bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman studies of nucleic acids. XII. Conformations of oligonucleotides and deuterated polynucleotides
Authors: Prescott B. , Gamache R. , Livramento J. , Thomas G. J. 
Published: May 2005

AbstractLaser Raman spectra of the trinucleoside diphoshate ApApA and dinucleoside phosphates ApU, UpA, GpC, CpG, and GpU are reported and discussed. Assignments of conformationally sensitive frequencies are‐facilitated by comparison with spectra reported here of poly(rA), poly(rC), and poly(rU) in deuterium oxide solutions. The significant spectral differences between ApU and UpA, and between GpC and CpG, reveal that the sequence isomers have nonidentical conformations in aqueous solution. In UpA at low temperature the bases are stacked and the backbone conformation is similar to that found in ordered polynucleotide structures and RNA. In ApU no base stacking can be detected and the backbone conformation differs from that found in UpA, both in the orientation of phosphodiester linkages and in the internal conformation of ribose. At the conditions employed neither ApU nor UpA exhibits base pairing in aqueous solutions. In both GpC and CpG the bases are stacked and the phosphodiester conformations are similar to those encountered for UpA and RNA. However, major differences between spectra of GpC and CpG indicate that the geometries of stacking and ribosyl conformations are different. In GpC the Raman data favor the formation of hydrogen bonded dimers containing GC pairs. Protonation of C in GpC is sufficient to eliminate the ordered conformation detected by Raman spectroscopy. Despite the ordered backbone conformation evident in GpU, this dinucleoside apparently contains neither stacked nor hydrogen bonded bases at the conditions employed here. The Raman data also confirm the stacking interactions in ApApA, poly(rA), and poly(rC) but suggest that the backbone conformation in poly(rC) differs qualitatively from that found in most ordered polynucleotide structures and is thermally more stable. The present results demonstrate the sensitivity of the Raman technique to sequence‐related structural differences in oligonucleotides and provide additional spectra–structure correlations for future conformational studies of RNA by laser Raman spectroscopy.
Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations
Authors: Poland Douglas 
Published: May 2005

AbstractThe problem of calculating detailed probability profiles giving the probability of each unit in the chain to be in the ordered state (and all other average quantities as well including the fraction of strand association) for specific‐sequence macromolecules requiring statistical weights that correlate up to the total number of units in the chain (e.g., DNA, collagen) is formulated in terms of recursion relations for appropriate a priori and conditional probabilities, thus generalizing the approach of Lacombe and Simha for nearest‐neighbor correlations in specific sequence macromolecules. The technique allows the probability profiles for chains of thousands of units to be calculated in minutes making no approximation in the basic model.
Cooperative elution of oligoadenylic acid in poly U immobilized chromatography
Authors: Okada Shozo , Husimi Yuzuru , Tanabe Sachiko , Wada Akiyoshi 
Published: May 2005

AbstractCharacterization of polyU immobilized chromatography was performed in order to use this technique as an analytical device. A method of analysis of the elution profile related to thermodynamic parameters was also developed.Sites of attachment of polyU to agarose gel activated by cyanogen bromide were studied using uridine diphosphate and adenine. Independent equilibrium dialysis of ApA for different states of polyU, in solution and immobilized in gel, were carried out. These results show that the immobilized polyU is attached to agarose only at the 5′‐terminal phosphate groups and behaves as it does in solution.Column chromatography of ApA with the immobilized polyU was performed at several temperatures and concentrations. To analyze the elution profile, the theory of cooperative binding of oligonucleotides to polynucleotides was extended to the frame‐work of plate theory. A computer simulation for the elution profiles was performed using thermodynamic parameters obtained by equilibrium dialysis. This simulation duplicated the experimental results. This fact shows that the peculiar leading form of elution profile is due to the cooperative binding. The thermodynamic parameters of the polyU–ApA system were obtained from the “peak trajectory.”
The ESR determination of protein α‐helicity
Authors: Lvov K. M. , Kim Yu. A. 
Published: May 2005

AbstractExperimental data are summarized on decay kinetics of uv‐induced paramagnetic centers in globular proteins. The PC decay rate in the absence of oxygen in α helical regions is shown to differ always by about two orders from that in nonhelical regions of the polypeptide chain. This effect can be utilized to estimate the degree of α helicity in the dry state, in solution, and in the frozen solution of proteins.
Fluorescence correlation spectroscopy and Brownian rotational diffusion
Authors: Aragón S. R. , Pecora R. 
Published: May 2005

