bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics of the helix‐coil transition in DNA
Authors: Record M. Thomas , Zimm Bruno H. 
Published: December 2004

AbstractThe kinetics of the helix‐coil transition have been investigated for T2 and T7 phage DNA in a formamide‐water‐salt mixed solvent using a slow temperature perturbation technique (applicable to kinetic processes with rate constants ⩽ 3 min−1). In this solvent degradation of the DNA is effectively suppressed. Complex kinetic curves are observed by absorbance and viscosity measurements for the response to denaturing perturbations in the transition region. Analysis of the decay curves indicates that the denaturation reaction in this time range can be treated as a first‐order reaction with a variable first‐order rate parameter, k, the derivative of the logarithm of the absorbance or viscosity change with respect to time. In the approach to denaturation equilibrium in the transition region, the rate parameter is determined only by the instantaneous extent of denaturation of the molecules. Near equilibrium, the rate parameter assumes a constant value characteristic of the equilibrium state. In this region, where the denaturation reaction proceeds as a simple first‐order process, both the decay of absorbance (reflected local conformational change) and the decay of solution viscosity (reflecting macromolecular conformational change) are characterized by the same constant value of k. In 83% formamide, 0.3M Na+, the rate parameter k for T2 DNA decreases from an extrapolated value of 2.0 min−1 at 0% denaturation to 0.11 min−1 at 90% denaturation. Rate parameters determined for T7 DNA at the same counterion concentration and fraction of denaturation are approximately five times as large as those cited for T2 DNA, indicating an inverse proportionality of rate constant to molecular length. On the other hand, simple first‐order kinetic responses with constant k are obtained for renaturing perturbations within the transition, indicating that the mechanism of rewinding differs, in most cases, from that of unwinding. Only in the limit of very small perturbations about a given equilibrium position are the rate constants k obtained from denaturing and renaturing perturbations equal. For perturbations of finite size, it appears possible that an intramolecular initiation or nucleation event may precede rewinding and limit the rate of this reaction. The rate parameters again are approximately inversely proportional to molecular weight. The one exception to the first‐power dependence on molecular weight appears when temperature jumps are made upward into the post‐transition region. Here the molecular‐weight dependence is second power, but complications arising from the different strand‐separation properties of T2 and T7 DNA's make interpretation difficult. The previously used model of friction‐limited unwinding appears to fit all the observations except for the molecular‐weight dependence.
On the kinetics of helix formation between complementary ribohomopolymes and deoxyribohomopolymers
Authors: Lee Cheng H. , Wetmur James G. 
Published: December 2004

AbstractThe rate of double helix formation by single‐stranded poly A plus poly dT, poly dA plus poly U, poly dA plus dT, poly G plus poly dC, poly dG plus poly C, and poly dG plus poly dC have been investigated and compared to rates of ribohomopolymer helix formation rates. After correction for molecular weight, comparisons of rate data at 30°C below the melting temperature of the double helix show that:

Rates of helix formation by all combinations of guanine plus cytosine homopolymers are the same.
The rate of helix formation for poly dA plus poly dT is three times faster than the rate for poly A plus poly U. Rates of formation of DNA‐RNA hybrid molecules are intermediate between these two rates, but closer to the poly dA plus poly dT rate.
The effect of temperature on the rate of helix formation is interpreted in terms of a steady‐state model for helix propagation. The results are consistent with a mechanism in which the formation of the second base pair is the rate‐determining step.
Extrinsic cotton effects of acridine orange bound to helical sodium desoxycholate
Authors: Zinner Klaus , Cilento Giuseppe 
Published: December 2004

AbstractAcridine orange bound to helical sodium desoxycholate polymers shows several Cotton effects which in some cases stongly resemble the ones seen with glycosaminoglycans. The dye molecules are probably bound to the outside core of the helix through electrostatic interactions. The strong Cotton effect in the 540‐nm region arises from dye‐dye interactions. Subtle factors, including shaking, affect CD and ORD spectra of these complexes.
Optical anisotropy of polypeptide chains
Authors: Ingwall R. T. , Flory P. J. 
Published: December 2004

