bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solvent effects on the dynamics of (dG‐dC)3
Authors: Freier Susan M. , Albergo Diane Deprisco , Turner Douglas H. 
Published: December 2004

AbstractThe kinetics of the coil‐to‐helix transition of (dG‐dC)3 in M NaCl, 45 mM sodium cacodylate, pH 7, were measured in H2O, D2O, 10 mol % ethanol, 10 mol % urea, and 10 mol % glycerol. At 43°C in H2O the recombination rate is 1.3 ± 0.2 × 107 M−1 s−1; the dissociation rate is 68 ± 10 s−1. The destabilization of the helix in 10 mol % ethanol and 10 mol % urea relative to water is primarily due to a large increase in the helix‐dissociation rate. In 10 mol % glycerol, the destabilization of the helix is due to a decrease in the recombination rate and an increase in the dissociation rate. Above 20°C, two exponential decays longer than 1 μs are observed after a temperature jump. The slower relaxation time is 4–10 times faster than the bimolecular component and is independent of oligomer concentration. We attribute this relaxation to a rapid equilibrium between two helical states. At low temperatures and oligomer concentrations of 1 mM or greater, the helices aggregate in 1M NaCl. Experimental data are presented under conditions where aggregation is unimportant and evidence is given that the ΔH‐determined spectroscopically is unaffected by aggregation.
Translational friction of rigid assemblies of spheres: Derivation and application of new hydrodynamic interaction tensors
Authors: De Haën Christoph , Easterly Russell A. , Teller David C. 
Published: December 2004

AbstractIn connection with our goal of calculating by practical methods the frictional properties of biopolymers from surface shells composed of spheres, we have investigated by the method of reflections the low‐Reynolds‐number hydrodynamic interaction between two unequal‐sized spheres in translation. Previous results, in which the velocities were used as independent variables and which have the form of truncated infinite power series, were substantially extended. By inversion of the power series, new power series with better convergence properties were obtained. Equivalence of these inverted power series with those previously reported based on the method of reflections, when forces are used as independent variables, was demonstrated, and the solutions were again substantially extended. Applying the Lagrange interpolation to data generated from exact theories for the hydrodynamic inteaction between two spheres, it was demonstrated that the various forms of the method of reflections do not just give reasonable power series, but actually yield optimal ones. These findings constitute a unification of diverse approaches and show methods of interconversion of results. On the basis of the power series obtained, a set of new hydrodynamic interaction tensors for two unequal spheres were derived. While the new tensors described the case of two unequal spheres with considerably more accuracy than those previously reported, direct application of these tensors to objects composed of more than two spheres revealed some unexpected problems resulting from overcorrection in the fourth‐order term. However, when the tensors were preaveraged over all orientations of the multisphere object, a formula for the scalar translational friction coefficient was obtained that outperformed all but the most involved earlier approaches. It thus constitutes an improved and practical solution to the problem of computing translational friction coefficients of objects describable by a surface shell of many spheres, such as proteins.
Calculations of the spatial distribution of charge density in the environment of DNA
Authors: Klein Brian J. , Pack George R. 
Published: December 2004

AbstractA technique for modeling the structured environmental charge distribution about isolated polyions of arbitrary geometry is presented and applied to B‐DNA. It describes the three‐dimensional variation of the continuous space charge and allows estimation of local electrostatic potentials and fields that the electrolytic environment induces at nuclei of the polyion. Calculations involve an iterative solution to the set of equations coupling electrostatic potential and average charge density in space. By dividing the region around a DNA segment into finite volume elements, sets of numerically stable atmospheric charge densities have been obtained over a range of concentrations of added monovalent salt. Results are in good agreement with those of Poisson‐Boltzmann calculations on comparable systems and are consistent with findings from Monte Carlo simulations of DNA.
Vibration of DNA polymer in viscous solvent
Authors: Dorfman B. H. , Van Zandt L. L. 
Published: December 2004