AbstractA theroy relating rotational Brownian motion to the time autocorrelation function of the intensity of radiation from a fluorescent system composed of spherical rotors is presented. The calculation shows three relaxation times, two associated with the rotational diffusion, and the third associated with the natural decay of the fluorescence. The correlation function contains terms that relax independently of the fluorescence decay time, thus arbitrarily extending the time range over which rotational diffusion can be studied by fluorescence.
The solution conformation of poly(L‐lysine). A Raman and infrared spectroscopic study
Authors: Painter Paul C. , Koenig Jack L. 
Published: May 2005

AbstractThe Raman and infrared spectra of poly(L‐lysine) and poly(DL‐lysine) in solution are reported and the effects of various salts are investigated. The results demonstrate that α‐helix formation in solution is induced by specific salts and the spectral data support the hypothesis of regions of local order for poly(L‐lysine) in aqueous solutions of low ionic strength.
Thickness and density of protein films by optical mixing spectroscopy
Authors: Uzgiris E. E. , Fromageot H. P. M. 
Published: May 2005

AbstractThe adsorption of protein films on polystyrene latex spheres was studied by optical mixing spectroscopy. With this technique, we show that both the hydrodynamic thickness of protein films and their optical density can be measured. Thus, we found that films of the glycoproteins isolated from the human erythrocyte membrane were four times as thick as films of either human serum albumin or bovine serum albumin for about the same surface coverage. This result suggests an end‐on orientation for the adsorbed glycoprotein molecules, which is consistent with the model proposed by others for the orientation of these molecules at the surface of the red blood cell itself.
Salt effects on the denaturation of DNA. V. Preferential interactions of native and denatured calf thymus DNA in Na2SO4 solutions of varying ionic strength
Authors: Fu Joseph C. C. , Gruenwedel Dieter W. 
Published: May 2005

AbstractPrecision density measurements were performed at 25°C on Na‐DNA‐Na2SO4 mixtures in the presence of either 0.005 m cacodylic acid buffer (pH 6.8) or in the presence of 0.1 m NaOH (pH 12.3). From measurements executed under equilibrium dialysis conditions, the so‐called “density increments” (∂ρ/∂c2)μ0 for native (pH 6.8), heat‐denatured (pH 6.8), and alkali‐denatured (pH 12.6) Na‐DNA were evaluated as a function of Na2SO4 concentration. (∂ρ/∂c2)μ0 for native DNA was found to decrease almost linearly with ionic strength I1/2 of the supporting electrolyte. The density increment for Na‐DNA at pH 12.6, on the other hand, increases in more or less linear fashion with I1/2. (∂ρ/∂c2)μ0 for heat‐denatured DNA at pH 6.8 is not affected very much by increasing salt strength. From density measurements performed on the Na‐DNA–Na2SO4 mixtures at fixed concentrations of diffusible components, the partial specific volumes ν2° of native (pH 6.8), heat‐denatured (pH 6.8), and alkali‐denatured (pH 12.6) Na‐DNA were determined as a function of Na2SO4 concentration. All ν2° values, irrespective of the secondary structure of the DNA, increase with increasing salt concentration although the increase for heat denatured DNA (pH 6.8) is barely noticeable. ν2° of both native and heat‐denatured DNA (pH 6.8) extrapolates to a value of 0.50o ml/g at vanishing salt concentration; ν2° of DNA in 0.1 m NaOH, on the other hand, assumes the value 0.2o ml/g.Distribution coefficients of diffusible components, expressed in terms of preferential water and salt interaction, were evaluated from the (∂ρ/∂c2)μ0 data, solvent densities, and partial specific volumes of all solution components. All interaction parameters depend strongly on salt concentration and on the conformation of DNA. From data collected and from information available in the literature it is concluded that Na2SO4, for instance, displaces water of hydration from native DNA much more readily with increasing salt concentration than does NaCl. The solvation properties of the denatured forms of Na‐DNA are rather complex but appear to be in harmony with whatever information can be gathered from the literature.
Length and dipole moment of TMV by laser signal‐averaging transient electric birefringence
Authors: Newman Jay , Swinney Harry L. 
Published: May 2005

