bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dilute solution of amylose in dimethylsuldoxide
Authors: Fujii M. , Honda K. , Fujita H. 
Published: December 2004

AbstractMeasurements of light scatting, sedimentation equilibrium, sedimentation velocity, and viscosity were carried out on fractions of native amylose in dimethylsulfoxide at 25°C. The data for statistical radius as a function of weight‐average molecular weight Mw suggested a stiff nature of this biopolymer in the solvent studied when interpreted in terms of Kirste's recent calculations with a stiff chain model. The data for sedimentation coefficient were consistent with this suggestion, and when analyzed in terms of the theory Hearst and Stockmayer for wormlike chain, a value of 233 Å2 was obtainedd for a/λ, where a is the length of a monomer unit projected on the chain axis and (2λ)−1is the persistence length of the wormlike chain. The intrinsic viscosity data gave a high a value as 0.91 for the exoponent in the Houwink‐Mark‐Sakuarada equation, in Substantial agreement with Cowie's prenious work.We attempted to interpret these data by use of the Eizner‐Ptitsyn equation for wormlike chains, with omission of the free‐drainage term and introduction of the a/λ value obtained from sedimentation data. It was found that, except in the region of Mw above one million, the observed values were fitted well by the E‐P theory with a = 1.4 Å and (2λ)−1 = 87 Å. The disagreement in the high‐molecular‐weight region was tentatively attributed to excluded volume effect. The a value obtained suggests that the molecular conformation of amylose in dimethylsulfoxide is predominantly helical, in contrast to that of the same polymer in aqueous solutions of simple electrolyte. It was also found that a similar value of a was derived from our data for the second virial coefficient and partial specific volume if the molecule was assumed to be essentially rodlike.
Syn–Anti effects on the spatial configuration of polynucleotide chains
Authors: Olson Wilma K. 
Published: December 2004

AbstractSemiempirical energy calculations have beeb performed on model nucleic acid systems to assess the preferred conformation of the rotation χ about the glycosidic linkage and also the effect of this rotation on the spatial configuration of the sugar‐phosphate chain backbone. The rotation angle ϕ˝ about bond C5′–C4′ in purine polyribonucleotides and 5′‐monoribonucleotides is found to depend on whether the conformational range of χ is syn or anti. The preferred conformation of χ in these molecules is also found to depend upon the nature of the attached base. The orientation of χ in poly rA chains is predicted to be predominantly anti, whereas in poly rG the syn conformer is expected to occur in significant proportions. The syn conformer is preferred almost exclusively in certain unusual purine polynucleotides, such as poly 8Br‐rA. It is noted that the preferred conformation of x in polynucleotides is not necessarily the same as that calculated for 5′‐mononucleotides and nucleosides. On the basis of these calculations, the influence of the orientation and nature of a purine base on the spatial configuration of a polynucleotide chain as a whole has been examined. The random coil dimensions of a syn polynucleotide chain are found to be larger than those of an anti chain as a consequence of the effect of a syn base on the local conformation of the chain skeleton. Finally, it is found that the occurrence of a syn base in an ordered polynucleotide chain may prevent the formation of normal stacking with the preceding base.
Conformational studies on guanosine nucleotides and polynucleotides. The effect of the base on the glycosyl and backbone conformations
Authors: Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractPotential energy calculations have been carried out on guanosine 5′‐monophosphate and guanosine 3′,5′‐diphosphate by simultaneous variation of the rotation angles χ and ψ to assess the influence of the base on the glycosyl and the sugar–phosphate backbone conformations and their possible interdependence. The results obtained predict that guanine containing nucleotides tend to favor the syn glycosyl conformation in sharp contrast to the anti conformation found for adenine and the common pyrimidine nucleotides. This characteristic behavior of guanine nucleotides is largely a result of increased non‐bonded van der Waals' and electrostatic attractive interactions between the 5′‐phosphate and the amino group of the base. As seen previously [N. Yathindra and M. Sundaralingam, Biopolymers, 12, 297 (1973)] changes in the glycosyl conformation mainly affects the C(4′)–C(5′) bond rotations of the backbone. The most favored (χ,ψ) conformer corresponding to the global minimum both in 5′‐GMP and 3′,5′‐GDP is syn‐gg, (190°,80°) for C(2′)‐endo rings and (180°,50°) for C(3′)‐endo rings. It is noteworthy that the syn angle is different from the usually observed range of 210–260°. The next significant minimum in the (χ,ψ) energy surface corresponds to the syn‐gt conformational combination (the syn angle now in the normal range), indicating that the occurrence of the normal syn conformer induces a distortion in the backbone c(4′)‐c(5′) bond conformation from the preferred gg. These studies reveal the significant influence of the base not only on the glycosyl conformation but also on the backbone conformations of polynucleotides.
Hydration of stratum corneum
Authors: Anderson R. L. , Cassidy J. M. , Hansen J. R. , Yellin W. 
Published: December 2004