AbstractOptical anisotropies γ2 of N‐t‐butylacetamide (tBA), N‐Methylacetamide (MA), and N, N‐dimethylacetamide (DMA) have been determined from the Rayleigh ratios for depolarzed scattering by dilute solutions of the amides in p‐dioxane. Traceless optical polarizability tensors \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for the amides are derived from these results in conjunction with the Kerr constant for tBA determined by LeGèvre and co‐workers. It is shown that the tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}i for the glycyle unit in a polypeptide chain may be identified with \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}MA. Methods for deriving corresponding tensors for other peptide units are indicated and the traceless polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for a polypeptide chain in any specified configuration is formulated.
Study of the interaction of polynucleotide chains with oligomers by means of chromatography
Authors: Bresler S. E. , Chernajenko V. M. , Saminski E. M. 
Published: December 2004

AbstractA new method of measurement of the binding constant of oligonucleotides with complementary polynucleotide chains was developed using a gel filtration procedure. Data for complexing of poly U with triplets ApApA are presented and analyzed by means of a simple statistical theory of cooperative adsorption deduced by the Bethe‐Guggenheim method. The complexes are triple, they contain two polymer chains bound by oligomers. The energy of stacking is found equal to 1300 cal/mol in fair agreement with earlier data of Ts'o. The energy of binding of a single triplet to both complementary chains is equal to 14,000 cal/mol.
Dielectric properties of polyelectrolytes. III. Effect of divalent cations on dielectric increment of polyacids
Authors: Minakata Akira 
Published: December 2004

AbstractDielectric dispersion of polyacrylic acid (PAA) and polystyrene sulfonic acid (PSS) was measured in the presence of divalent cations. Effects of divalent ions were studied by neutralization with varying ratios of sodium hydroxide and divalent base concentration, addition of salts of divalent cations, and neutralization with divalent bases only. Two dispersion regions were observed in all cases, i.e., low‐frequency dispersion (102–104 Hz) and high‐frequency dispersion (105–106 Hz). The dielectric increment increases in the presence of sodium and alkaline earth metal ions together, but not with sodium and transition metal ions. This is due to the increment of low‐frequency dispersion and is attributable to the fluctuation of bound counterions which is explained by our theory previously reported.1 In the case of PAA neutralized with large fractions of divalent ions, or with divalent ions only, the increment is very small because of reduction of the fluctuation by interaction between bound ions at the neighboring sites and reduction of the effective length of polyion probably due to chelation by divalent ions. There are some differences among the effects of Mg++, Ca++, and Ba++ on dielectric increment which may result from affinity or chelating ability of these ions.
Far‐infrared spectra of sequential copolymers of amino acids with alkyl group side chains
Authors: Itoh Koichi , Katabuchi Hiroaki 
Published: December 2004

AbstractFar‐infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L‐Ala‐L‐Ala‐Gly)n, (L‐Ala‐Gly)n, (L‐Ala‐Gly‐Gly)n, (L‐Val‐L‐Ala‐L‐Ala)n, and (L‐Val‐L‐Ala)n, have the antiparallel pleated sheet structures and that the backbone conformations of (L‐Val‐L‐Val‐L‐Ala)n and (L‐Val‐L‐Val‐Gly)n are the same as that of poly‐L‐valine. The far‐infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly‐L‐alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x‐ray powder‐diffraction patterns of these samples.
The hydrolysis of poly (L‐prolyl‐glycyl‐L‐prolyl) by bacterial collagenase
Authors: Harper Elvin , Berger Arieh , Katchalski Ephraim 
Published: December 2004

AbstractPoly (L‐Prolyl‐Glycyl‐L‐Prolyl), a polymer which resembles collagen by physical and immunochemical criteria, has been shown to serve as a substrate for the highly specific bacterial collagenase obtained from Clostridium histolyticum. The postulated reaction products Gly Pro, Gly Pro Pro, and Pro Gly Pro Pro have been isolated. The enzyme has been employed as an analytical tool in elucidating the sequence of synthesized polymers of proline and glycine.
Effect of non‐complementary nucleotides on the rate of helix formation: Kinetics of formation of poly (I)·poly (C,I) and poly (I)·poly (C,U) complexes
Authors: Kallenbach Neville R. , Drost Stanley D. 
Published: December 2004

