bluuebunny/crossref_metadata_2025 huggingface dataset:
The conversion of two‐stranded poly (A + U) to, three‐strand poly (A + 2U) and poly A by heat
Authors: Stevens Charles L. , Felsenfeld Gary
Published: December 2004

It is shown that the formation of the three‐strand poly (A + 2U) complex is accompanied by a decrease in optical absorbance at 280 mμ, while the format ion of poly (A + U) is not. This difference makes it possible to demonstrate that in dilute solutions (∼10−4 monomolar), a 1 : 1 mixture of poly A and poly U always forms poly (A + U) at room temperature. At higher temperatures in solutions containing more than about 0.2M sodium ion, poly (A + U) is converted to poly (A + 2U) and free poly A. These results are consistent with the observations reported by Miles and Frazier, using infrared absorption spectra, at much higher polymer concentrations. It is concluded that most of the physicochemical studies of 1 : 1 mixtures of poly A and poly U in dilute aqueous solution refer to the two‐stranded species.

A simple thermodynamic analysis is developed to explain the two‐ to three‐strand conversion, and with the use of a “phase diagram” showing conditions of stability of the various poly A–poly U structures as a function of salt and temperature, it is possible to estimate the value of the enthalpy of formation of poly (A + 2U).
A physical study of the degradation of periodate–oxidized amylose
Authors: Erlander Stig R. , Griffin H. L. , Senti F. R.
Published: December 2004

Changes in the viscosity of amylose that had been oxidized In an aqueous medium at pH 3.0 by sodium metaperiodate were followed as a function of time. Levels of 20, 40, 60, 80, and 100% periodate oxidation were attained. The rate of hydroxyl ion cleavage of the periodate oxidized amylose [(d1/[η]2)/dt = k] is proportional to the square of the degree of oxidation. That is, the hydroxyl ion hydrolysis of periodate oxyamylose occurs predominately at the site where two or more oxidized units exist side by side. A reaction mechanism is postulated to account for this slow breakdown of an isolated oxidized unit and for the fast degradation of two adjacent oxidized glucose; units. When two or more oxidized units exist side by side, the free aldehyde at carbon atom 3 is believed to be in equilibrium with a hydrate instead of a hemiacetal structure as in the case of a single, isolated, oxyglucose unit in amylose. The greater reversibility of the hydrate to the free aldehyde structure results in a greater possibility of β‐alkoxycarbonyl elimination at sites where two or more oxidized glucose units exist side by side.
A polynucleotide helix containing polinosinic acid and protoated polycytidylic acid
Authors: Giannoni Giovanni , Rich Alexander
Published: December 2004

Titration studies of the 1 : 1 helical polynucleotide complex of polyinosinic acid and polycytidylic acid reveal that these two polymers form a complex when the polycytidylic acid is protonated near pH 3. Sedimentation studies show that the protonated complex also has a 1 : 1 stoichiometry. However, the protonated complex is more stable than the unprotonated neutral complex as judged by its thermal stability. The molecular structure of the protonated complex is not the same as the neutral form. Study of the kinetics of the reaction of the protonated complex with formaldehyde suggests that the amino group of cytosine is involved in hydrogen bonds which hold the polynucleotide strands together.
The dynamics of the helix‐coil transition in poly‐α, L‐glutamic acid
Authors: Lumry R. , Legare R. , Miller W. G.
Published: December 2004

Temperature jump measurements employing optical rotation to follow transients show an upper limit of 10μsec. on the half time of the helix‐random coil relaxation in poly‐α, L‐glutamic acid. No relaxations are observed under conditions where the polymer exists in completely helical or completely random coil form. Assuming that the helix‐coil transition can be described kinetically as a pure growth process, expressions for the relaxation time are derived for three special cases. A comparison is made between the rate of the helix‐coil transition and the rate of imide proton exchange.
Statistical mechanics of noncovalent bonds in polyamino acids. IX. The two‐state theory of protein denaturation
Authors: Poland Douglas C. , Scheraga Harold A.
Published: December 2004

