Kiwamu Yamaoka

Electric dichroism of DNA in aqueous solutions: electric field dependence

: The ionic strength and molecular weight dependence of the electric field dichroism of DNA, using native and sonicated calf thymus DNA, has been examined in the range of 0.09-1.0 mM NaCl solutions for molecular weights ranging from 1.24 x 10(5) to 44 x 10(5). The application of a classical theoretical analysis implies that the orientation results from an induced moment which appears to saturate at moderate fields of several killivolts per centimeter and that the induced moment is at least partly characteristic of that expected of a polyion whose charge is partially counterion compensated. The orientation leads to dichroism values which are in accord with other observations and are lower than expected for a B-form rod of DNA. These values, however, are not uniquely interpretable as resulting from base tilting.

Ionic strength and counterion repulsion as factors in the behavior of polyions in orienting electric fields

The effect of counterion-counterion repulsion on the orientation of DNA, a polyion of high charge density is examined by electric-field orientation experiments. The charge species of the counterion and the ionic strength effect the orientation in a manner consistent with a theoretical treatment of the polarization of high charge density polyelectrolytes in terms of the effect of the applied field on the equilibrium distribution of condensed counterfoils on the polyion.

Reversing‐pulse electric birefringence of disklike suspension in the low electric field region: An extension of the ion‐fluctuation model

A rigorous theory is formulated for the reversing‐pulse electric birefringence (RPEB) for the ionized macroion of cylindrical symmetry, according to the idea of the coupled rotational (with the molecular relaxation time τθ) and ion‐atmosphere dynamics of rodlike macroion, developed previously by Szabo et al. [J. Chem. Phys. 85, 7472 (1986)]. The present theory is based on the interaction of applied electric pulse with two electric dipole moments of the macroion; one is due to the ion‐atmosphere polarizability α3 with a single relaxation time τI for the distortion of ion‐atmosphere along the longitudinal axis, as originally proposed, and the other is newly considered as being due to the intrinsic molecular, or instantaneously field‐induced, polarizability anisotropy Δα’ between the longitudinal and transverse axes of the macroion. The RPEB expressions were derived with the electric and hydrodynamic parameters (α3/Δα’ and τI/τθ) for the low‐field region. Theoretical curves were calculated with appropriate v...

The electric dipole moment of DNA-binding HU protein calculated by the use of NMR database

Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein databases. The dipole moments of globular proteins have hitherto been calculated with X-ray databases and NMR data have never been used before. The advantages of NMR databases are: (a) NMR data are obtained, unlike X-ray databases, using protein solutions. Accordingly, this method eliminates the bothersome question as to the possible alteration of the protein structure due to the transition from the crystalline state to the solution state. This question is particularly important for proteins such as HU protein which has some degree of internal flexibility; (b) the three-dimensional coordinates of hydrogen atoms in protein molecules can be determined with a sufficient resolution and this enables the N-H as well as C = O bond moments to be calculated. Since the NMR database of HU protein from Bacillus stearothermophilus consists of 25 models, the surface charge as well as the core dipole moments were computed for each of these structures. The results of these calculations show that the net permanent dipole moments of HU protein homodimer is approximately 500-530 D (1 D = 3.33 x 10(-30) Cm) at pH 7.5 and 600-630 D at the isoelectric point (pH 10.5). These permanent dipole moments are unusually large for a small protein of the size of 19.5 kDa. Nevertheless, the result of numerical calculations is compatible with the electro-optical observation, confirming a very large dipole moment in this protein.

Electric linear dichroism. A powerful method for the ionic chromophore–colloid system as exemplified by dye and montmorillonite suspensions ☆

Abstract The electric linear dichroism (ELD) measures the anisotropic absorption of a chromophore in solution under externally applied electric pulse field, which orients the solute molecule (particle) rotationally to the field direction. The ELD method is used to study at 20°C the binding mode and electrooptic properties of a nonlinear optical molecule (DAES), 4-[2-[4-(dimethylamino)phenyl]ethenyl]-1-ethylpyridinium, in the presence of montmorillonite K10 (MK-10) in the absorption region at mixing ratios ( D / S ) between 0.1 and 0.97, where D is the concentration of DAES and S is the cation exchange capacity of MK-10. Descriptions are given on a new home-built ELD apparatus. The measured quantities are the wavelength (600–300 nm) and field-strength (0–3 kV cm −1 ) dependence of the reduced dichroism, Δ A / A . The optical transition moment directions of bound DAES is determined from the observed ELD spectra relative to the symmetry axis of the field-oriented disklike MK-10 particle. Discussion is given both on the field-strength dependence of Δ A / A and on the ELD spectral analysis in terms of the tilt, roll, and inclination angles of the molecular plane of DAES bound to the surface and/or interlayer of MK-10 particle. The DAES molecule is not bound flatly on the surface or between the layers, but inclined at 35–39°, tilted by ±21°, and rolled by ±(27–33)° relative to the clay plane. The DAES–MK-10 system is no more associative than the clay itself on the basis of the electric-dichroism-average relaxation time, evaluated from the field-off decay signal, of DAES bound to MK-10 particle in solution.