AbstractA model for the hydration behavior of human stratum corneum has been developed from measurements on in vitro samples isolated in a manner which minimized tissue treatment and trauma. Water sorption/desorption rate measurements as a function of water activity, temperature, and tissue integrity are reported. These data, together with thermodynamic data (infrared and nmr results reported earlier) are consistent with a model in which rapidly sorbed/desorbed water (ca. 0.5 mg water/mg stratum corneum) is associated with (“bound” by) the tissue, while slowly sorbed/desorbed “free” water (up to 12 mg water/mg stratum corneum) is kinetically restricted and probably intracellular in location. Both equilibrium water binding and desorption kinetic data suggest structural changes of this cellular water barrier upon hydration. Evidence for hysteresis in water sorption isotherms (reported by others) could not be reproduced.
Metastable secondary structures in ribosomal RNA: A new method for analyzing the titration behavior of rRNA
Authors: Revzin Arnold , Neumann Eberhard , Katchalsky Aharon 
Published: December 2004

AbstractThe pH titration behavior of E. coli rRNA in the acid range has been analyzed by combining spectrophotometric and potentiometric titration data. The “simplest” model for the system, which considers as possible reactions the protonation of adenine (A), cytosine (C), and guanine (G) residues along with the opening of A·U and G·C base pairs, does not adequately account for the titration properties. It is postulated that extra reactions may occur in addition to those in the “simplest” model, and a new analytical method was developed to deal with this situation. Our approach yields the ultraviolet spectral changes which accompany the extra reactions, from which the nature of these reactions can in principle be deduced. The calculations also give, at each pH, the extents of the extra reactions as well as the extents of those reactions which comprise the “simplest” model.We infer that in acidic RNA solutions of 0.1M ionic strength there occur at least two extra reactions, each of which involves G residues. We propose that in the pH range 6.0 ≥ pH ≥ 3.8 triple‐stranded helical sequences, presumably protonated G·C·G, are formed. These regions are replaced at lower pH by acid‐stable structures involving G·G and A·A base pairs. In solutions of lower ionic strength (I = 0.01M) no triple strands are formed, but G·G and A·A regions seem to develop even at pH values as high as 6.0. At I = 0.1M, an acid–base titration cycle between pH 7 and 2.8 is not reversible; rRNA shows true hysteresis behavior. We conclude that in ribosomal RNA's, which are generally G‐rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures.
Fluorescence correlation spectroscopy. I. Conceptual basis and theory
Authors: Elson Elliot L. , Magde Douglas 
Published: December 2004

AbstractWe describe a method for determining chemical kinetic constants and diffusion coefficients by measuring the rates of decay of spontaneous concentration fluctuations. The equilibrium of the system is not disturbed during the measurement. We measure the number of molecules of a specified type in a defined open volume as a function of time and compute the time course of the deviations from the thermodynamic mean concentration. The method is based on the principle that the rates of decay of spontaneous microscopic fluctuations are determined by the same phenomenological rate coefficients as those of macroscopic departures from equilibrium which result from external perturbations. Hence, an analysis of fluctuations yields the same chemical rate constants and diffusion coefficients as are measured by conventional procedures. In practice the number of the specified molecules is measured by a property such as absorbance or fluorescence which is specific and sensitive to chemical change. The sample volume is defined by a light beam which traverses the cell. As the molecules appear in or disappear from the light beam, either due to diffusion or chemical reaction, their concentration fluctuations give rise to corresponding fluctuations of the intensity of absorbed or emitted light. This paper presents the theory needed to derive chemical rate constants and diffusion coefficients from these fluctuations in light intensity. The theory is applied to three examples of general interest: pure diffusion in the absence of chemical reaction; the binding of a small rapidly diffusing ligand to a larger slowly diffusing macromolecule; and a unimolecular isomerization. The method should be especially useful in studying highly cooperative systems, relatively noncooperative systems with intermediate states closely spaced in free energy, small systems, and systems not readily subject to perturbations of state.
Fluorescence correlation spectroscopy. II. An experimental realization
Authors: Magde Douglas , Elson Elliot L. , Webb Watt W. 
Published: December 2004