AbstractTransient electric birefringence experiments have been performed on well‐characterized highly monodisperse samples of tobacco mosaic virus (TMV). Experiments and calculations are presented that show that the sensitivity and accuracy of the traditional transient electric birefringence technique can be enhanced by several orders of magnitude through the use of a low‐powered laser and crystal polarizing optics, signal averaging, and digital data processing. Measurements of the field‐free decay of the birefringence yield for the rotational diffusion coefficient, DR = 318 ± 3 sec−1. The length of the rodlike virion, calculated from the Broersma equation with this value of DR and a rod diameter of 15 nm, is 292.5 ± 1.0 nm. Measurements of the growth of the birefringence when an electric field is applied across the sample yield μ2/kT(α∥ − α⊥) = 0.47 ± 0.07, where μ is the permanent dipole moment (assumed parallel to the symmetry axis of the virus) and α∥ − α⊥ is the electrical polarizability anistropy of the virus. Using the value of α∥ − α⊥ measured by O'Konski et al., we then obtain μ = 2.5 × 10−14 esu cm.
Analysis of derivative binding isotherms. Theoretical considerations
Authors: Sturgill T. , Biltonen R. L. 
Published: May 2005

AbstractThe basic theoretical groundwork for the use of derivative binding isotherms in the analysis of ligand binding is presented. The derivative binding isotherm is defined as Γ (Y) = df/dy where f = fractional degree of saturation and y = natural logarithm of the free ligand concentration. Since Γ (y) is a positive function, which goes to zero as y → ±∞, the mean value of y, 〈y〉, and the second and third moments, μ2 and μ3 about 〈y〉 are well defined.For a macromolecular system consisting of N equivalent and independent binding sites, Γ (y) is a symmetrical bell‐shaped function with one maximum. The maximum occurs when y = −ln Kassoc; μ2 = π2/3, and μ3 = 0. For multiple sets of independent binding sites, Γ (y) is a superposition of Γ‐type functions. If the sets are sufficiently well separated in binding free energy, multiple extrema may be seen at positions corresponding to the logarithms of the dissociation constants for the individual sets. In any case, 〈y〉 is equal to the mean value of the logarithms of the dissociation constants for the sets; μ2 > π2/3 and equal to π2/3 plus the variance of the logarithms of the dissociation constants about their mean value; and μ3 is, except by coincidence, not equal to zero and equals the third moment of the distribution of logarithms of the dissociation constants about their mean value.Analysis of Γ(y) for the case of cooperative interactions within a set of binding sites was investigated by examining (1) the Hill model (whose mathematical representation is equivalent to that used to describe antibody heterogeneity except that in the latter case the parameter a, the Sips, constant, is constrained (0 < a ≤1);(2) a common model for cooperativity in which the cooperative free energy is a linear function of the fraction bound; and (3) a general representation of cooperative interactions within a set of sites in terms of ϕ(f), a smooth function that gives the interaction free energy in units of RT.For the Hill model (or Sips model) Γ(y) is a symmetrical function with one maximum at y = (−1)/a)lnK, μ2 = π2/3a2; and μ3 = 0. For the case in which the cooperative free energy is a linear function of f [ϕ(f) = cf], 〈y〉 = −ln K0 + (c/2); μ2 = (π2/3) + c[(c/12) + 1] where c > −4; and μ3 = 0. General expressions for the moments in terms of ϕ(f) are derived. In general, μ2 < (π2/3) for positive cooperativity and μ2 > (π2/3) for negative for negative cooperativity. Γ(y) will be symmetrical if and only if the cooperative free energy is introduced symmetrically about f = 0.5.
Generation of continuous ligand–macromolecule binding isotherms. Use of exponential concentration gradients
Authors: Mountcastle Donald B. , Freire E. , Biltonen R. L. 
Published: May 2005

AbstractContinuous exponential concentration gradients, accurate, precise, and reproducible to better than 1% over at least a 103–104 concentration range, can be easily produced. In fact, it appears that these gradients may be substantially better than this. Such gradients have been used to generate a continuous ligand binding isotherm for the system Mg++ + Eriochrome Black T over a 106 ligand concentration range. This continuous isotherm is shown to be sufficiently precise to provide a first derivative function Γ(y), which is precise to 0.4%. The moments of Γ(y) were calculated and found to be extremely accurate. For example, the second moment about the mean was calculated to be 3.32 and 3.30 for two different experiments compared to a theoretical value of 3.29. The general application of these techniques to generate continuous ligand binding isotherms is discussed.
1H Nuclear magnetic resonance studies of histidine‐containing di‐ and tripeptides. Estimation of the effects of charged groups on the pKa value of the imidazole ring
Authors: Tanokura Masaru , Tasumi Mitsuo , Miyazawa Tatsuo 
Published: May 2005

