The effect of acridine dyes on the molecular structure of DNA]

DNA--acriflavin complexes have been investigated by the methods of flow birefringence and viscometry. The intrinsic viscosity and the optic anysotropy of the complex increase with the increasing quantities of binding dye. Experimental data are treated on the basis of different models of binding. At high ionic strength (mu = 0,1) one type of binding takes place which is described by the intercalation model. In this case the thermodynamic rigidity of DNA-molecule within the complex is proportional to "r". In solutions of low ionic strength (mu = 0,001), two types of DNA-acriflavin binding occur: intercalation and external binding. At low ionic strength, the spectrophotometric titration technique is shown to give a reduced value of "r".     

Diphasic transformations of F-actin. Effects of urea and MgCl2 on F-actin.

Asakura, Taniguchi and Oosawa [1]proposed that muscle actin polymer under sonic vibration is in a different state from that of the ordinary double stranded helical structure (F-actin), characterised by partially interrupted structures of F-actin, a state of "f-actin". In order to confirm different states for actin polymers [1, 2], physicochemical studies were made by measurements of viscosity, flow birefringence, electric birefringence, fluorescence, electron microscopy, quasielastic light scattering and ATP splitting. The following results were obtained. (1) F-actin polymers can undergo two processes of depolymerization upon treatment with urea and various salts as judged by measurements of flow birefringence and viscosity: one is a rapid process in a solution containing K+ or Ca2+ and urea; the other is a slow process following a brief rapid one in a solution containing Mg2+ and urea. (2) In the presence of Mg2+ and a suitable concentration of urea, F-actin (FMU-actin) appeared to exhibit different properties than ordinary F-actin; it had lower viscosity and lower flow birefringence and it had on the whole a more flexible polymer structure, also judging from experiments of quasielastic light scattering, electric birefringence. The different structure was confirmed directly be electron microscopic observation. The aromatic side chains of FMU-actin were also more mobile than those of F-actin judging from fluorescence measurements. The transformation between F-actin and FMU-actin was reversible. (3) The state of FMU-actin polymers was also characterized by ATP splitting; FMU-actin split about one mole of ATP into ADP and inorganic phosphate per mole of actin monomer at room temperature, where F-actin did not. A molar excess of Mg2+ with respect to actin monomer at room temperature, where F-actin did not. A molar excess of Mg2+ with respect to actin monomer is required for ATP splitting. F-actin in solutions containing K+ or Ca2+ and urea did not split ATP. FMU-actin activated on Mg-ATP-ase of myosin at nearly the same rate as that of F-actin. (4) We have postulated a flexible filament model (f-actin). The relationships between the structure of f-actin and its functional role for force generation during contraction are discussed.     

Steady-state opticohydrodynamic properties of DNA: Molecular weight dependence and the internal viscosity problem

Extinction angles, flow birefringence, and intrinsic viscosities are compared for linear, bihelical DNAs from viral and other sources that span a range in molecular weight from ～10⁵ to 1.3 × 10⁸. This range effectively spans the region over which transition from rigid-rod to expanded-coil hydrodynamic property behavior occurs. All DNAs are in identical, phosphate–EDTA, neutral-pH buffers, 0.1M in NaCl. The extinction angle is a hydrodynamic property only and is thus particularly sensitive to effects of kinetic chain rigidity or internal viscosity. Our extinction angle results cannot be interpreted by any simple, single-function theoretical expression. Rather, they must be divided into distinct high- and low-molecular-weight domains. The low-molecular-weight region is typical of rigid-particle opticohydrodynamic property behaviour characterized primarily by particle orientation. The high-molecular-weight domain shows evidence for a finite internal viscosity effect, however, which can be interpreted as very nearly Kuhnian using Cerf's amplification of the Gaussian subchain model to include internal viscosity. It is found that the high-molecular-weight, monodisperse viral DNAs from T7, T5, and T2 bacteriophage show an internal viscosity contribution to the limiting extinction angle–shear rate ratio of ～3 × 10^?3 s. An effect of this magnitude may be marginally important in interpreting extinction angle and certain other hydrodynamic property data for high-molecular-weight DNA systems. Internal viscosity effects do not appear to be manifest in the ratio of flow birefringence to intrinsic viscosity, however, and the persistence length of the high-molecular-weight DNAs is found to be independent of molecular weight to within estimated experimental uncertainty.     