AbstractThis paper describes the first experimental application of fluorescence correlation spectroscopy, a new method for determining chemical kinetic constants and diffusion coefficients. These quantities are measured by observing the time behaviour of the tiny concentration fluctuations which occur spontaneously in the reaction system even when it is in equilibrium. The equilibrium of the system is not disturbed during the experiment. The diffusion coefficients and chemical rate constants which determine the average time behaviour of these spontaneous fluctuations are the same as those sought by more conventional methods including temperature‐jump or other perturbation techniques. The experiment consists essentially in measuring the variation with time of the number of molecules of specified reactants in a defined open volume of solution. The concentration of a reactant is measured by its fluorescence; the sample volume is defined by a focused laser beam which excites the fluorescence. The fluorescent emission fluctuates in proportion with the changes in the number of fluorescent molecules as they diffuse into and out of the sample volume and as they are created or eliminated by the chemical reactions. The number of these reactant molecules must be small to permit detection of the concentration fluctuations. Hence the sample volume is small (10−8 ml) and the concentration of the solutes is low (∼ 10−9 M). We have applied this technique to the study of two prototype systems: the simple example of pure diffusion of a single fluorescent species, rhodamine 6G, and the more interesting but more challenging example of the reaction of macromolecular DNA with the drug ethidium bromide to form a fluorescent complex. The increase of the fluorescence of the ethidium bromide upon formation of the complex permits the observation of the decay of concentration fluctuations via the chemical reaction and consequently the determination of chemical rate constants.
α‐Glutamyl oligopeptides: Preparation by the solid‐phase method
Authors: Bonora G. M. , Toniolo C. , Fontana A. , Di Bello C. , Scoffone E. 
Published: December 2004

AbstractThe synthesis of the oligomeric peptides (Glu)n–Phe(NO2)–Phe (up to n = 4) by the solid‐phase method is reported. Fractionation by ion‐exchange column chromatography of the crude materials cleaved from the resin and subsequent amino acid analysis revealed that the desired peptides were obtained, although contaminated by several by‐products whose number depends on the length of peptide chain and on the experimental conditions.
Analysis of circular dichroism spectra of homopurine: Homopyrimidine DNA's for sequence information and comparison of results with heterobase DNA
Authors: Allen Fritz Schreyer , Daub Guido William 
Published: December 2004

AbstractProcedures are developed which make a first neighbor frequency analysis possible from a CD spectrum of homopyrimidine: homopurine DNA's. The contribution to the CD spectrum from the various first neighbor frequencies present in homopyrimidine: homopurine‐type DNA's has been determined, and hence the CD spectrum for any DNA of this type with known first neighbor frequencies can easily be calculated. An identical analysis is presented for the determination of extinction coefficients. It is further shown that unlike the more usual heteropurine–pyrimidine DNA's a random sequence does not lead to a simplified formalism. Finally, it is concluded that the homopyrimidine: homopurine DNA's have a structure that is different from that of the more usual heterobase DNA's.A procedure capable of determining first neighbor frequencies from a CD spectrum for heterobase and/or homopurine: homopyrimidine DNA's is described. This procedure is used to determine that there is only minimal interference between these two types of DNA in the first neighbor analysis.
Stability and thermodynamics of polyuridylic acid–deoxyadenosine complexes in aqueous neutral salt solutions
Authors: Schleich Thomas , Gould Gene R. 
Published: December 2004