AbstractThe nmr titration curves of chemical shifts versus pH were observed for the protons of various histidine‐containing di‐ and tripeptides. With these results, the macroscopic pKa values and the chemical shifts intrinsic to each ionic species were determined by a computer curve‐fitting based on a simple acid dissociation sequence. The pKa value of the imidazole ring in N‐acetyl‐L‐histidine methylamide was assumed to represent the intrinsic (or unperturbed) pKa of the imidazole rings of histidine having peptide linkages at both the CO and NH sides. The pKa values of the imidazole rings observed for most di‐ and tripeptides were reasonably reproduced by simple calculations using the intrinsic value and the perturbations due to the CO2− and NH3+ groups located at various positions. Some other factors affecting the pKa value of the imidazole ring are also discussed.
Cooperative ligand binding by ferrihemoglobin: An experimental artifact?
Authors: Anusiem Alphonso C. I. , Beetlestone John G. 
Published: May 2005

AbstractWe have carried out a detailed study of ligand binding of ferrihemoglobins under various conditions. Our results show that n varies with time and that this variation is paralleled by changes in the spectrum of methemoglobin. This suggests some form of structural perturbation. The time‐dependent value of n is discussed in terms of the observed spectral changes accompanying prolonged equilibration.
The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking
Authors: Olson Wilma K. 
Published: May 2005

AbstractA single virtual bond scheme set forth previously for the treatment of average properties of randomly coiling polynucleotides is here applied to the calculation of helical parameters which characterize a regularly repeating polynucleotide molecule. Only a fraction of the enormous number of conformationally feasible helixes fulfill the geometric criteria of vertical base stacking usually associated with ordered polynucleotide chains. Detailed examination of the nature and mode of base stacking feasible in a single helical backbone structure indicates that the handedness of a base stacking arrangement does not correlate either quantitatively or qualitatively with the handedness of the polymer backbone. A number of polynucleotide chains which exhibit lefthanded base stacking patterns in nmr and CD studies may, in fact, be righthanded helixes.
Dielectirc relaxation of DNA in aqueous solutions
Authors: Sakamoto Masanori , Kanda Hirohsi , Hayakawa Reinosuke , Wada Yasaku 
Published: May 2005

AbstractUsing a four‐electrode cell and a new electronic system for direct detection of the frequency differences specturm of solution impedance, the complex dielectric constant of calf thymus DNA (Mr = 4 × 106) in aqueous NaCl at 10°C is measured at frequencies ranging from 0.2 Hz to 30 kHz. The DNA concentrations are Cp = 0.01% and 0.05%, and the NaCl concentrations are varied from Cs = 10−4 M to 10−3 M. A single relaxation regions is found in this frequency range, the relaxation frequency being 10 Hz at Cp = 0.01% and Cs = 10−3 M. At Cp = 0.05% it is evidenced that the DNA chains have appreciable intermolecular interactions. The dielectric relaxaton time τd at Cp = 0.01% agrees well with the rotational relaxation time estimated from the reduced visocisty on the assumption that the DNA is not representable as a rigid rod but a coiled chain. It is concluded that the dielectric relaxiatioinis ascribed to the rotation of the molecule. Observed values of dielectric increment and other experimental findings are reasonably explained by assuming that the dipole moment of DNA results from the slow counterion fluctuation which has a longer relaxation time than τd.
Electric field‐induced conformational change of poly(L‐lysine) studied by transient electric birefringence
Authors: Kikuchi Kazuo , Yoshioka Koshiro 
Published: May 2005