The two‐state theory of protein denaturation, in which it is assumed that a protein exists as two species, native and denatured, is examined by three approaches in this paper. First, the point is made that denaturation of an isolated molecule involves a continuous shift in the probabilities of occurrence of many states generated by the partition function for the protein. It is argued that the maximum term approximation does not lead to a two‐state mechanism of denaturation, and that the extent of cooperation implied by the two‐state theory should give very much sharper transitions than are actually found in proteins. Second, the two‐state theory is applied to the various model systems treated in this series of papers, and is found to be inadequate. Since the detailed behaviour of the models is known, it is possible to deduce the effect of the incorrect application of the two‐state theory to a system that “denatures” by gradual unwinding. This exercise is useful when, thirdly, we examine experimental data that seem to depart radically from a two‐state interpretation. We conclude that a mechanism of gradual unwinding is the most generally valid assumption, and that the two‐state theory has no theoretical or experimental support.
Interaction between proteins and salt solutions. I. Thermodynamic parameters of dilution for gelatin and collagen
Authors: Rajagh L. V. , Puett D. , Ciferri A.
Published: December 2004

Intrinsic viscosity–temperature studies for isoelectric gelatin in KCl and KSCN aqueous solutions and equilibrium degree of swelling, ν−1, measurements for amorphous crosslinked rat tail tendons in the same solutions were carried out. On increasing salt concentration Cs, both [η] and ν−1 increase, go through a maximum, and then decrease at high Cs, KCl being more effective than KSCN in bringing about this decrease. The trend observed is similar to the variation of solubility of polypeptides and soluble proteins with Cs. By regarding a water–salt solution of a given Cs as a single diluent interacting with the protein modified by solvation and binding of ions, usual polymer solution theories were applied to the experimental results. Thus, quantities related to the entropy and enthalpy components of the excess chemical potential of the diluents were obtained. The data indicate that the initial increase of [η] and ν−1 with Cs results from the balance of an enthalpy component which, on increasing Cs, becomes less favorable to dilution and an entropy component which, conversely, becomes more favorable. The subsequent decrease of [η] and ν−1 with Cs is due to the prevailing of the enthalpy component. The maximum is reached at higher Cs for KSCN than for KCl, primarily because of the large increase in the entropy component operated by the former salt. The increase of the entropy parameter with Cs is associated to a breaking down of the coordinated water structure and to an alteration of the conformation of the macro molecules due to ion–dipole interaction and to ion absorption. The decrease in exothermicity of dilution with Cs indicates a reduced thermodynamic affinity of the diluent toward the polymer which probably results from alteration of the nature of both polymer and diluent.
Influence of counterion radius on the polyelectrolyte behavior of synthetic polypeptide solutions
Authors: Botré C. , Solinas M. , Ascoli F.
Published: December 2004

The influence of counterion radius on the polyelectrolyte behavior of poly‐L‐cysteate in aqueous solution under different conditions was investigated. A linear relationship was found between a critical concentration in solution of the synthetic charged poly‐peptide and the crystallographic radius of different counterions, indicating that the stability of this macromolecule is inversely proportional to the size of the cations.
Rendement quantique, temps de vie de fluorescence et heterogeneité des sites de fixation de la proflavine sur le DNA
Authors: Weill G.
Published: December 2004

The binding of Acridine Orange (AO) to DNA at a phosphorus:dye molar ratio higher than 60 results in an increase of the quantum yield of fluorescence of the bound dye with respect to the free dye. The binding of proflavine (Pro) under the same conditions results, on the contrary, in a large decrease of quantum yield. This difference is surprising in view of the common increase of quantum yield of Acridine Orange and proflavine on going from aqueous to glycerol solution, the latter being a solvent with higher viscosity and lower dielectric constant. A comparative study of the spectra, lifetime of fluorescence τ, and quantum yield of fluorescence ϕ of the free and bound dye can shed light on this specific interaction and discriminate between a uniform exaltation or quenching of the dye molecules and a heterogeneity in the binding sites. For AO, the ratio τ/ϕτ0, where τ0 is the “natural” lifetime calculated from absorption spectra, remains constant for free and bound dye, a test for uniform exaltation. For proflavine, τ remains constant (4.4 ± 0.4 × 10−9 sec.), while ϕ drops from 0.7 to 0.23. This result shows that two molecules out of three are bound on a site producing almost complete quenching while the third exhibits “normal” fluorescence, comparable to that of the free dye. It is suggested that intercalation between two adenine thymine base pairs could account for the quenching. Fluorescence techniques would be valuable to study the equilibrium between the binding sites as a function of ionic strength and DNA base composition. By taking advantage of the accuracy of the lifetime determination by a photon‐sampling technique, comparison of τ for direct and sensitized excitation of fluorescence of the bound dye has been performed. No difference has been observed, which indicates a transfer time faster than 0.1 × 10−9 sec., a result in agreement with singlet singlet transfer and with the very low quantum yield of fluorescence of DNA alone at room temperature.
Effect of temperature on the spin‐lattice relaxation times of aqueous solutions of ribonuclease and human serum albumin
Authors: Blears D. J. , Danyluk S. S.
Published: December 2004