AbstractUsing the thermodynamic analysis and methodology of Hill (Biopolymers, 12, 257 (1973)) for the treatment of optical thermal transition data the effects of various neutral salt additives on the stability and thermodynamics of the poly U–deoxyadenosine interactions that lead to the formation of triple‐stranded helical polymer–monomer complexes have been studied. In order of increasing molar effectiveness as polyU–deoxyadenosine complex stability perturbants (pH 7 and in the presence of 1 M NaCl), the various ions may be ranked: SO4−2 < Cl− < Br− < ClO4−; and (CH3)4 N+ < Li+ < Rb+ ∼ Na+ < K+ < (CH3 CH2)4 N+ < urea < Guan+ ∼ (CH3(CH2)2)4 N+. Destabilizing neutral salt additives (e.g., NaClO4) caused a decrease in the absolute magnitude of the apparent enthalpy and entropy of binding relative to the values determined in the presence of NaCl. By contrast, stabilizing additives (e.g., Na2 SO4) had the opposite effect on these parameters. Along a melting curve the apparent differential heat of complex formation calculated for the binding of deoxyadenosine to poly U in 1 M NaCl appeared to vary linearly with θ, the extent of fractional binding. For such a linear dependence it can be shown that the integral heat (usually determined calorimetrically) equals the differential heat at θ = 0.5. Correcting the apparent differential heat calculated at θ = 0.5 for ligand activity resulted in values for the integral heat of binding of deoxyadenosine to poly U in 1 M NaCl of −13 to −16 kcal/mol. Binding isotherms determined in the presence of different inorganic electrolytes could be superimposed provided that different temperatures were compared. However, the additive (CH3)4NCl, which has been shown to interact preferentially with A‐T rich regions of DNA (Shapiro, Stannard, and Felsenfeld, Biochemistry, 8, 3233 (1969)) resulted in a considerably broadened binding isotherm indicating less cooperativity.
All‐valence‐shell molecular orbital calculations on the chiroptical properties of substituted and unsubstituted 2,5‐diketopiperazine structures
Authors: Richardson F. S. , Pitts W. 
Published: December 2004

AbstractThe chiroptical properties of L‐3‐methyl‐2,5‐diketopiperazine (L‐alanylglycyl anhydride) are examined on a theoretical model in which the electronic wave functions are obtained from semi‐empirical all‐valence‐shell molecular orbital calculations. The INDO molecular orbital model is used to perform SCF‐MO calculations on the ground states of six conformation isomers of L‐3‐methyl‐2,5‐diketopiperazine and two chiral conformational isomers of unsubstituted 2,5‐diketopiperazine. Excited‐state wave functions are constructed in the virtual orbital‐configuration interaction approximation. The rotatory strengths, dipole strengths, oscillator strengths, and dissymmetry factors of the first eight singlet–singlet transitions for each of the eight structures are calculated and reported. Additionally, ground‐state dipole moments, net atomic charges, and the first four ionization potentials (calculated according to Koopman's theorem) are computed for each structure. The signs and the magnitudes of the rotatory strengths are found to be extremely sensitive to the conformation of the piperazine ring as well as to methyl substitution at the α carbon of the ring. Spectra–structure relationships based on the calculations reported here are discussed, and the available experimental CD data on dissymmetric 2,5‐diketopiperazine are examined in terms of our theoretical results.
The strand‐separation transition of T7 DNA
Authors: Kallay Michael , Record M. Thomas 
Published: December 2004

AbstractThe strand‐separation transition of T7 DNA has been investigated by temperature shift and viscosity measurements in two formamide–water solvents. The strand‐separation region is quite narrow, and follows directly at the end of the denaturation transition observed by absorbance. The kinetics of strand separation of T7 DNA are slow and complex in the strand‐separation transition. Similarities and differences in the behavior of T2 and T7 DNA in strand separation are indicated and discussed. Briefly, the time course of strand separation and the conformational changes observed in the population undergoing strand separation are similar for the two molecules. However, the transition breadths and the interval between the helix–coil transition and the strand‐separation transition differ markedly. Both DNA molecules exhibit hysteresis in the strand‐separation region. For both molecules, it appears that strand separation involves the coupled denaturation and disentanglement of the two‐stranded form found at the end of the helix–coil transition.
Studies of deoxyribonucleoproteins progressively depleted of proteins in solutions of various ionic strengths
Authors: Frisman E. V. , Sibileva M. A. , D'Iakova E. B. , Vorob'ev V. I. , Turoverova L. V. 
Published: December 2004