AbstractTransient electric birefringence measurements on poly(L‐lysine hydrobromide) in methanol–water mixtures have been carried out at various solvent compositions in the vicinity of the helix–coil transition region (from 87 to 98 vol % methanol). Anomalous birefringence transients were observed between 90 and 95 vol % methanol above a threshold field strength. A distinct difference between the responses to weak and strong electric fields was noticed over a narrow range of the solvent composition. The effects of polymer concentration and temperature on the field‐strength dependence of the birefringence were studied at a solvent composition of 90 vol % methanol where the anomalous transients appeared most clearly. The double logarithmic plots of the steady‐state specific birefringence versus the square of field strength for different concentrations and temperatures could be superimposed by shifting them horizontally along the abscissa. The threshold field strength which was determined from the shift factor decreased with decreasing concentration. The results provide further evidence that strong electric fields can cause a helix–coil transition in this system under favorable conditions.
Induced circular dichroism of acridine orange bound to double‐stranded RNA and transfer RNA
Authors: Zama Mitsuo , Ichimura Sachiko 
Published: May 2005

AbstractThe induced circular dichroism (CD) in the visible region of acridine orange bound to the double‐stranded RNA from cytoplasmic polyhedrosis virus and to yeast tRNA has been measured as a function of RNA phosphate‐to‐dye ratio (P/D), under the conditions of 0.01 M Na+ at pH 7.0. The shape of the CD spectrum of acridine orange bound to the double‐stranded RNA was quite different from the spectrum of the dye bound to DNA. The CD spectral features of acridine orange bound to the double‐stranded regions in tRNA closely resembled those of the double‐stranded RNA‐dye complex, suggesting that the dyes bind similarly to the two RNA's. It was further found that the CD spectrum of the tRNA‐dye complex at sufficiently high P/D ratios, which is assignable to monomeric, intercalated dye to the base‐paired parts in tRNA, is also distinct from the corresponding spectrum of the DNA‐dye complex.
The spatial distribution of moving macromolecules undergoing isomerization
Authors: Mitchell R. M. 
Published: May 2005

AbstractIn this paper we use probabilistic arguments to derive and discuss the spatial distribution of molecules which are undergoing electrophoresis or centrifugation while at the same time they are switching back and forth between two configurational states. An exact solution is obtained for arbitrary values of the diffusion coefficients of the two isomerizing states. The traditional analytic method of solving this problem, namely, by use of “master equations,” is not completely satisfactory because one can find only the Fourier transform of the solution rather than the solution itself. Our treatment yields the answer one would get if it were feasible to perform the inversion of the Fourier transform.
An easy method for retrieving atomic coordinates from CPK space‐filling molecular models
Authors: De Haën Christoph , Swanson Eric , Teller David C. 
Published: May 2005

AbstractConnectors for CPK space‐filling molecular models have been supplemented with pointed steel wires (ϕ = 1.59 mm) of appropriate lengths and positions to represent atomic bonds. For illustration purposes, the polypeptide backbone of glucagon was equipped with such wire‐core connectors and given a possible conformation. The molecular model was packed into a cubic box and, using a clinical instrument, X‐ray films were taken from three orthogonal directions. Atomic coordinates on the films were then corrected to real‐space coordinates.This method for retrieving atomic coordinates from space‐filling models of modium‐sized polypeptides is easy and can be done wih equipement available everywhere. Coordinates obtained in this way should be useful as starting points for energy minimization, for the calculation of frictional coefficients, and in attempts to solve crystal structures by X‐ray diffraction, using molecular replacement methodology.
Kinetics of proflavin binding to bacteriophages T2L and T4D
Authors: McCall Philip J. , Bloomfield Victor A. 
Published: May 2005

AbstractWe have measured the kinetics of proflavin binding to T‐even bacteriophages—the 700 S and 1000 S forms of T2L, T4D, and T4D os41—by difference spectroscopy at 430 nm. Measurements were carried out from 22° to 37°C. Binding is very slow to encapsulated DNA compared to free DNA, requiring hours to reach equilibrium. The kinetic data are compatible with the two‐step mechanism

where P is proflavin, N is nucleotide, and PN1 and PN2 are complexes. Computer integration of the rate equations allows evaluation of the rate constants; previous equilibrium measurements gave thermodynamic parameters. For all phage studied, the bimolecular step is endothermic with high positive entropy; the second, unimolecular step is highly exothermic with small negative entropy change. Both forms of T2L bind proflavin with essentially the same rate, as do T4D and the osmotic shock resistant mutant T4D os41. This suggests that the encapsulated DNA is equally accessible to proflavin in both forms of each phage. However, T4D binds dye appreciably faster than T2L, indicating that capsid permeability or DNA environment (glucosylation or packing) is different in the two species.