AbstractThe problem of viscous damping of vibrating DNA polymer in solution is solved in the low‐amplitude limit for all acoustic branches of the spectrum. The acoustic spectrum covers the microwave region of frequencies. Analytic solutions are obtained for a model describing the DNA polymer as a smooth circular cylinder. Numerical solutions are presented for a model describing the DNA polymer as a twisted cylinder of elliptical cross section. The amount of mass loading is determined for both models and the damped spectrum for the mass‐loaded oscillator is calculated. The viscous damping is found to be a strong function of frequency, singular at very low frequencies for all modes except the torsional mode of the circular cylinder. All acoustic modes are overdamped, implying that the observation of well‐defined resonances in DNA requires either highly structured water on the molecular level or very dry material.
Theoretical studies of nucleic acid interactions. I. Estimates of conformational mobility in intercalated chains
Authors: Taylor Eric R. , Olson Wilma K. 
Published: December 2004

AbstractA combined geometric and potential‐energy analysis has been carried out to identify the torsional arrangements of the nucleic acid chain that can accommodate the intercalation of small planar moieties. In contrast to previous theoretical efforts, which detail local conformations after adjacent bases are positioned in space, the likely geometries are found here on the basis of the base orientations that result from all feasible combinations of the nine torsional variables of the basic dinucleotide intercalation unit. The relatively mobile nature of the sugar‐phosphate backbone, together with the fairly long stretches of chemical bonds between adjacent units, is apparently responsible for the large number of feasible binding geometries. Some previously overlooked conformations with unusual sugar‐puckering combinations and various phosphodiester arrangements are found in the survey. A large proportion of the energetically favored intercalation states are closely related to the backbone conformations of familiar double‐helical models such as A‐, B‐, and Z‐DNA, as well as the Watson‐Crick model. Moreover, the intercalated forms are found to interconvert smoothly along a continuous conformational pathway. The intercalation structures derived from x‐ray crystallographic analyses of drug‐oligonucleotide complexes, in contrast, are stiff three‐dimensional forms essentially frozen in a single domain of conformation space. Specific ligand‐nucleic acid interactions that may be responsible for the experimental observations are not included in this study. The classical intramolecular potential energies reported here are highly approximate, providing only rough gauges of the relative importance of the many competing conformations.
A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double‐ and single‐stranded DNA
Authors: Levy George C. , Craik David J. , Kumar Anil , London Robert E. 
Published: December 2004

AbstractThe nature of internal and overall motions in native (double‐stranded) and denatured (single‐stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular‐dynamics modeling using 13C‐nmr spin‐relaxation data obtained over the frequency range of 37–125 MHz. The broad range of 13C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T1 values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double‐stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τx = ∼10−6 s;τZ = ∼1.8 × 10−8s), which is in good agreement with values calculated from hydrodynamic theory (τx = ∼1.8 × 10−6 s; τZ = ∼2.7 × 10−8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual CH vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τw = ∼4 × 10−9 s, θcone = ∼21°) or as a bistable jump (τA = τB = ∼2 × 10−9 s, θ = ∼15°). We discuss the critical role in molecular‐dynamics modeling played by the angle (β) that individual CH vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τW = ∼0.2 × 10−9 s, θcone = ∼50°), and overall motion is affected by becoming essentially isotropic (τx = τZ = ∼5 × 10−8 s) for the single‐stranded molecules. Since 13C‐nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.
Magnetic birefringence study of the electrostatic and intrinsic persistence length of DNA
Authors: Maret G. , Weill G. 
Published: December 2004

