bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physicochemical properties of N4 virus solutions. I. Viscosity–temperature behavior
Authors: Rialdi Giovanni , Profumo Pietro , Ciferri Alberto 
Published: December 2004

AbstractThe viscosity–temperature behavior of N4 virus solution was investigated by using a Zimm type viscometer. The role of ionic strength (LiBr) and pH in the viscosity–temperature behavior was determined. Supporting measurements of the sedimentation coefficient, infectivity, and optical density are presented. The viscosity–temperature behavior generally includes a region of low viscosity, characteristic of the intact virus, followed, upon increasing temperature, by a rather abrupt increase of viscosity which corresponds to the ejection of native DNA from the protein shell, presumably through a suitable opening in the capside. The viscosity remains constant upon further increase of temperature until a second abrupt increase is observed which is shown to correspond to the degradation of the empty protein shell (ghost). Finally, at a still higher temperature, denaturation of DNA occurs. This sequence of events can be altered by changes in pH and ionic strength. Increasing LiBr concentration reduces the temperature of ghost degradation and raises the temperature of DNA ejection and DNA de naturation. It is suggested that polyelectrolyte effects play a controlling role in the ejection of native DNA and that the conformation of the latter within the protein shell is stabilized by a decrease of the electrostatic free energy due to the swamping effect of the co‐ions.
Extraction, separation and labeling with 14C‐glucose of hela cell polyglucose, RNA and DNA and comparison of the molecular weights and buoyant densities of polyglucose from poliovirus‐infected and noninfected cultures
Authors: Graves I. L. 
Published: December 2004

AbstractThe aqueous phase of phenol extracts of HeLa cells contains polyglucose (CHO)n, RNA, and DNA. These macromolecules were precipitated together and removed from 50% (v/v) ethanol solutions with a stirring rod. The viscous precipitate had the classical white appearance of DNA, but contained an average of 439, 670, and 220 μg (from 3 × 107 cells) of (CHO)n, RNA, and DNA, respectively. The (CHO)n was separated from the RNA, either by CsCl density gradient centrifugation or by precipitating the RNA with trichloroacetic acid (TCA). Both methods of separation resulted in preparations of (CHO)n with similar specific activities (radioactive counts/μg min). However, electron micrographs showed that the (CHO)n separated by using TCA had a greater variation in particle size when compared with (CHO)n separated by CsCl centrifugation. With the CsCl methods, the number‐average molecular weights, as determined by electron microscope particle‐counting, and the buoyant densities of (CHO)n whose synthesis was stimulated by poliovirus infection and (CHO)n from noninfected cultures, were found to be similar. When the (CHO)n was extracted from HeLa cells with TCA, rather than phenol, the yield was 1.68‐fold greater and its specific activity was an average of twice that of the (CHO)n extracted with phenol. The time at which cells were pulse‐labeled with 14C‐glucose, after reducing the glucose in the culture medium to 0.01 of normal, was found to be important, in that the specific activity of the (CHO)n increased 23.4‐fold over a 4‐hr period and the amount extracted decreased 8.2‐fold. The increase in the specific activities of RNA and DNA was not as large as that of the (CHO)n and the amounts extracted were not significantly changed. The sedimentation coefficients of RNA and (CHO)n which were separated from each other with TCA were 6.4 and 116 S, respectively, whereas, without separation, two peaks were seen, with values of 25.4 and 31.4 S. Chloride ions reduce the sensitivity of the Burton test for DNA. However, the Burton reagent will detect (CHO)n even in the presence of DNA if the assay mixture is heated. Chloride ions increase the sensitivity of the Burton reagent to detect melizitose and, at concentrations above l.5M, synthetic‐ polyglucose by increasing the absorption of the colored (CHO)n reaction product(s).
Circular dichroism of acridine orange bound to DNA
Authors: Zama M. , Ichimura S. 
Published: December 2004