Low‐field expressions for reversing‐pulse electric birefringence of ionized polyions with permanent, ionic, and electronic dipole moments: A further extension of the ion‐fluctuation theory and the application to poly(α,L‐glutamic acid)

A rigorous theory was further extended for the reversing‐pulse electric birefringence (RPEB) of the ionized polyion of cylindrical symmetry with the permanent dipole moment μ3, in addition to two previously considered electric dipole moments, i.e., the root‐mean‐square‐average moment 〈m23〉1/2 resulting from the fluctuation of ion–atmosphere along the longitudinal (3)axis of the polyion with a single relaxation time τI, as originally proposed by Szabo et al. [J. Chem. Phys. 85, 7472 (1986)], and the electronic moment from the intrinsic covalent polarizability anisotropy Δα between the longitudinal and transverse axes of the polyion by Yamaoka et al. [J. Chem. Phys. 101, 1625 (1994)]. The extended RPEB expressions were derived with three electric and hydrodynamic parameters (p=μ23/kTΔα, q=〈m23〉1/2/kTΔα, and τ*=τI/τθ) in the Kerr‐law region. Calculated with appropriate values to these parameters, the theoretical curves show such new features that either maxima or minima appear in the buildup and reverse proc...

Effect of aliphatic alcohols on the conformation of poly (l-ornithine hydrobromide) as studied by square-pulse and reversing-pulse electric birefringence

Abstract The electric birefringence and circular dichroism spectra of poly( l -ornithine hydrobromide) have been measured in ethanol/water, 2-propanol/water and tertiary butyl alcohol/water mixtures of various compositions. This charged polypeptide underwent a transition from the coil conformation to the helical conformation at high alcohol content in every case tested. Anomalous birefringence signals, indicative of a field-induced helix-to-coil transition. were observed at high electric fields only in the case of ethanol/water mixtures. The reversing-pulse electric birefringence of this polypeptide has been studied in ethanol/water mixtures and in neutral aqueous solution. Upon rapid reversal of the pulse field, no transient could be observed. This confirms that the electric-field orientation of poly( l -ornithine hydrobromide) results predominantly from the contribution of the counterion-induced dipole moment, regardless of its molecular conformations. It is very probable that the backbone permanent dipole moment of the helical conformation is largely suppressed by the counterion-induced dipole moment in the ionized form.

Adsorption of deoxyribonucleic acid and poly(cytidylic acid)•Poly(inosinic acid) onto the poly(styrene) latex

Abstract Adsorption of native and heat-denatured calf thymus DNA (Mw = 2.5 × 105 and 4.5 × 106) and poly(cytidylic acid) · poly(inosinic acid) ((C)n · (I)n, Mw = 1.5 × 105, and 7.7 × 105) duplex onto the negatively charged poly(styrene) latex was examined at 4°C with emphasis on the effect of the molecular chain length, the species of added salts (NaCl, CaCl2, and MgCl2), and their ionic strengths ((1–10) × 10−3). The amount of adsorbed nucleic acids was determined photometrically from teh difference in the concentrations before and after mixing with the latex (average diameter, 471 nm; surface charge density, −3.52 μC/cm2). For native DNA, the higher the molecular weights and ionic strengths were, the more was adsorbed, the effect of the added ions being Mg2+ > Ca2+ ⩾ Na+. For denaturated DNA, the adsorption behavior was qualitatively the same but the adsorbed amount was less. These trends were reversed for (C)n · (l)n, but the effect of added ions remained the same as that for DNA. The divalent cations play a role of a binder between two types of negative charges on nucleic acids and on latex.

Metachromasy of crystal violet in the presence of poly(α-L-glutamic acid) and the bound-dye spectra determined by the principal/component-analysis method

In order to study quantitatively the metachromatic behaviour of crystal violet (CV) in the presence of poly (alpha-L-glutamic acid), (poly (Glu)), four sets of the absorption spectra of the poly(Glu)-CV system were analyzed by the extended principal-component-analysis (PCA) method. Two classes of CV-Glu complexes, i.e., the bound-CV species, are present in poly(Glu) regardless of its helical and random-coiled conformations over a wide range of the mixing ratios of Glu residues to CV (P/D). The spectra of the bound CV in a low P/D range < 100 (complex I), extracted by the PCA method, are conformation-dependent showing three absorption bands at 506, ca. 550, and 610-620 nm. The spectra of the bound CV in a high P/D range > 100 (complex II) are closely related to, but not identical with, the free CV. The molar fractions of free CV and complexes I and II, evaluated in the P/D range of 0-150, indicate that CV binds more to the random-coiled poly(Glu) than to the helical one. Metachromasy of CV results from a complicated interplay of an unbound and two differently bound species.

Electric field orientation of sonicated κ-carrageenan in aqueous solution: ionic polarization of loosely bound counterions

Abstract The electric field orientation of κ-carrageenan in aqueous solution was investigated by the reversing-pulse electric birefringence method at 633 nm and 33°C. The observed field orientation was attributed to the fast-induced polarization of the counterions (K + ions) in the ionized polymer domain. Since the charge density parameter ξ of non-helical and elongated κ-carrageenan is 0.66, the fast-induced ionic polarization is probably due to the counterions loosely bound by Debye-Huckel type electrostatic forces, but not due to the condensed counterions.