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This study presents a new framework for extracting single ion diffusion coefficients in ion exchange membranes from experimental ion sorption, salt permeability, and ionic conductivity data. The framework was used to calculate cation and anion diffusion coefficients in a series of commercial ion exchange membranes contacted by aqueous NaCl solutions. Counterion diffusion coefficients were greater than co-ion diffusion coefficients for all membranes after accounting for inherent differences due to ion size. A model for ion diffusion coefficients in ion exchange membranes, incorporating ideas from counterion condensation theory, was proposed to interpret the experimental results. The model predicted co-ion diffusion coefficients reasonably well with no adjustable parameters, while a single adjustable parameter was required to accurately describe counterion diffusion coefficients. The results suggest that for cross-linked ion exchange membranes in which counterion condensation occurs condensed counterions mi...

Myotonic dystrophy type 1 (DM1) is a multisystemic disease caused by an expanded CTG repeat in the 3′ UTR of the dystrophia myotonica protein kinase (DMPK) gene. Short, DNA-based antisense oligonucleotides termed gapmers are a promising strategy to degrade toxic CUG expanded repeat (CUGexp) RNA. Nucleoside analogs are incorporated to increase gapmer affinity and stability; however, some analogs also exhibit toxicity. In this study, we demonstrate that the 2′,4′-BNANC[NMe] (BNANC) modification is a promising nucleoside analog with high potency similar to 2′,4′-LNA (LNA). BNANC gapmers targeting a nonrepetitive region of the DMPK 3′ UTR show allele-specific knockdown of CUGexp RNA and revert characteristic DM1 molecular defects including mis-splicing and accumulation of RNA foci. Notably, the BNANC gapmers tested in this study did not induce caspase activation, in contrast to a sequence matched LNA gapmer. This study indicates that BNANC gapmers warrant further study as a promising RNA targeting therapeutic.

A previously unrecognized function of normal human hemoglobins occurring during protein assembly is described, i.e. self-regulation of subunit pairings and their durations arising from the variable strengths of their subunit interactions. Although many mutant human hemoglobins are known to have altered subunit interface strengths, those of the normal embryonic, fetal, and adult human hemoglobins have not been considered to differ significantly. However, in a comprehensive study of both types of subunit interfaces of seven of the eight normal oxy human hemoglobins, we found that the strengths, i.e., the free energies of the tetramer-dimer interfaces, contrary to previous reports, differ by 3 orders of magnitude and display an undulating profile similar to the transitions ("switches") of various globin subunit types over time. The dimer interface strengths are also variable and correlate linearly with their developmental profile. Embryonic hemoglobins are the weakest; fetal hemoglobin is of intermediate strength, and adult hemoglobins are the strongest. The pattern also correlates generally with their different O(2) affinities and responses to allosteric regulatory molecules. Acetylation of fetal hemoglobin weakens its unusually strong subunit interactions and occurs progressively as its level of expression diminishes and adult hemoglobin A formation begins; a causal relationship is suggested. The relative contributions of globin gene order and competition among subunits due to differences in their interface strengths were found to be complementary and establish a connection among genetics, thermodynamics, and development.

We give approximate solutions for some problems in polyelectrolyte theory involving nonuniform charge distributions. Distributions of condensed counterions and electrostatic free energies are found for line-charge models of oligomers, end segments, junctions separating regions of different charge densities, and two semi-infinite line charges approaching each other end-on. The end-on potential of mean force in the latter case is screened by the Debye length. With that exception, we find little correlation between the Debye screening length and the much smaller distances marking the onset of significant end effects. We suggest a biological application to DNA unwinding by helicases.

In a previous paper, we have shown that counterions condense on charged spheres and planes as well as on the linear polyelectrolyte models of charged lines and cylinders, provided that the surface charge densities exceed a critical value. Here we give a more complete calculation resulting in the electrostatic free energies of all of these geometric shapes. We consider a macroion immersed in salt solution and also a macroion in the presence only of its own counterions. For a sphere, cylinder, and plane with equal surface charge densities, the sphere has the lowest electrostatic free energy and the plane the highest. We apply the results to the coil-to-globule transition and to the growth of spheres by fusion of two smaller spheres to form a larger one.