AbstractMagnetic birefringence experiments were performed on solutions of DNA of intermediate molecular weight at several concentrations (cp) over a wide range of ionic strengths (of NaCl and MgCl2). The specific Cotton‐Mouton constant (CM/cp) is found to be independent of cp when contributions from cp to the ionic strength (μeff) are taken into account according to the concept of counterion condensation. For μeff ≳ 10−2M, CM/cp is also independent of the ionic strength; the plateau value results in an acceptable value of the intrinsic persistence length, when a revised theoretical expression for the magnetic birefringence of wormlike chains is used, combined with new experimental data for the monomeric optical and magnetic anisotropy. For μeff < 10−2M, CM/cp strongly, or wealky, increases with decreasing μeff, depending on the valency of the counterion used (Na+ or Mg2+, respectively). This increase agrees quantitatively with the variation of the electrostatic persistence length as predicted by Odijk [(1977) J. Polym. Sci. Polym. Phys. Ed. 15, 477–483], Odijk and Houwaart [(1978) J. Polym. Sci. Polym. Phys. Ed. 16, 627–639], and by Skolnick and Fixman [(1977) Macromolecules 10, 944–948]. A comparison with other experimental data seems to reveal the importance of excluded‐volume effects, which are particularly pronounced in the low‐salt regime.
Interacalation of ethidium ion into DNA and RNA oligonucleotides
Authors: Nelson Jeffrey W. , Tinoco Ignacio 
Published: December 2004

AbstractThe thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo‐oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest‐neighbor exclusion. For the ribo‐oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo‐oligonucleotide showed all sites equivalent and no cooperativity. For the ribo‐oligonucleotides the enthalpy for ethidium binding is −14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M−1 for the two strong sites (4 × 103M−1 for the weak site) or K = 2.5 × 105M−1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo‐oligonucleotide the enthalpy of binding is ‐9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M−1).
Characterization of DNA structures by laser Raman spectroscopy
Authors: Prescott B. , Steinmetz W. , Thomas G. J. 
Published: December 2004

AbstractOriented fibers drawn from aqueous gels of calf‐thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A‐DNA and B‐DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm−1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D2O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A‐ and B‐DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation‐sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700‐cm−1 interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000‐cm−1 region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A‐ and B‐DNA structures. The results are extended to Z‐DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleoproteins and viruses are considered.
Structure of hydrated Na+ ions around a region of A‐ or B‐DNA helix
Authors: Lee W. K. , Gao Y. , Prohofsky E. W. 
Published: December 2004

AbstractA molecular‐dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A‐ or B‐DNA helix with one Na+ counterion per nucleotide. Four Na+ ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ ions were assumed to be Lennard‐Jones spheres that also carried charges. Stillinger four‐point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B‐DNA and 20, 32, and 46 in A‐DNA fragments. The arrangements of the Na+ ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of DNA molecules.
Variation of longitudinal acoustic velocity at gigahertz frequencies with water content in rat‐tail tendon fibers
Authors: Cusack Stephen , Lees Sidney 
Published: December 2004

AbstractBrillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high‐humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799–2815] with the variations of the sonic velocity with water content.
Contributions of the PO ester and CO torsion angles of the phosphate group to 31P‐nuclear magnetic shielding constant in nucleic acids: Theoretical and experimental study of model compounds
Authors: Giessner‐Prettre Claude , Pullman Bernard , Parado Fernando Ribas , Cheng Doris M. , Iuorno Virginia , Ts'O Paul O. P. 
Published: December 2004

AbstractThe magnetic shielding constant of the 31P nucleus of the dimethylphosphate anion is calculated by an ab initio method for different values of the torsion angles about the PO ester bond and different orientations of the methyl groups. The results obtained tend to show that both types of conformational parameters contribute to the value of σ31P. The largest shielding is obtained when the methyl groups are staggered with respect to the PO bond; the smallest, for the eclipsed arrangement. Measurements carried out on the 16 deoxyribodinucleoside monophosphates show that in the majority of cases σ31P is shifted toward lower field for the dimers having large values of 3JPH3′ and 3JPH5′(5″). The theoretical results are discussed in relation to experimental data for polynucleotides and nucleic acids.
Ion transport through liquid membrane by cyclic octapeptides
Authors: Kimura Shunsaku , Imanishi Yukio 
Published: December 2004