AbstractApparent second‐order rate constants for complex formation between poly (I) and poly (C) and copolymers of C containing non‐complementary I or U residues have been determined spectrophotometrically. The rate constants decrease as the concentration of either I or U in the C strands increases–the effect seems insensitive to the species of residue involved, when differences in the thermal stabilities of the poly (I) poly (C,I) and poly (I). poly (C,U) complexes are taken into account. These results suggest that low concentrations of relatively stable defects can alter the apparent kinetic “complexity” of polynucleotides as determined by hybridization methods (C0t analysis).
Model connective tissue system: The effect of proteoglycan on the diffusional behavior of small non‐electrolytes and microions
Authors: Preston B. N. , Snowden J. Mck. 
Published: December 2004

AbstractThe diffusional behavior of low‐molecular‐weight solutes through gel membranes containing polyanionic material has been studied as a model for connective tissue. A steady‐state isotopic flux measurement is used. Results indicate that the presence of solutions of “native” proteoglycans within a gelatin‐agarose matrix has negligible effects on the diffusion of non‐electrolytes but markedly affects the behavior of ionic species. The permeabilities of counter‐and coions are discussed in terms of a Donnan equilibrium. It is evident that not all the counterions of the polyionic salt can be regarded as mobile in terms of the Donnan effect. The polyelectrolyte theories of Katchalsky et al. are applied to the behavior of the gel membranes to explain this observation. These quantitative interpretations suggest that counterion fixation by the proteoglycans occurs.
Criteria for the crystallization of polysaccharides
Authors: Atkins E. D. T. , Wills H. H. , Mackie W. 
Published: December 2004

AbstractThe relationship between crystallization and the annealing process is well established in the synthetic polymer field. This relationship appears to have been somewhat neglected in studies on biopolymers. Results are presented to show the effect of both humidity and temperature in promoting structural changes in polysaccharide system. Three different polysaccharides have been used as examples of how crystallization may be speeded up by annealing at elevated temperatures.
Solution properties of synthetic polypeptides. XII. Enthalpy changes accompanying helix‐coil transition of polypeptide
Authors: Teramoto Akio , Norisuye Takashi 
Published: December 2004

AbstractFor helix‐coil transitions of polypeptide in binary mixtures consisting of helix‐forming solvent and coil solvent, the transition enthalpy ΔH(T,x) has been found to depend significantly on temperature (T) and solvent composition (x). For such systems, calorimetric measurements may yield some averages of ΔH(T,x) which are no longer amenable to direct comparison with ΔH itself. Theoretical equations relating calorimetric data to ΔH(T,x) are derived and tested favorably with experimental data. It is demonstrated that the transition enthaply from heat capacity measurements is approximately equal to ΔHcfm, while those from heat of dilution and heat of solution measurements are equal to ΔHc. Here ΔHc denotes the value of ΔH at the transition point and fm represents the maximum helical content attained in a thermally induced transition. The discrepancies among calorimetric data are also discussed.
Conformational studies on copolymers of L‐leusine and L‐leucine: Circular dichroism and potentiometric titration studies
Authors: Snell Christopher R. , Fasman Gerald D. 
Published: December 2004

AbstractConformational aspects of a series of copolymers of L‐Leucine and L‐leucine [poly‐(LysxLeuy)] containing 0 to 0.41 mole fraction L‐leucine have been studied by circular dichroism (CD) and potentiometric titration in 0.05M KF solution. CD studies on the α‐helical conformation showed a dependence of the magnitude of the CD ellipticity band at 222 nm on copolymer composition; the [θ]222 decreasing with higher leucine contents. This was interpreted as the result of an increase of the hydrophobicity of the environment of the amide group due to the presence of the leucyl residues. Values of the Zimm‐Rice parameter, σ, for the copolymers were obtained from the potentiometric titrations and used to fit theoretical curves to the experimental data. Using the variation of σ with polymer composition, a value of σ for the leucyl residue was estimated to be 6.3 × 10−2, assuming independence of σ on the amino acid sequence in the copolymer. The free energy change for the conversion of one mole residue from uncharged helix to uncharged coil, ΔGhc°, was also obtained from the titration data for each copolymer up to a leucine mole fraction of 0.16; a value of 385 cal mole−1 was estimated for ΔGhc° for a leucyl residue. These values for σ and ΔGhc° are compared with other values in the literature for various amino acid residues obtained from titration and melting curve data.
Coformational aspects of polypeptide structure XL. The synthesis of poly[(S)‐thiazolidine‐4‐carboxylic acid]
Authors: Goodman Murray , Su Kai‐Chiang 
Published: December 2004