Optico-hydrodynamic properties of high molecular weight DNA from steady-state flow birefringence and viscosity at extremely low velocity gradients

The flow birefringence, extinction angles, and shear-dependent viscosity over a velocity gradient range of approximately 0.1–3 sec^?1 have been obtained for T2 bacteriophage DNA at low concentration in neutral aqueous buffer. The data are found to be interpretable and self-consistent in terms of subchain dynamical theory, including hydrodynamic, interactions and excluded volume, and the parameters characterizing these phenomena are in good agreement with the results of other hydrodynamic experiments and theoretical calculations. No necessity for modification of the subchain model in terms of limited extensibility or internal viscosity is found for high molecular weight DNA at the velocity gradients studied, although the latter cannot be ruled out on the basis of the present data. The Kuhn statistical segment length is determined from the intrinsic optical anisotropy and is estimated as 930 Å. Implications of these findings and their relation to appropriate dynamical models for DNA are discussed.     

Low velocity gradient flow birefringence and viscosity changes in hyaluronate solutions as a function of pH.

The flow birefringence and extinction angle over a velocity gradient range of approximately 5–100 sec^?1, and the zero shear-viscosity have been obtained from human umbilical cord hyaluronic acid at concentrations of 0.25, 0.125 and 0.0625%, and pHs 6.0, 6.5, 7.0, 7.5, 8.0, and 8.5 and constant ionic strength 0.1. The data indicate a large change in optical anisotropy as a function of pH, with most of the transition in the pH range 7.0–7.5, i.e., across the physiological range. The sign of the anisotropy changes between pH 8.0 and 8.5. These results, together with changes in the extinction angle and intrinsic viscosity as a function of pH, suggest a pH-dependent structural change in the system. Due to the abruptness of the transition, as evidenced by the intrinsic viscosity and flow birefringence, it is probable that the structural transition is cooperative. If the data are interpreted in terms of the Rouse-Zimm Gaussian subchain theory, a modification of the model in terms of the Haller-Cerf concept of internal viscosity is required. Thus, the demonstrated properties of hyaluronate solutions indicate a system with memory of stress. Due to the presence of large concentration effects discernible in the extinction angle measurements, hyaluronic acid probably exists as a network in solution. The results are discussed with respect to the mechanoelectrical transducing properties of hyaluronates and stress-dependent changes in ORD already reported.     

Intrinsic Birefringence of Poly-γ-Benzyl-l-Glutamate, A Helical Polypeptide, and the Theory of Birefringence

The intrinsic birefringence of macromolecules can be obtained directly from flow birefringence measurements in a solvent whose refractive index matches that of the solute. A small and positive value (approximately 0.01) was found for the helical polypeptide, poly-γ-benzyl-L-glutamate. The birefringence in solvents of varying index calculated from the Peterlin-Stuart theory using this value of the intrinsic birefringence did not agree with experimental values. Considerations of polydispersity and shear deformation indicated that the discrepancy could not be attributed to these effects. Also it could not be explained in terms of specific solvent effects. It is concluded that optical properties cannot be derived from the continuum model employed by Peterlin and Stuart. Much better agreement was obtained with a helical dipole necklace model.     

In vitro polymerization of flagellar and ciliary outer fiber tubulin into microtubules.

About 10--20% of the total protein in the outer fiber fraction was solubilized by sonication in a solution containing 5 mM MES, 0.5 mM MgSO4, 1.0 mM EGTA, 1.0 mM GTP, and 0 or 50 mM KC1 at pH 6.7. The sonicated extract was shown by analytical centrifugation to consist largely of a 6 S component (tubulin dimer), having a molecular weight of 103,000, as determined by gel filtration, and possessing a colchicine-binding activity of 0.8 mole per tubulin dimer. The tubulin fraction failed to polymerize into microtubules by itself. Addition of a small amount of the ciliary outer fiber fragments or reconstituted short brain microtubules, however, induced polymerization, as demonstrated by viscosity of flow birefringence changes as well as light or electron microscopic observations. The growth of heterogeneous microtubules upon mixing outer fiber tubulin with DEAE-dextran-decorated brain microtubules was observed by electron microscopy. Microtubules were reconstituted from outer fiber tubulin without addition of any nuclei fraction when a concentrated tubulin fraction was warmed at 35degree. A few doublet-like microtubules or pairs of parallel singlet microtubules that were closely aligned longitudinally could be observed among many singlet microtubules. Unlike other fiber microtubules, the reconstituted polymers were depolymerized by exposure to Ca2+ ions, high or low ionic strength, colchicine, low temperature or SH reagents. No microtubules were assembled under these conditions.     