AbstractThe circular dichroism (CD) spectra of DNA–acridine orange (DNA–AO) complex in the visible region were measured at DNA phosphate‐to‐dye ratios (P/D) from 1 to 550. The CD spectrum of DNA–AO complex in the P/D ratio between 1 and approximately 40 consists of four components, i.e., positive CD bands centered at 510 and 480 mμ, and negative CD bands at 497 and 468 mμ. The CD bands at 510 and 468 mμ are optimum at P/D = 4, and the change of ε1 − εr with P/D suggests that both of them are induced from the interaction between dye molecules bound to adjacent DNA binding sites, each of which is composed of four nucleotides. This is supported by the fact that the values of ε1 − εr for both decrease with increasing temperature or increasing methylene blue concentration added to the complex. The negative Cotton effect at, 497 mμ is most favored at larger P/D ratio (∼8), and the suggested assignment is to the interaction between two dye molecules bound with an empty site between them. A positive Cotton effect at 480 mμ is observed at P/D ratio of less than 4 and is optimum at 1. Above P/D ratio of 40, the CD spectrum of the complex can not be resolved into its components and even at sufficiently high P/D ratio (550) the complex shows a small Cotton effect.
Kinetic equations for surface adsorption
Authors: Nossal Ralph , Ninham Barry 
Published: December 2004

AbstractWe investigate the time‐dependent solution of a set of equations used to approximate the binding of flexible polymers to the surface of suspended targets. The equations account, for the possibility that the first adsorption step can be a rate limiting step. Rate constants for other steps of adsorption and desorption are proportional to the number of free and occupied polymer binding sites, respectively.
Measurement of flow birefringence at very low velocity gradients
Authors: Harrington R. E. 
Published: December 2004

AbstractInstrumentation and associated techniques are described for the measurement of flow birefringence and extinction angles of high molecular weight polymer systems at extremely low velocity gradients. Precision of less than one degree in the extinction angles is obtained for birefringence smaller than 10−11, based upon studies of very dilute high molecular weight DNA solutions over a range of velocity gradients from 0.1 to 3 sec−1. Extinction angles approaching 44° are also observed with at least this degree of reliability for these systems. A relatively simple method of data reduction is outlined which permits explicit correction for solvent effects and for residual instrument birefringence and background; only the latter are found to be necessary at the shear rates reported in this communication. Applicability of the techniques to other macromolecules of biological interest is discussed.
Aggregation of poly(γ‐benzyl‐L‐glutamate) in mixed solvent systems
Authors: Powers John C. , Peticolas Warner L. 
Published: December 2004

AbstractThe aggregation of poly(γ‐benzyl L‐glutamate) has been studied by measuring the specific Kerr constants (B/c) over a tenfold range of concentration and the intrinsic viscosities of solutions of a low molecular weight sample of the polymer in four solvent mixtures, viz., benzene–dimethylformamide (DMF), benzene–ethylene dichloride (EDC), dioxane–DMF and dixoane–EDC. Sharp changes are found in the experimentally determined quantities on the addition of small amounts of polar solvent to solutions of the polymer in either benzene or dioxane; this implies that lyotropic phase changes are occuring. The aggregation in benzene produces a birefringent, viscous solution which is probably a smeetic liquid crystal. This changes on addition of polar solvent to an aggregation involving only a few molecules; the second aggregate is most likely antiparallel. Aggregation in dioxane is antiparallel; the existence of a smectic phase is ruled out by the low intrinsic viscosities.
Helix–coil transition in heterogeneous chains. II. DNA model
Authors: Eichinger B. K. , Fixman M. 
Published: December 2004

AbstractMelting curves are calculated for infinitely long DNA‐like random copolymers composed of AT and GC pairs of nucleotides. The entropy of random coil rings formed on melting is explicitly included through use of the Jacobson‐Stockmayer ring‐weighting factors. Transition curves are calculated for values of the cooperativity parameter σ in the range 10−2 ⩽ σ ⩽ 10−4. Ninety percent of the melting occurs in ca. 0.2°C for σ ⩽ 10−3 regardless of the mole fraction of GC. We conclude that observed breadths of thermal denaturation curves for native DNAs result from a superposition of essentially all‐or‐none melting of various regions of the molecule. It is argued that refined approximations to the ring‐weighting factors are probably not important when compared with the effects produced by long‐range base sequence correlations which are known to occur in native DNA.
A new approach to the study of sequence‐dependent properties of polynucleotides
Authors: Gray Donald M. , Tinoco Ignacio 
Published: December 2004