AbstractThe synthesis of poly[(S)‐thiazolidine‐4‐carboxylic acid] is described. The polymer is obtained by the polymerization of the N‐carboxyanhydride of (S)‐thiazolidine‐4‐carboxylic acid in pyridine or nitrobenzene using triethylamine as an initiator. The amino acid is prepared by the condensation of cysteine and formaldehyde. N‐Acetyl‐(S)‐thiazolidine‐4‐carboxylic acid methyl ester is also prepared as a model compound by standard acetylation and esterification reactions.
Non‐empirical valence bond calculation of hydrogen bond energy in polypeptides
Authors: Takashima Shiro 
Published: December 2004

AbstractAn approximate ab‐initio valence bond calculation of hydrogen bond energy was carried out and the results are discussed. The total bond energy of a simplified NH…O structure is calculated for various NH and N…O distances and the potential energy profiles are obtained. The hydrogen bond energy, ie, the delocalization energy gained by the formation of one hydrogen bond is found to be 8.7–12.0 kcal/mole. The potential energy is characterized by a deep minimum at 1.6–1.8 a.u. from the nitrogen and the second trough is found to be considerably higher than the first.
High shear rate viscosity measurements with dilute solutions of bovine fibrinogen
Authors: Lederer Klaus , Schurz Josef 
Published: December 2004

AbstractViscosity measurements at a rate of shear between 104 and 5 X 105 sec−1 were carried out with solutions of bovine fibrinogen (c = 8.0–18.4 mg/ml). The degree of anisotropy of the fibrinogen molecule estimated from the data is less than expected for Hall and Slayter's molecular model of fibrinogen. A tentative interpretation is offered in terms of Köppel's model of fibrinogen.
Comparison of the UV flow dichroism spectra of TMV and several of its mutants
Authors: Gabler Raymond , Bendet Irwin 
Published: December 2004

AbstractThe dichroic ratio spectra of TMV and four of its mutants (YTAMV, GTAMV, HR, and CV4) were determined from 320 to 240 nm. Measurements were also made on particles of ATMV (TMV protein reconstituted with polyadenylic acid) and rods of repolymerized TMV, YTAMV and GTAMV protein, respectively. These cylindrical molecules were oriented in a flow gradient with their degree of orientation being determined from anisotropic light scattering measurements. Taking length distributions into account, the dichroic ratios were then extrapolated to values characteristic of perfect particle alignment.Due to the large number of overlapping absorbing bands in the whole viruses, it is very difficult to separate out specific contributions to the total spectra. Since, however, the spectra for the whole viruses were similar, this would suggest an overall likeness in structure for all the virus particles studied. Because the repolymerized proteins did not have the four RNA chromophoric groups present, their spectra would be more sensitive to protein contributions to the total spectrum. Repolymerized rods of YTAMVP yielded results similar to those for TMVP, while the spectrum for repolymerized rods of GTAMVP was significantly different from that obtained for TMVP.Dichroic ratio spectra of the nucleic acids, as they exist within the whole particles, were also calculated by subtracting protein absorptivities from their respective viral absorptivities. The spectra indicates similar results for the various nucleic acids in all the particles studied.
The Circular Dichroism of Complexes of 2,7‐Di‐tertiary‐Butyl Proflavine with DNA
Authors: Dalgleish D. G. , Feil M. C. , Peacocke A. R. 
Published: December 2004

AbstractThe binding isotherm of 2, 7‐di‐tert‐butyl proflavine on calf thymus DNA has been measured by dialysis equilibrium. The CD spectra of complexes of the dye and DNA have been measured, and the variation of the induced circular dichroism of the dye with the amount of dye bound (r) has been found. The results show that di‐tert‐butyl proflavine binds to DNA in a completely different manner from proflavine itself, since both the visible and ultraviolet CD spectra of complexes of the two dyes with DNA differ markedly. The conformation of the nucleic acid is not affected by the binding of di‐tert‐butyl proflavine. It is possible that these results may allow determination, by using CD spectroscopy, of whether molecules intercalate into DNA.
Raman studies of nucleic acids. VII. Poly A · poly U and poly G · Poly C
Authors: Lafleur L. , Rice J. , Thomas G. J. 
Published: December 2004

