bluuebunny/crossref_metadata_2025_split huggingface dataset:
Denaturation of RNA with dimethyl sulfoxide
Authors: Strauss James H. , Kelly Regis B. , Sinsheimer Robert L. 
Published: December 2004

AbstractThe 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

AbstractA 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

AbstractThis 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

AbstractWe 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

AbstractThe 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

AbstractThe 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

AbstractAcridine 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

AbstractThe 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

AbstractWhen 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

AbstractThree 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

AbstractElectro‐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

AbstractHelix–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

AbstractThe 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.
Anisotropic scattering by single starch granules. II. Layered granule structure
Authors: Finkelstein R. S. , Sarko A. 
Published: December 2004

AbstractThe study of anisotropy light scattering from tapioca and potato starches has continued with the recording of more detailed experimental single‐granule Hv scattering patterns and, for the first time, single‐granule Vv patterns. Quantitative analysis of the higher order scattering maxima to the granule morphology, permitting an analysis of the latter in terms of a lyered structure. For tapioca starch, this analysis indicates that if layering is present at all, the layer thickness is comparable to the wavelength of the incident radiation, and most likely is considerably less than 0.5 μ in thickness. On the other hand, the potato starch morphology is characterized by a relatively coarse layering with few layers and considerable difference in the anisotropy between successive layers. The models for the two starches in best agreement with experimental data are as follows: almost perfectly spherulitic anisotropic structure with very thin shell‐like layers—if any—for tapioca, and alternating layers of varying anisotropy several microns in thickness and probably simultaneously present with an isotropic center, for potato starch. The Vv pattern for tapioca starch is in agreement with this model, although its information content is lower owing to the experimental difficulty of recording higher order maxima. Suggestions for further morphological study of starches are presented.
Dynamic studies of the unwinding of a DNA‐like strand
Authors: Ree Francis H. , Chay Teresa Ree 
Published: December 2004

AbstractFollowing Simon and Zimm's recent work, both molecular dynamic and Monte Carlo methods are used to simulate on a computer the unwinding of a DNA‐like (N + 1)‐unit helical strand. The strand unwinding is assumed to obey (N + 1)‐coupled Langevin equations of motion (N = 10–50). The present computer “experiment” was done to elaborate dependence of unwinding behavior of the helix upon (i) configurations of its complementary strand [represented here by a square cylinder (Simon‐Zimm model), a circular cylinder, and a fixed helix (double‐helical model)]; (ii) interstrand potentials (a hard‐cylinder potential, an inverse twelfth‐power soft repulsion with or without an inverse third‐power attractive tail); (iii) amplitudes of the Brownian motions, and (iv) the molecular weights of the unwinding strand.We found that (i) the Brownian motions strongly couple with the interstrand potentials to produce a shorter “unwinding time” (τ0) (which characterizes an expotential decay of the unwinding) for a longer renged repulsive potential (without the Brownian motions, no such effect was present); (ii) addition of an attractive tail to the repulsive potentials further reinforces the unwinding, thereby giving a reduced value of τ0; (iii) τ0 can be expressed as a product of two factors–unwinding time for a one‐dimensional spring‐bead model, which mostly accounts for the N 2‐dependence in τ0, and a factor which depends on the Brownian motions and the interstrand potentials; (iv) among the three models described above, under similar situations, the three‐dimensional double‐helical model has the smallest τ0; and (v) unless the maximum Brownian displacement exceeds a certain value, the unwinding around a square cylinder takes place in a (unrealistic) stair‐step manner whose τ0 decreases with increase in the Brownian displacements.The N 2‐dependence of τ0 agrees with the Simon and Zimm's machine results as well as Crother's experimental data on T2 DNA; however, it contradicts experimental data of Massie and Zimm, and others. Further possible improvements in connection with the computer simulation are suggested.
The conformation fo poly‐L‐alanine in hexafluoroisopropanol
Authors: Parrish Joseph R. , Blout Elkan R. 
Published: December 2004

AbstractHigh‐molecular‐weight poly‐L‐alanine dissolved in hexafluoroisopropanol exhibits infrared, ultraviolet, circular dichroism, and optical rotatory dispersion spectra which are unique and unlike any other previously reported polypeptide spectra. Strong evidence that a helical conformation is present is shown by the high degree of hypochromism in the 187mμ absorption peak and by the positions of the amide infrared bands. The CD and ORD spectra are also similar to those of α‐helical polypeptides, though important qualitative and qualitative differences are observed. To explain the novel spectra, which are not mixtures of the spectra of previously reported polypeptide conformations, a new α‐helix‐like conformation is proposed. The postulated conformation (a doubly hydrogen‐bonded helix) is a distorted α‐helix in which the peptide carbonyl groups point slightly out from the helix axis and are hydrogen bonded simul taneously both to the NH of the fourth peptide residue to the carboxyl terminal side (as in the classical α‐helix), as well as to a solvent molecule's hydroxyl hydrogen.
Infrared spectroscopy of human amyloid fibrils and immunogolbulin proteins
Authors: Termine J. D. , Eanes E. D. , Ein D. , Glenner G. G. 
Published: December 2004