Aqueous solutions of ribonuclease and human serum albumin were subjected to periods of controlled heating and the nuclear magnetic spin‐lattice relaxation times, T1, of the water protons measured. The heat treatment causes an initial increase in the relaxation times of the water protons. These T1 variations indicate that a configurational change, compatible with a disordering of the protein structure occurs, which involves an increase in various modes of internal mobility. The T1 measurements also indicate a close, ordered association of the water molecules and the protein.
Spectrophotometric, potentiometric, and density gradient ultracentrifugation studies of the binding of silver ion by DNA
Authors: Jensen Ronald H. , Davidson Norman
Published: December 2004

The 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

The 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

The 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

Poly‐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

Measurements 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

Studies 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

Studies 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

The 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

By 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

The 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

A 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

The 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).2,3

In 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

Poly‐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

The 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

The 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

Single 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

The 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

The 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

In 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

The 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

A 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

The 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.
Denaturation of RNA with dimethyl sulfoxide
Authors: Strauss James H. , Kelly Regis B. , Sinsheimer Robert L.
Published: December 2004

The denaturation of single‐stranded and double‐stranded RNA's in solutions with varying proportions of dimethyl sulfoxide has been followed by changes in absorbancy, optical rotation, and—with a double‐stranded form of bacteriophage of MS2 RNA— infectivity for bacterial spheroplasts. By these criteria the RNA's studied, including the synthetic polynucleotide rG:rC, are completely denatured at room temperature in high concentrations of this solvent. In lower concentrations, the Tm of the RNA preparation is decreased only slightly as the dimethyl sulfoxide concentration is raised until a critical concentration is reached. The Tm falls sharply with small further increases in dimethyl sulfoxide concentration. Sedimentation studies can be conducted directly in these media. The determination of sedimentation velocity in 99% dimethyl sulfoxide containing 0.001M EDTA provides a reliable estimate of RNA molecular weights.
Conformational aspects of polypeptides. XXV. Solvent and temperature effects on the conformations of copolymers of benzyl and methyl L‐aspartate with nitrobenzyl L‐aspartate
Authors: Toniolo Claudio , Falxa Martin L. , Goodman Murray
Published: December 2004

A series of copolymers of β‐p‐nitrobenzyl L‐aspartate with β‐benzyl L‐aspartate and with β‐mcthyl L‐aspartatc in helix‐supporting and helix‐breaking conditions have been reexamined by using ultraviolet isotropic, absorption, optical rotatory dispersion, and circular dichroism techniques. Many different conformations are apparent, depending on solvent and temperature. Chloroform, trifluoroethanol, and methylene dichloride support the left‐handed helical conformation of the copolymers containing less than about 20 mole‐% nitroaromatic residues and the right‐handed helical conformation of the copolymers containing more than approximately 30 mole‐% nitroaromatic residues. In trifluoroacetic acid all the copolymers are in a random‐coil conformation. In hexa‐fluoroacetone trihydrate and in trimethyl phosphate, the copolypeptides with low nitroaromatic residues content are predominantly in a disordered conformation, while those with high nitroaromatic residues content show a right‐handed helical array. Reversible helix‐ramlom‐coil transitions are observed with increasing temperature in trimethyl phosphate. An example of right‐handed‐left‐handed helix reversible transition with temperature is reported in a chloroform‐trimethyl phosphate (2:1) mixture. Nitrobenzyl‐nilrobenzyl side‐chain interactions in chloroform, but not in trifluoroacetic acid or in trimethyl phosphate, have been confirmed. For the first time we report the circular dichroism spectra in which the n‐π* peptide band of a left‐handed helical conformation is almost completely evident.
Interaction between parallel rodlike macroions
Authors: Oosawa Fumio
Published: December 2004