AbstractLaser‐excited Raman spectra of the double‐helical complexes poly A·poly U and poly G·poly C are reported for 2H2O and H2O solutions. The spectra are discussed in relation to their use as quantitative reference spectra for determining the dependence of the Raman scattering of RNA on secondary structure. The Raman line at 815 cm−1, due to the phosphodiester group, exhibits the same intrinsic intensity in spectra of poly A·poly U and poly G·poly C and is thus dependent only upon the amount of ordering of the helix and not on the kinds of nucleotides involved. The hypochromic Raman lines in spectra of poly A·poly U are identified and their intensity changes are determined quantitatively over the temperature range 32–85°C. Comparison of the spectra in the 1500–1750 cm−1 region reveals that the Raman lines from carbonyl group vibrations of uracil are about sevenfold more intense than those of guanine and cytosine for both paired and unpaired states and will thus dominate the spectra of RNA. The Raman frequencies in this region are also compared with previously reported infrared frequencies and give evidence of being strongly perturbed by base‐stacking interactions in the helices.
Side chain interactions in aromatic dipeptides
Authors: Deber Charles M. , Joshua Henry 
Published: December 2004

AbstractA study of the 100‐MHZ nuclear magnetic resonace spectra in D2O solution was made of a series of linear dipeptides of the types L‐phenylalanine‐L‐and‐D‐X, and L‐phenylalanine‐L‐and‐D‐Y, where X comprised a group of amino acid residues with polar side chains (X = glutamine, glutamic acid, arginine, and Nε‐acetyllysine) and Y comprised amino acid residues with purely aliphatic side chains (Y = α‐aminobutyric acid and norvaline). It was found that regardless of the side chain length, resonances due to the α‐methylene protons in the X and Y side chains of the L‐Phe‐D‐Y series consistently exhibited upfield shifts greater than any other protons in these side chains, when compared to the corresponding side chain resonances of the nonaromatic dipeptide series L‐Ala‐L‐X and L‐Ala‐L‐Y. The magnitudes of these shielding effects were consistently and considerably greater for the L‐Phe‐D‐X series than for the L‐Phe‐D‐Y series. An intramolecular complex–formed by association of armatic π‐electrons with the positive end of the dipole in the polar side chains—was proposed as one plausible interpretation of the enhanced shielding effects. An increase in temperature from 32 to 70–80° was sufficient to overcome the enhanced shielding attributable to the suggested complex.
Adsorption of single‐stranded and double‐helical polynucleotides on the mercury electrode
Authors: Brabec V. , Paleček E. 
Published: December 2004

AbstractThe adsorption of single‐stranded polynucleotides and double‐helical DNA on the dropping mercury electrode has been studied with the aid of Breyer's alternating current (a.c.) polarography. Our results indicate that all three constituents of polynucleotides (residues of bases, sugar, and phosphoric acid) are involved in the adsorption. At neutral pH their participation in adsorption depends on the ionic strength, the potential of the electrode, and the conformation of the polynucleotide in the solution.At an ionic strength of about 0.1, double‐helical DNA is adsorbed electrostatically on a positively charged electrode surface by inadequately masked negative charges of the phosphate groups. At a higher ionic srength (about 0.5), this electrostatic adsorption is no longer detectable by using a.c. polarography; under these conditions it is probable that native DNA is adsorbed around the potential of the electrocapillary maximum with the aid of sugar residues and a few bases. Single‐stranded polynucleotides, on the other hand, are primarily adsorbed by means of the bases.Desorption of double‐helical DNA occurs around a potential of −1.2 V against SCE. At this potential, the helical regions of single‐stranded polynucleotides are also desorbed. Desorption of the disordered regions of single‐stranded polynucleotides occurs at more negative potentials. Adsorption and desorption of a small number of bases released from double‐helical DNA was evident in the a.c. polarograms only at elevated temperature, or at room temperature after degradation of DNA by sonication.