AbstractA sequence‐dependent properly of any long polynucleotide can be related to the properties of a limited number of other polynucleotides. The properties of the constituent sequence subunits need not be individually known. Only the properties of a set of linearly independent sequence combinations in polymers need be known. The number of independent sequences depends on the number of neighboring bases (or base pairs) contributing to the property and on the number of different bases (or base pairs) allowed. General formulae are derived. If only nearest neighbors contribute to a property, there are 13 linearly independent single‐strand sequences with four different bases and there are 8 linearly independent double‐strand sequences with two different base pairs. The study of independent sequences in polymers should be especially useful with double‐stranded polynucleotides. It should be possible by this polymer approach to estimate nearest‐neighbor frequencies from the circular dichroism of double strands and also to investigate the relation between solution conformation and double‐strand sequence.
Theory of chromatography of macromolecules with rigid structures on hydroxyapatite columns. I. Static part
Authors: Kawasaki Tsutomu 
Published: December 2004

AbstractA theory for the chromatography of rigid macromolecules on hydroxyapatite columns has been developed under the assumptions of instantaneous thermodynamic equilibrium between adsorbed phase and solution and of negligible longitudinal diffusion of macro‐molecules. In the first or static part of this theory the adsorption isotherm of macro‐molecules was studied as a function of phosphate concentration in the solvent.
Determination of molecular weight distributions and particle scattering factors of the various species of an aggregating system from light‐scattering and low‐angle X‐ray scattering data
Authors: Magar Magar E. 
Published: December 2004

AbstractSeveral methods are presented for the determination of molecular weight distributions from light‐scattering and low‐angle x‐ray scattering data. These methods are also applicable to the experimental determination of the particle scattering factors of various aggregates provided the molecular weight distribution of the aggregates is known. The statistical analyses pertinent to these methods are appended.
On the helix–coil equilibrium in two‐ and three‐stranded complexes involving complementary poly‐ and oligonucleotides
Authors: Damle Vinayak N. 
Published: December 2004

AbstractThe helix–coil equilibrium in molecular complexes formed between long homopoly‐nucleotides and short complementary oligonucleotides is discussed. Each oligomer is allowed to bind to polymer(s) in an all‐or‐none fashion. The formal treatment of Lifson and Zimm is used as a basis for derivations. Approximations for long polymer(s) yield simple formulae describing the transition. The theory is applied to both a two‐stranded complex (i.e., a complex, one strand of which is a long polymer and the other of which consists of a number of short oligomers) and to a three‐stranded complex (i.e., a complex, two strands of which are long polymers and the third of which consists of a number of short oligomers). For the two‐stranded complex, simple expressions result for average quantities when the interruption constant is much smaller than unity. For the three‐stranded complex the matching and the mismatching models are considered in the case where the non‐bonded segments of polymer chains may form closed loops, and it is shown that true phase transitions occur under certain conditions. For a highly cooperative transition the slope of the melting curve is shown to be independent of the cooperativity parameter, provided that residue molar concentrations of the polymer and oligomer are of comparable magnitude. It is thus possible to obtain the enthalpy of the transition directly from the slopes of the melting curves. Some experimental results on two‐ and three‐stranded complexes are compared with the theory and yield the enthalpy and the entropy for the formation of base pairs and triplets.
Theoretical structure of the polar regions of the tropocollagen molecule
Authors: Hopfingkr A. J. , Walton A. G. 
Published: December 2004