This paper gives a very simple method based on the characteristic property of the electric free energy to calculate the repulsive force between parallel rodlike macroions in a solution as a function of the charge density on rods. The total extensive force (∂f/∂X) of an assembly of m rods of length l and charge number n (charge density − neo /l) at small extension X in the absence of low molecular sals is given by
magnified image
where z is the valency of counterions and Q (= neO2/εkTl) is a dimensionless quantity representing the charge density. The repulsion between two parallel rods is given by putting m = 2. At large charge densities the repulsion is very much smaller than the direct coulomb force between charged rods, even at small distances. The addition of low molecular salts does not depress the repulsion appreciably, as long as the average concentration of salt ions is much smaller than the concentration of counterions accumulated in the space between rods. The effect of fluctuation of the coumerion distribution is also analyzed, and it is found that the attractive force due to the ion fluctuation may predominate over the above repulsive force in the case of polyvalent counterions and rods of high charge densities at small distances.
Conformational studies of proteins with aromatic side‐chain effects
Authors: Goodman Murray , Toniolo Claudio
Published: December 2004

We present here a brief analysis of ultraviolet isotropic absorption and related circular dichroism of the n–π* and π–π* transitions for the peptide (amide) chromophore in the 185–240 mμ region. Investigations by ultraviolet absorption and circular dichroism techniques on natural amino acids with aromatic chromophores in their side chains are also reported. By taking into account both the peptide and aromatic transitions we discuss the conformational studies of proteins with aromatic side‐chain effects. Our attention is largely focused on the optical rotatory dispersion and circular dichroism spectra of these proteins in the near ultraviolet region, where characteristic aromatic side‐chain bands occur. The 185–240 mμ region is also discussed when evidence exists of overlapping Cotton effects of aromatic and peptide groups.
Dielectric properties of oxyhemoglobin and deoxyhemoglobin in aqueous solution at microwave frequencies
Authors: Von Casimir W. , Kaiser N. , Keilmann F. , Mayer A. , Vogel H.
Published: December 2004

The complex dielectric constant of aqueous hemoglobin solution was measured at 9.5 GHz. A microwave technique allowing phase and attenuation settings with an accuracy of 0.3° and 0.03 db was used. The shift of the relaxation wavelength and the hydration values of horse hemoglobin were determined for native and lyophilized hemoglobin solution and erythrocytes suspensions as well. The isotope effect of light and heavy water on these parameters was detected. The influence of buffers was studied. Relative measurements, with the sensitivity increased by a factor of 20, were made with alternating oxygenated and deoxygenated human hemoglobin solutions. The oxygenation of hemoglobin was found to leave the hydrated molecule volume invariant within ±250 Å3, while a shift of the relaxation wavelength of 0.0025 ± 0.0015 cm occurs for a hemoglobin concentration of 107 g/l. The results are discussed in terms of the structure and function interrelationship of hemoglobin and the current picture of water structure.
Effect of oxygen binding on the dielectric properties of hemoglobin
Authors: Schlecht Peter , Vogel Helmut , Mayer Adalbert
Published: December 2004

The dielectric properties of horse hemoglobin have been investigated in the frequency range for 100 kcps to 15 Mcps at varying degrees of oxygenation. A linear dependence of the specific increment on the degree of oxygenation was found under a variety of experimental conditions, the increment of oxygenated hemoglobin being about 10% larger than that of deoxygenated hemoglobin. A similar difference was obtained with human adult and fetal hemoglobin. No variation of the dielectric parameters as reported by Takashima and Lumry could be detected.
Broadening by acridine orange of the thermal transition of DNA
Authors: Stewart Charles R.
Published: December 2004

Acridine Orange, at appropriate intermediate concentrations, causes a substantial broadening of the thermal transitions of Bacillus subtilis DNA and of dAT. Experiments in which the two polymers are healed together show that the broadening is the result of the transfer of acridine orange molecules from denatured to native DNA molecules.
Oligonucleotide interactions. I. Structure of 2 : 1 complexes between polyuridylic acid and oligoadenylic acid
Authors: Cantor Charles R. , Chin William W.
Published: December 2004

The circular dichroism of a number of 1:2 complexes between oligoadenylic acid and polyuridylic acid has been measured. The structure of these complexes, as evidenced by their optical properties, is independent of the chain length of the oligonucleotide throughout all ranges of chain lengths from adenosine to high molecular weight polyadenylic acid. A similar structure was found for the complex (Ap)5A:2(Up)5U.
Physico‐chemical description of a condensed form of DNA
Authors: Dore E. , Frontali C. , Gratton E.
Published: December 2004