Intrinsic viscosity of bead models for macromolecules and nanoparticles

The calculation of the intrinsic viscosity by means of classical treatments of bead models, typically composed of a number of identical beads, presents some problems when applied to models where the beads are unequal and their number is not very large. A correction to this problem was proposed 10 years ago (García de la Torre and Carrasco in Eur Biophys J 27:549–557, 1998). This so-called volume correction, which consisted of adding a term proportional to the volume of the model, was proved to be rigorous in physico-mathemathical terms, and produced improved results in some circumstances, but not always. Recently, the volume correction is being reconsidered so that with some deduced or empirical modifications, it can allow for safer predictions of the intrinsic viscosity. This paper contributes a discussion and further improvements of that correction for the intrinsic viscosity.     

Hydrodynamic properties of DNA and DNA-lipid complex in an elongational flow field

The aim of this study was to determine the difference between hydrodynamic properties of DNA-cetyltrimethylammonium (CTA) complex and those of DNA, which may be related to the difference in fibre-forming ability of DNA-CTA from that of DNA. Responses of DNA and DNA-CTA complex to an elongational flow field were investigated. In both solution systems, results suggesting a coil-stretch transition were obtained. From a critical strain rate value, the radius of gyration of DNA-CTA molecules in ethanol-glycerol solution was revealed to be 0.3-0.5 times of that of DNA in aqueous NaCl solution. Shear viscosity of DNA-CTA solution was much smaller than that of DNA solution, also suggesting a smaller size of DNA-CTA in ethanol-glycerol solution than that of DNA in aqueous NaCl solution. The plateau birefringence value of the DNA-CTA system, a parameter that indicates the local molecular conformation and the molecular arrangement, was only about 1/10 of that of the DNA system. There is an empirically determined molecular model of DNA-CTA complex in which a DNA molecule is sheathed by a cylindrical crust made of CTA chains. This structure reduces the DNA molecular density in a pure elongational flow field region but cannot explain the observed reduction of birefringence intensity. The small plateau birefringence value of DNA-CTA compared with that of DNA was attributed to the reduced molecular polarizability by the particular conformation of DNA molecules and CTA chains in the DNA-CTA system such as that expected by the conformational models.     

Membrane viscoplastic flow.

In this paper, a theory of viscoplasticity formulated by Prager and Hohenemser is developed for a two-dimensional membrane surface and applied to the analysis of the flow of "microtethers" pulled from red blood cells attached to glass substrates. The viscoplastic flow involves two intrinsic material constants: yield shear and surface viscosity. The intrinsic viscosity for plastic flow of membrane is calculated to be 1 X 10(-2) dyn-s/cm from microtether flow experiments, three orders of magnitude greater than surface viscosities of lipid membrane components. The fluid dissipation is dominated by the flow of a structural matrix which has exceeded its yield shear. The yield shear is the maximum shear resultant that the membrane can sustain before it begins to deform irreversibly. The yield shear is found to be in the range 2-8 X 10(-2) dyn/cm, two or three orders of magnitude smaller than the isotropic tension required to lyse red cells.     

Numerical simulation of non-Newtonian blood flow dynamics in human thoracic aorta

Three non-Newtonian blood viscosity models plus the Newtonian one are analysed for a patient-specific thoracic aorta anatomical model under steady-state flow conditions via wall shear stress (WSS) distribution, non-Newtonian importance factors, blood viscosity and shear rate. All blood viscosity models yield a consistent WSS distribution pattern. The WSS magnitude, however, is influenced by the model used. WSS is found to be the lowest in the vicinity of the three arch branches and along the distal walls of the branches themselves. In this region, the local non-Newtonian importance factor and the blood viscosity are elevated, and the shear rate is low. The present study revealed that the Newtonian assumption is a good approximation at mid-and-high flow velocities, as the greater the blood flow, the higher the shear rate near the arterial wall. Furthermore, the capabilities of the applied non-Newtonian models appeared at low-flow velocities. It is concluded that, while the non-Newtonian power-law model approximates the blood viscosity and WSS calculations in a more satisfactory way than the other non-Newtonian models at low shear rates, a cautious approach is given in the use of this blood viscosity model. Finally, some preliminary transient results are presented.     

