequencies with various velocity gradients. The conductance increment decreased when the shear was applied perpendicular to the electrical field. The conductance change is converted into the unit of dielectric constant; it was found that the dielectric increment of DNA solution decreases by as much as 85 percent. From these observations, it is concluded that the direction of the dipole moment in DNA is longitudinal rather than transverse. The same experiment was repeated with the random coil DNA and no anisotropy in the dielectric increment was observed.
The effect of acridine orange on the structure of ribosomes
Authors: Tal Moshe , Rotem Haim , Alfasi Matya , Berg Robert A. 
Published: May 2005

AbstractExposure of Escherichia coli MRE‐600 ribosomes to acridine orange (AO) at low ionic strength (1mM Tris‐acetate pH 7.4) results in quantitative binding of the dye. Under our experimental conditions about a few hundred dye molecules can be bound to any one of the 30, 50, or 70‐S particles. AO causes the 30 and the 50‐S subunits to form ribosomal aggregates of approximate sedimentation constants of 70 and 100‐S.
Synthèse et Caractérisation des Trois Premiers Oligomermères de l'Acide α‐L‐Glutamique. I
Authors: Rinaudo M. , Domard A. , Spach G. 
Published: May 2005

AbstractIn the present work, the synthesis of the three primary oligomers of α‐L‐glutamic acid is described; the general formula is the following:
magnified image

The choice of protective groups at the both ends of the chain allows for the good solubility in the water and the liberation of free carboxyl groups on the side chain. Thus, models are obtained for the study of thermodynamic properties of solutions and especially of the interactions between polyanions and cations. The prepared products are characterized by different techniques such as mass spectrometry potentiometry, tonometry, and thin‐layer chromatography. The results are in agreement and lead to the conclusions that the molecules have the general formula of [I] and are stereoregular.
Isokinetic relationships for the effect of inorganic phosphate adn protons on the deoxygenation rate of human hemoglobin
Authors: Salhany J. Mitchell 
Published: May 2005

AbstractThe rate of hemoglobin deoxygenation is measured as a function of inorganic phosphate concentration, pH, and temperature. Isokinetic relationships (enthalpy‐entropy compensation) are searched for by applying the method of O. Exner and, for comparative purposes, the conventional method of plotting the energy of activation (E*) versus the natural log of the pre‐exponentional factor of the Arrhenious equation (In A). Both plots indicate compensation between the activation parameters. However, unlike the conventional plot, the Exner treatment is able to distinguish between two types of compensation. Furthermore, when extrapolated rate constants based on all the data in an Exner plot are transposed into E* vs. In A plots, so‐called “turn‐around” behavior is predicted for the effect of increasing phosphate concentration at constant pH. Such “turn‐around” behavior in E* vs. In A plots has been observed experimentally by Beetlestone and co‐workers for anion binding to human hemoglobin as a functin of pH. Lastly, the compensation temperatures obtained from these data all fall within the Vaslow‐Doherty compensation range (250–350°K) which is thought to indicate that the solvent, water, is involved in the reaction mechanism. Thus, Exner plots appear to further resolve isokinetic temperatures of the Vaslow‐Doherty type. Differences in the electrostriction of solvent in the activated state is suggested as one possible physical source for the Vaslow‐Doherty type compensation observed in this work.
Nuclear magnetic resonance study on the model compounds for poly(N‐alkylglycine)s
Authors: Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu 
Published: May 2005

AbstractCis‐trans isomerism was investigated with N‐acetyl and N‐propionyl, N‐alkylglycine dimethylamides as model compounds for poly(N‐alkylglycine dimethlamides as model compounds for (N‐alkylglycine)s using n.m.r. spectroscopy. The population of the cis isomer measured in benzene and methylene chloride solutions did not show any marked dependence on the bulkiness of N‐alkyl substituents. This contrasts with polyN‐alkylglycine)s, whose cis isomer population increased with the introduction of bulky N‐alkyl groups. Kinetics of the Cis‐trans isomerization was also investigated with N‐acetyldimethylamides of sacrosine, N‐n‐propylglycine, and N‐isopropylglycine in tetrachloroethane solution. The δG‡ values for Cis‐trans isomerization in these amides were 18 ∼ 19 kcal/mole, which were virtually the same as that of polysacrosine.