When exposed to a low pH, in various ionic strength conditions and in sufficiently dilute solutions, DNA undergoes a transition, revealed by an increase in optical density. A careful analysis shows that, associated with this transition, there is an effective decrease in absorbance, overcompensated by an increase in scattering. The conditions for the new transition can be summarized conveniently by a graph in a pH–Na+ molarity diagram. If the pH of a DNA solution is progressively lowered at constant Na+ concentration, one finds first the melting transition (I), and at lower pH values, the new transition (II). If the same experiment is performed on pre‐denatured DNA, only transition II will be found. If native DNA is brought directly to the low pH conditions, without allowing it to denature irreversibly at intermediate pH values, transition II is reversible (with a small hysteresis effect). DNA, initially native, neutralized after prolonged exposures to the low pH, recovers the buoyant density value of native DNA, along with the absorption and scattering properties of the native state. The experiments are consistent with the interpretation that a new state exists in which DNA, still double stranded, assumes a very compact shape (of the order of 1500 Å in diameter for T2 DNA), with a hyperchromicity value of 10–14% above the native value. Nearly monodisperse suspensions of DNA molecule in this apparent state may be obtained only at very low concentrations (∼0.25 μg/ml). At 1 μg DNA/ml aggregation is noticeable. The possible connection with the condition of intraphage DNA is discussed.
The β‐conformation and association of low‐molecular‐weight poly‐γ‐benzyl‐L‐glutamate in Solutions
Authors: Ikeda Shoichi , Imae Toyoko
Published: December 2004

Three samples of poly‐γ‐benzyl‐L‐glutamate have been prepared from γ‐benzyl‐N‐carboxy‐L‐glutamate anhydride with n‐hexylamine initiation at anhydride‐to‐initiator molar ratios, [A]/[I], of 3, 4, and 8, and their conformation and association in ethylene dichloride and dioxane have been investigated by means of infrared spectra and vapor‐pressure osmometry. Two conformations, σ‐and β‐forms, are present in those solvents, and the content of β‐form increases with increasing A/I value and concentration. At infinite dilution molecular association is absent, but the number‐average molecular weight increases with cocentration, markedly in ethylene dichloride and, to a lesser extent, in dioxane. The fraction of residues involved in associated molecules have been estimated as a function of concentration. Combination of the content of β‐structure with the fraction of association leads to the following results. The A/I 3 and 4 polymers form intermolecularly hydrogen‐bonded aggregates, in which hydrogen‐bonded residues are in the β‐structure. The A/I 8 polymer has the intramolecularly hydrogen‐bonded β‐structure at very low concentrations, but it also forms intermolecularly hydrogen‐bonded aggregates at high concentrations.
Electric birefringence and dichroism of acridine orange and methylene blue complexes with polynucleotides
Authors: Bradley D. F. , stellwagen N. C. , O'konski C. T. , Paulson C. M.
Published: December 2004

Electro‐optic measurements are reported for the polynucleotides poly A, poly U, poly G, and NaDNA, and their complexes with acridine orange (AO). Measurements were also made on the methylene blue (MB) complex with NaDNA. Poly U, poly G, and NaDNA complexes with AO as well as the NaDNA–MB complex were found to exhibit positive birefringence and perpendicular dichroism indicating the dye molecules are oriented with their long axes perpendicular to the applied electric field. The opposite was found for the AO complex with poly A, which showed positive birefringence and parallel dichroism, indicating that in this case the dye molecules are oriented with their long axes parallel to the field.
The helix–coil transitions of poly (dA). Poly (dT) and poly (dA‐dT). Poly (dA‐dT)
Authors: Wartell Roger M.
Published: December 2004

Helix–coil transition curves are calculated for poly (dA) poly(dT) and poly (dA‐dT) poly (dA‐dT) using the integral equation approach of Goel and Montroll.5 The transitions are described by the loop entropy model with the exponent of the loop entropy factor, k, remaining an arbitrary constant. The theoretical calculations are compared with experimental transition curves of the two polymers. Results indicate that the stacking energies for these two polymers differ by about 1 kcal/mole of base pairs. Also, a fit between theory and experiment was not possible for k > 1.70.
Circular dichroism of DNA: Temperature and salt dependence
Authors: Studdert David S. , Patroni Maria , Davis Robert C.
Published: December 2004

The temperature dependence of the circular dichroism and ultraviolet absorbance of calf thymus DNA and poly dAT were measured in aqueous solutions of various 1–1 electrolytes. Although there was very little change in absorbance, the circular dichroism changed dramatically as a function of both temperature and solvent. There is a correlation of the heat of hydration of the cation and the magnitude of the temperature dependence of the circular dichroism. Our results are interpreted in terms of a large number (possibly a continuum) of intermediate secondary structures.