Optico-hydrodynamic properties of high molecular weight DNA. II. Effect of aqueous glycerol solvents

The optical and hydrodynamic properties of T2 bacteriophage DNA have been determined by steady-state flow birefringence and viscosity in glycerol–aqueous buffer solvents at 25°C. Flow birefringence and extinction angle data were obtained over a velocity gradient range of 0.1 to 5 sec^?1 and at concentrations from 3 to 55 μg/ml in solvents containing approximately 30, 42, and 48 vol-% glycerol. Large optical backgrounds were observed in the mixed solvent flow birefringence studies which presented special experimental difficulties; these are described and their effect upon the flow birefringence data are discussed. The data on extinction angle provide no evidence for an internal viscosity effect on the stationary-state hydrodynamic properties of high molecular weight DNA over a range of solvent viscosity from 0.9 to 4.6 cP. Both the optical and hydrodynamic properties under present conditions of measurement appear to be self-consistent in terms of the values for these quantities in neutral aqueous buffer solution. Interpretation of the birefringence is complicated by uncertainties inherent in calculating the form anisotropy of DNA in non-aqueous solvents, but the data imply no large changes in helical structure with increasing glycerol concentration. Both intact and slightly degraded DNA samples were investigated, and no significant polydispersity effects were observed under the experimental conditions described.     

DNA interaction with low molecular ligands of different structure. II. Complexes of DNA with actinomine and its analogs

DNA-complexes with actinomine and its analogues containing omega-dialkylaminoalkyl groups at 1,9 positions of the phenoxazone moiety were studied by technique of spectrophotometry, viscometry and flow birefringence. In the process of spectrophotometry titration two groups of spectra corresponding to different DNA--ligand ratio in a complex were observed. According to the experimental data the investigated compounds are bounded to DNA by means of intercalation and external binding. There within a region of low degrees of binding the intercalation type of the ligand--DNA interaction prevails. In virtue of the spectrophotometry data the intercalation binding share was calculated. The intrinsic viscosity of a complex increases in the case of ligand intercalation and does not change as it joins to the DNA double-helix from outside. Optical anisotropy of DNA molecule increases linearly irrespective of the way of ligand binding. Data on the flow birefringence permits to conclude that under external binding the angle between the normal to the ligand chromophore plane and the axis of DNA double-helix is about zero. During ligand intercalation the equilibrium rigidity of DNA molecules increases.     

Conformation of the denatured DNA molecule in solutions of different ionic strengths]

The conformation of the denatured DNA molecule of different molecular weights in the solutions of various ionic composition was studied by the methods of viscometry, light scattering and flow birefringence. Formaldehyde purified from metallic ions with the help of ionites was used for fixation of the denatured state of the DNA molecule. It has been shown that theories developed for flexible macromolecules are in a sufficient accordance with hydrodynamical and optical data. The unperturbed dimensions, equilibrium rigidity of the macromolecule in solutions of different ionic strengths, mu, were determined. In the range of mu greater than or equal to 0.005 the length of Kuhn's segment (A) is equal to approximately 40 A and its value increases with an increase of mu. At mu 0.001 A approximately 60 A and mu 0.0005 A approximately 85 divided by 100 A. A relation between intrinsic viscosity and molecular weight of the denatured DNA molecule was established. Data on the flow birefringence in the solutions of the denatured DNA have shown that the sigh of optical anisotrophy of the macromolecule depends on the ionic strength. The observed dependency may be explained only by assuming that ionic strength influences the equilibrium orientation of nitrogen base planes with respect to the main chain of the macromolecule.     

Process and molecular data of branched 1,3-β-D-glucans in comparison with Xanthan