AbstractThe conformation of deoxyribonucleoprotein (DNP) from calf thymus at different stages of deproteinization was studied.The dissociation of the first portion of histone produces no effect on the hydrodynamical and optical behavior of DNP particles. The conformational transition of a macromolecule was observed as soon as the ratio of protein to DNA ⩽ 0.9.The effect of ionic strength on the conformation of DNP particles with high protein content was more strongly pronounced than that for DNA. On the contrary, DNP particles depleted of proteins (protein/DNA < 0.9) were found to be less sensitive than DNA to the variation of ionic strength. These data imply that the DNP molecules rich in proteins possess a superstructure that is destroyed as the protein/DNA ratio becomes 0.9.The data were analyzed in view of current theories on various model concepts. The most probable model to describe the DNP molecule was chosen by comparing the calculated and experimentally obtained parameters. We believe that DNP is best described as a “compressed coil,” possibly including superhelical regions.
The thermal induced helix—β transition of poly(Nε‐methyl‐L‐lysine) and poly(Nδ‐ethyl‐L‐ornithine) in aqueous solution
Authors: Yamamoto Hiroyuki , Yang Jen Tsi 
Published: December 2004

AbstractUncharged poly(Nε‐methyl‐L‐lysine) (PMLL) and its isomer, poly(Nδ‐ethyl‐L‐ornithine) (PELO), in alkaline solution (pH ca. 12) undergo a helix‐to‐β transition upon mild heating at 50°C or higher in a manner similar to that of poly(L‐lysine) (PLL). The rate of conversion follows the order: PMLL < PELO < PLL. The helix can be regenerated upon cooling near zero degrees, for instance, after more than 12 hr at 2°C. At concentrations less than 0.02% the β form is intramolecular, but at higher concentrations both intra‐ and intermolecular β forms are generated. Poly(Nδ‐methyl‐L‐ornithine) (PMLO), an isomer of PLL, behaves like poly(L‐ornithine); uncharged PMLO in alkaline solution is partially helical and becomes disordered at elevated temperatures.
Crystal and molecular structure of V‐anhydrous amylose
Authors: Winter William T. , Sarko A. 
Published: December 2004

AbstractThe conformation and crystalline packing of V‐anhydrous amylose has been investigated by a combination of linked atom model building and X‐ray diffraction analysis. The unit cell, the P212121 space group, the left‐handed sixfold helical conformation with all O(6) in gt rotational positions, and the intrahelical O(2)‐‐‐O(3) and O(2)‐‐‐O(6) hydrogen bonds are substantially in agreement with previous studies. A new model for packing of the chains in the unit cell and the presence of crystallographic water is proposed. Packing appears to be stabilized by corner‐to‐center chain O(2)‐‐‐O(2) hydrogen bonds. The nature of the transition from the amylose–DMSO complex to Va‐amylose was considered and it is shown that the transition involves translation of the amylose chains parallel to the a and b unit cell axes with only slight changes in the orientation of the helix. No significant conformational changes result from the transition.
Crystal and molecular structure of the amylose–DMSO complex
Authors: Winter William T. , Sarko Anatole 
Published: December 2004

AbstractThe crystal and molecular structure of the complex of amylose with dimethyl sulfoxide has been studied by a combination of stereochemical analysis, potential energy, and X‐ray diffraction methods. The complex crystallizes in a pseudotetragonal unit cell with a = b = 19.17 Å and c (fiber axis) = 24.39 Å, with two antiparallel chains per unit cell and space group P212121. The amylose chain is a left‐handed 61(1.355) helix with three turns per crystallographic repeat. The O(6) rotational position is approximately gt. Dimethyl sulfoxide is located inside the helix with one DMSO molecule for every three glucose residues. An additional four DMSO molecules and eight water molecules each are located in the large interstices between chains, and it is the interaction of these molecules with the helix that results in the pseudotetragonal chain packing. The interstitial DMSO is the source of the previously reported additional layer lines, which are not consistent with the 8.13‐Å amylose repeat distance. The final R factor for the layers with amylose contribution to the structure factors was 0.29, while the overall R factor was 0.35. The stereochemical packing analysis provided suitable phasing models for the subsequent X‐ray refinement.