AbstractCation transport through a chloroform liquid membrane by cyclic octapeptides—cyclo(Leu‐Pro)4, cyclo(Phe‐Pro)4, and cyclo[Lys(Z)‐Pro]4—was investigated. All of these cyclic octapeptides transported K+ and Ba2+, and the rate of cation transport was correlated with the ability to extract cations from the aqueous phase to the chloroform phase. Among them, cyclo (Leu‐Pro)4 was the most efficient and transported K+ and Ba2+ selectively from other alkali and alkaline earth cations, respectively. The rate of K+ transport by cyclo(Leu‐Pro)4 was about one‐third as fast as that by dicyclohexyl 18‐crown‐6. Picrate anion transport against its concentration gradient was observed by cyclo(Leu‐Pro)4, which is conjugated with the selective transport of K+. Complex formation in a liposome between cyclo(Leu‐Pro)4 and Ba2+ was observed, but the binding constant was low.
Viscometry and sedimentation equilibrium of partially hydrolyzed hyaluronate: Comparison with theoretical models of wormlike chains
Authors: Cleland Robert L. 
Published: December 2004

AbstractFractionated samples of sodium hyaluronate of low molecular weight were used to calibrate the carbazole method for glucuronyl analsis and to determine the density increment (based on dry weight) of 0.444 (±0.003) mL/g in water and 0.386 (±0.003) mL/g for samples dialyzed against 0.2M NaCl. Weight‐average molecular weights obtained by high‐speed sedimentation equilibrium were used to calibrate the limiting viscosity number [η] in 0.2M NaCl, which gave [η]/Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 105. Experimental data from this work and the literature, including viscosity and light‐ and small‐angle x‐ray scattering measurements, were compared to theoretical chain models of the Kratky‐Porod (KP) wormlike and the helical wormlike (HW) chain, as treated by Yamakawa and collaborators. Although either model could be fitted to experimental data about equally well with consistent parameters, provided those for the HW chain were of weakly helical nature, calculation of the unperturbed meansquare end‐to‐end distance as a function of chain length from a conformational model favored the KP chain alternative. The parameters that provide the best fit to experimental data for the KP wormlike model are a persistence length of 4.5–5 nm and a diameter of 1.1 nm. The latter is resonable for a hydrated hydrodynamic cylinder in view of the approximate unhydrated value of 0.7 nm estimated from the density increment.
Effects of viscous solvent on DNA polymer in a fiber
Authors: Dorfman B. H. , Van Zandt L. L. 
Published: December 2004

AbstractThe viscous forces acting on a DNA macromolecule in a fiber are calculated. The DNA polymer is modeled as an infinite rod of elliptical cross section with a grooved surface. The viscous solvent is hydrodynamic water. Appropriate boundary conditions for determining the viscous forces on the acoustic vibrational modes are discussed. The viscous forces acting on each mode are then calculated as functions of both frequency and amount of water in the fiber. The mass loading of the DNA due to water in the grooves is shown to reduce the longitudinal acoustic velocity, which agrees with recent experimental results. The longitudinal modes are determined to be underdamped and correspondingly sharp over a range of frequencies and humidities appropriate to experimental conditions. The torsional and transverse acoustic modes are still strongly overdamped.
Kinetics of irreversible dissociation for proteins bound cooperatively to DNA
Authors: Balazs Anna C. , Epstein Irving R. 
Published: December 2004

AbstractWe consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one‐dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22, 1697–1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n−2) internal positions of an n‐cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero‐order dissociation kinetics predicted by the Lohman model.
Liquid crystallinity in collagen solutions and magnetic orientation of collagen fibrils
Authors: Murthy N. S. 
Published: December 2004

AbstractStudies of the optical birefringence of solutions of acid‐soluble collagen from rat‐tail tendon at 22°C in the pH range 1.0–6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt‐soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the magnetic field.
Dielectric properties of aqueous solutions of sonicated DNA above 40 MHz
Authors: de Xammar Oro Juan R. , Raul Grigera J. 
Published: December 2004

AbstractThe dielectric properties of sonicated calf‐thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix‐to‐coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.