AbstractThe theoretical conformations of poly (Gly‐Ala‐Glu) have been studied. This peptide was chosen as a model for the glycine led triads of the polar regions in collagen. The most favorable conformations are found to be based on the extended and folded forms of the 27 helix (27a and 27b). It is suggested that triple‐strand structures of folded 27 helices exist in the polar collagen regions, and a structural model is presented which is in accord with recent ultrastructural deformation studies. It is a necessary condition for this structure that glycine occur in the lead of the peptide triads. In regions of the collagen molecule where the primary sequence does not contain triads (e.g., in the telopeptide region), random structures based on energy minimization of peptide neighbors are considered briefly. It seems likely that such regions contain an admixture of left‐hand α, polyproline II, and 27 helix structures.
Volume changes accompanying thermal denaturation of deoxyribonucleic acid. II. Denaturation at alkaline pH
Authors: Chapman R. E. , Sturtevant J. M. 
Published: December 2004

AbstractThe change in apparent molal volume ϕ of DNA on thermal denaturation in carbonate buffer at pH 11.0 has been determined by the dilatometric method. It was found that ϕ increases sigmoidally during the helix–coil transition. Several methods, including a colorimetric technique that closely simulates the conditions used in the dilatometric experiments, were employed to estimate the protons lost by the DNA during the transition. These measurements indicated that the extent of the proton loss depends on the counterion present, increasing in the order Li+ < Na+ < K+ < Cs+. The major part of the volume changes observed during the denaturation is due to the volume changes expected to accompany the transfer of protons from the bases guanine and thym ne to carbonate ions. As has been previously reported for the denaturation of DNA at neutral pH, the volume change directly due to the change in shape of the polymer molecules is so small as to be experimentally undetectable.
Location of proline derivatives in conformational space. I. Conformational calculations; optical activity and NMR experiments
Authors: Madison Vincent , Schellman John 
Published: December 2004

AbstractIn order to develop methods of analysis applicable to the determination of the conformation of biological polymers in solution, a series of proline derivatives was studied. The steric constraints of the pyrrolidine ring limit these compounds to a relatively small set of conformations. This set was further reduced by eliminating conformations with large computed conformational energy. Computations revealed that the conformational energy of the proline derivatives fits into one of three classes, depending on the bulk and the polarity of the C‐terminal group. Three analogous classes of optical activity were observed. The optical activity data were analyzed in terms of conformations computed to be of low energy. In some cases qualitative theoretical considerations enabled molecular groups to be located. For example, solvent‐dependent isomerization of the carboxyl hydrogen of N‐acetyl‐L‐proline was detected. Nuclear magnetic resonance provided an experimental measure of the fraction of molecules which had cis unsymmetrically‐substituted tertiary amide groups. This information aided and confirmed the other measures of molecular conformation.
Density gradient proportionality constants for a number of aqueous binary solutions
Authors: Ifft James B. , Martin William R. , Kinzie Kathleen 
Published: December 2004

AbstractA computer program, based upon the method of Trautman, has been developed to calculate density‐gradient proportionality constants, β0, as a function of density for any salt for which density and activity coefficient data are available. Results are given for twenty 1:1 electrolytes at 25°C. These salts are the chlorides, bromides, iodides, and nitrates of the five alkali cations. The program is available for use for any other salt and for a variety of temperatures if the necessary data can be found or measured. Between six and eleven centrifuge runs at different densities were performed fur each of seven of these salts experimentally to determine β0. In general, the experimental and theoretical values agree within 3% except at the extremes of density. This demonstrates the validity of the computer program and is the first extensive demonstration that the thermodynamic calculation of density gradients is correct. Five new quadratic relationships between refractive index and density are given.
Quantitative flow dichroism. I. Correction for disorientation in a solution of rods
Authors: Mayfield John E. , Bendet Irwin J. 
Published: December 2004

AbstractFlow dichroism suffers from two ambiguities which have prevented it from being a useful analytical technique. One is imperfect particle orientation, and the other is the unknown importance of form dichroism. This paper presents a method for calculating from experimental data the dichroism which would be observed from a solution in which all rods were aligned parallel to one another. The procedure utilizes anisotropic light scattering as an independent measure of particle orientation and requires only that the solute particles may be approximated by thin rods.
Quantitative flow dichroism. II. Form dichroism at ultraviolet wavelengths
Authors: Mayfield John E. , Bendet Irwin J. 
Published: December 2004