AbstractThe presence of the antiparallel‐β‐pleated sheet coformation io isolated human amyloid protein fibrils has been confirmed by infrared spectroscopy. In most amyloid samples, this conformation was enhanced by acidic solution conditions. Infrared spectroscopy (Amide I and Amide V absorption bands) and x‐ray diffraction methods were also used to examine the immunoglobulin molecule for solid state‐β‐structure. It was found that both heavy chains and Bence Jones proteins exhibited some β‐pleated sheet content upon acid and/or heat treatment. Furthermore, pepsin digests comprising either the variable‐rich region (Fd′) of the immunloglobulin heavy chain or in particular, filamentous variable segments of κ and λ Bence Jones proteins were, as isolated, very similar to amyloid in β‐structure content. Data from other immunoglobulin‐derived sample did not exhibit extensive β‐pleated sheet content. On the other hand, most amyliod and immunoglobulin‐derived samples did display some β‐structure when cast from 50% HCOOH solution. Under these conditions, however, filamentous light chain‐variable segments exhibited well‐defined infrared patterns rich in antiparallel‐β‐pleated sheet structure and gave a “cross‐β” x‐ray diffraction pattern.
Limiting sedimentation and diffusion coefficients of polyelectrolytes. The charge effect
Authors: Varoqui R. , Schmitt A. 
Published: December 2004

AbstractGeneral expressions relating the sedimentation and diffusion constants of polyelectrolytes to the friction properties of ionic components in multicomponent systems have been derived. A quantitative explanation of the charge effect with respect to the addition of a low‐molecular‐weight salt is given; special attention is laid on limiting laws according to the salt‐to‐polymer concentration ratio. The theory is applied to a simple model, the infinitely long rod‐like model, to illustrate the peculiar aspect of the charge effect in presence of salt.
Far‐infrared spectra of copoly(‐α‐amino acids)
Authors: Itoh Koichi , Oya Masanao , Shimanouchi Takehiko 
Published: December 2004

AbstractFar‐infrared spectra in the region from 700 to 200 cm−1 were measured for the copolymers of L‐alanine and glycine, those of L‐alanine and L‐valine, those of L‐alanine and L‐leucine, and those of L‐alanine and L‐phenylalanine. The observed spectra were interpreted on the basis of the analysis of the far‐infrared spectra of the corresponding homopolymers, and the correlation between the conformations of the copolymers and the kinds of the component amino acids was discussed.
A Molecular Model for the Inversion of the CD Spectra of Actinomycin D in the Presence of gem‐diols
Authors: Ascoli F. , Desantis P. , Lener M. , Savino M. 
Published: December 2004

AbstractA molecular model for the inversion of the CD spectra of actinomycin D in the presence of gem‐diols is proposed, in terms of the inversion of chirality of the peptide groups directly connected to the phenoxazone ring.
The Structures and Properties of Poly‐5‐methylcytidylic Acid
Authors: Warshaw Myron M. , Noe Ralph 
Published: December 2004

AbstractThe optical rotatory dispersion properties of poly 5MeC, poly diMeC, and 5MeCMP‐(5′) in 0.1M Na+ have been studied at various pH values and temperatures. Poly 5MeC and poly diMeC have optical properties which are similar to those for poly C; however, poly 5MeC has a biphasic melting profile in the pH range from 3.8 to 5.4 similar to that observed for poly 51C. Using titration, ionic strength, and pH dependence measuements, the data for poly 5MeC are interpreted in terms of the following scheme at pH 4.0 and 0.1 ionic strength: triple‐strand helix 37°C double‐strand helix 79°C single‐strand coil. Support for this scheme is discussed. The effect of the methyl group is discussed in terms of similar structural possibilities for other polymers of cytidylic acid.
Chain conformation of poly‐L‐alanine in dichloroacetic acid
Authors: Nakajima Akio , Murakami Masahiko 
Published: December 2004

AbstractThe chain conformation of poly‐L‐alanine in dichloroacetic acid has been investigated by combining experimental data on optical rotatory dispersions, intrinsic viscosities, and sedimentation equilibria. Comparison of experimentally obtained characteristic ratio with that predicted from theory leads to the conclusion that poly‐L‐alanine molecules exist as interrupted helices in dichloroacetic acid.