Bioreactor cultivations were carried out with Schizophyllum commune and Xanthomonas campestris. Influence of process parameters and downstream processing on molecular data (molecular weight, intrinsic and shear viscosity) of the secreted exopolysaccharide are shown. Glucan formation of S. commune was enhanced by oxygen limitation. Depending on the type of agitator used, a maximum glucan formation rate of 0.12 kg/(m³ · h) was reached. During cultivation molecular weight and intrinsic viscosity went through a broad maximum with maximum data of 1.3 10⁷ g/mol and 15,400 cm³/g, respectively. After substrate consumption glucan degrading enzymes (glucananses) were released by S. commune. For washing out low molecular substances and concentrating cellfree glucan solutions cross-flow filtration technique with hollow fiber cartridges (molecular cut-off 100,000) were used. After this procedure the shear and intrinsic viscosity were decreased. In contrast to Xanthan, shear viscosity of glucan solutions was not affected by a change in pH from 2 to 12. The intrinsic viscosity of aqueous Xanthan and glucan solutions was opposingly altered by adding salt.List of Symbols A number of capillaries - C ^*g/(dm³ · h) formation rate - D ^–1 shear rate - k Pa/sⁿ consistency index - n flow behaviour index - MW g/mol molecular weight - R m radius - t h time - V dm³ volume - Y yield coefficient - mPas shear viscosity - [] cm³/g intrinsic viscosity - Pa shear stress Indices PS polysaccharide - X cell mass - S substrate - m maximum Dedicated to Prof. Dr. Fritz Wagner on his 60th birthday     

Flow birefringence and intrinsic viscosity of a T2 bacteriophage DNA–methylated bovine serum albumin complex

The flow birefringence, extinction angles, and intrinsic viscosity have been determined at low velocity gradients for a complex of T2 bacteriophage DNA and methylated serum albumin prepared in dilute solution to a stoichiometry of approximately 90 proteins per DNA molecule. Comparative data upon equivalent solutions of pure uncomplexed T2 DNA are also presented, and these data are completely in accord with the results of previous study. The experimental data are interpreted in terms of current dynamical theory and indicate that the complex has an essentially linear chain structure, consisting of approximately two DNA molecules, which is hydrodynamically indistinguishable from the pure DNA and that extensive internal or intramolecular binding in the complex does not occur. Although interpretation of the results is hampered by an apparent moderate degree of polydispersity in the complex preparations and by relatively large shear extrapolations, the data for both DNA and the complex are substantially in accord with dynamical theory for a nondraining bead subchain model having high kinetic segmental rigidity.     

Theory of optical ellipsometric measurements from muscle diffraction studies.

A theory of optical ellipsometry describing the complete phase shift and ellipticity of light diffracted from a single muscle fiber is developed. We show that both the phase shift information, described commonly by the birefringence of the fiber, and the ellipticity information, described by the differential polarizability ratio, are necessary to provide a complete picture of the complex contributions to the total optical anisotropy spectra from a diffraction pattern derived from the striated muscle cell. Both form and intrinsic contributions play significant roles in either the birefringence measurement or the differential field ratio measurement. However, we show that their relative weights in these two measured quantities are different, and measuring both of these parameters is necessary to obtain a more complete assessment of the cross-bridge structure and dynamics. The theoretical results have been tested for three different situations: solvent index matching, passive stretch of a resting fiber, and cross-bridge changes under isometric conditions. Comparisons between experimental data and simple model calculations provide much information regarding cross-bridge orientation and structure.     

Birefringence of actin.

The total strain birefringence of F-actin isolated from chicken gizzards was measured as a function of elongation in thin transparent films. Each film held at a certain elongation in a jig was allowed to swell in a penetrating but nondissolving liquid. Seven liquids with different refractive indices were employed. The thickness of the film in each swelling liquid was obtained once equilibrium was established. At each elongation, from 0 to 16%, a Wiener curve was obtained. The minima of the Wiener curves yielded the intrinsic birefringence of F-actin as a function of elongation. The intrinsic birefringence increases with elongation up to 16%, above which the thin films break. The form birefringence at a set refractive index also increases with elongation. The implication of the strain birefringence of F-actin is discussed as it affects the optical properties, mainly light scattering, of tissues such as the fiber cells of lens of the eye.     

Preservation of differences in the degree of polymerization of actin, isolated at different stages of ontogenesis after its purification]

Actin preparation from skeletal muscles of new-born, 10 days old and adult rabbits, containing less than or equal to 5% of inactivated actin and 1-2% of other myofibrillar proteins, were studied by means of flow birefringence and viscosimetry. It is found, that, like earlier studied crude preparations, purified actin preparations, isolated at different ontogenesis stages, differ in their intrinsic viscosity and extinction angle. These differences retain after the additional trypsin treatment. Non-polymerizing fraction of Straub F-actins, isolated from rabbit muscles of all ontogenesis stages studied, practically does not affect the polymerization in the course of ontogenesis, which is due to changes in its stucture.