AbstractForm dichroism has been predicted to make an important contribution to the dichroic spectra of rod‐shaped macromolecules. Ultraviolet flow dichroism experiments on tobacco mosaic virus and bacteriophage fd in solvents of different refractive indices were unable to detect the phenomenon, indicating that for these viruses form dichroism is much less important than had been postulated.
Ionic polysaccharides. III. Dilute solution properties of hyaluronic acid fractions
Authors: Cleland Robert L. , Wang John L. 
Published: December 2004

AbstractMolecular weights by osmometry (M̄n), light scattering (M̄w), and sedimentation‐diffusion (MsD) were determined for selected fractions and unfractionated samples of hyaluronic acid in the molecular weight range 3 × 104−1.7 × 106. For the determination of MsD from the sedimentation coefficient s, a calibration procedure based on the data of Laurent, Ryan, and Pietruszkiewicz gave the following relations in 0.2M NaCl: log (s−1)0 = 14.681 − 0.413 log MsD and log D0 = −3.828 − 0.568 log MsD, where subscript, zero refers to zero concentration and D is the diffusion coefficient. The average Mandelkern‐Flory parameter β in 0.2M NaCl is 3.0 × 106. Data for the intrinsic viscosity [η] may be fitted for M > 105 by [η] = K′Ma, where K′, a are in 0.2M NaCl, 0.0228, 0.816; in 0.5M NaCl, 0.0318, 0.777; in 0.1 M HCl, 0.0279, 0.763, respectively. Below M = 105, [η] appears to fall below the values calculated, possibly due to non‐Gaussian behavior of short chains. The second virial coefficient A2 in 0.5M NaCl approaches the ideal Donnan value, decreasing slightly with increasing molecular weight. The friction parameter P is about 20% smaller than that of uncharged polymers of similar dimensions. The flexible coiling nature of this polymer is confirmed.
Mechanochemical study of wet‐spun lithium‐DNA fibers
Authors: Rupprecht A. 
Published: December 2004

AbstractUniform LiDNA fiber specimens of nearly 20 m length have been prepared with a wet‐spinning method developed by the author. Samples immersed in the spinning bath (80% ethyl alcohol containing 0.4M LiCl) have been subjected to mechanochemical study involving stretching, relaxation, and contraction measurements. A special technique was developed to transfer the sample from the Teflon‐coated cylinder used in spinning to the sample column of the mechanochemical apparatus without stretching or removing the sample from the spinning bath. Force–strain curves of samples consisting of two fiber bundles showed an initial region of low slope followed by a region of high slope and a second region of low slope up to rupture. Some thicker specimens showed an aging effect which abolished the initial low‐slope region and was interpreted as indicative of crystallization. Force–strain curves of two‐bundle samples showed a strong influence of temperature with a complete loss of tensile strength of the LiDNA fibers in the spinning bath at about 55°C. Furthermore, samples at zero strain exhibited a contractile force when subjected to temperatures above about 40°C; the contractile process was pronounced with samples kept above 48°C. On contraction these samples obtained a zero‐force length 20–30% of the original. These data are taken as evidence for a helix‐to‐coil transition occurring in the DNA, the low melting temperature being caused by the chemical influence of the ambient aqueous alcohol–LiCl bath.
Diffusional boundary spreading in the ultracentrifuge
Authors: Weiss George H. , Dishon Menachem 
Published: December 2004

AbstractA common approximation for deriving solutions to the Lamm equation is to neglect diffusion. This paper presents a singular perturbation technique that allows one to estimate the band spreading due to nonzero diffusion coefficient. We illustrate the general mathematical technique by its application to sedimentation when pressure effects are important. Comparison of the approximate solution with accurate numerical solutions shows that the relative errors are of the order of 1% both for concentration and concentration gradient for parameters of chemical interest.