X-ray diffraction structures of the nucleosome core particle along with a variety of experiments are consistent with the idea that an important source of the free energy holding DNA to the superhelical ramp on the histone octamer surface is obtained from a relatively small amount of electrostatic neutralization of the DNA phosphate charge by positively charged histone groups, especially arginine residues. Here we present a theoretical analysis of a simple model that emphasizes the competition between the high degree of bending of the stiff DNA molecule required for its tight curvature on the histone octamer and the neutralization of the DNA phosphate charge by basic histone residues. Our calculation accounts for the strong influence of condensed counterions on the electrostatic interactions. We find that the minimum amount of free energy required to bend DNA into axial conformity with the superhelical ramp at physiological salt concentration can be provided by a scant 6% neutralization of the phosphate charge, in close correspondence to the stoichiometric neutralization of phosphate charge by the arginine side chain that intrudes into the inward-facing minor groove of each DNA double helical turn.

We present a simple model for the binding of persistence-length segments of a polyelectrolyte to an oppositely charged spherical macroion with radius of the same order as the polymer persistence length. The polyelectrolyte is taken as a rod with elastic bending capacity. The macroion is abstracted as an absolutely rigid circular arc. In the bound state, the polyelectrolyte bends onto the macroion, and some of the opposite charges are mutually neutralized. The curvature of the macroion imposes stability limits on the bound state. The model predicts transitions to bound-state stability in the same conditions (polyelectrolyte charge density and bare persistence length, macroion radius, salt concentration) under which they are observed in experimental studies of the binding of polyelectrolytes to oppositely charged micelles. The calculations also suggest why macroscopic phase separation occurs in experiments below a critical salt concentration but not above.

DNA dodecamers of the alternating d(CG).d(CG) sequence with six phosphate groups either charge-neutralized or substituted by neutral methylphosphonates across the major or minor groove have been subjected to energy minimization to determine the conformational effect of the asymmetric elimination of phosphate charge. We report bending angles, directions of bending, and detailed structural characteristics such as groove widths and local base-pair parameters. Our principal results are that charge neutralization on one face of the DNA induces significant bending toward the neutralized face, in agreement with theoretical predictions on a simplified model and experimental data on a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methylphosphonate substitutions is nearly the same as the conformation produced by charge neutralization of the phosphates. Individual isomers, however, cover a wide range of structures, with the magnitude and direction of overall bending sensitive to the precise stereochemical pattern of neutralization. Our simulation does not explicitly contain counterions, and the results therefore suggest that counterions can influence DNA structure by neutralizing the phosphate charge. These data provide new hints into the molecular mechanisms which underlie the deformations of DNA structure induced by the binding of positively charged proteins and other tightly associated cationic species.

We extend the theory of counterion condensation from the standard representation of a locally stiff rodlike polyion as a line of discrete charges to a helical lattice of charges. The number of counterions condensing on a helix with given axial charge density is the same as on a line of the same charge density, but the electrostatic free energy is substantially less for the helix than for the line. In fact, the free energy of assembling the helical charge lattice becomes negative at higher salt concentrations, indicating electrostatic stabilization of the helix due to the mixing entropy of condensed counterions. The electrostatic persistence lengths of the line and helix subjected to locally elastic thermal bending fluctuations differ only slightly. They have the same κ -2 dependence as the Odijk-Skolnick-Fixman persistence length but a different prefactor. It is commonly believed that elastic bending models for the persistence length are applicable to double-helical DNA, but we point out that DNA apparently has unique mechanical properties that do not conform to the elastic model of bending. On the other hand, the helical model and its subsequent generalization to a double helix will serve as a basis for the electrostatic free energy of DNA conformational transitions.

Monte Carlo simulations of the interactions of Na+ and Cl- ions with λ repressor protein and its DNA operator site have revealed an interesting effect [Jayaram, B.; DiCapua, F. M.; Beveridge, D. L. J. Am. Chem. Soc. 1991, 113, 5211−5215]. When the protein is close to its binding site on DNA, the presence of the small ions strengthens the electrostatic net attractive force between the formally charged protein residues and the phosphate groups on DNA. The effect has been interpreted as a manifestation of the release of counterions condensed on DNA. We show that although counterions are indeed released, the enhancement of the attractive force at short distances has a different origin. There is a direct attraction between DNA phosphates and positively charged protein residues, and a direct repulsion between DNA phosphates and negatively charged protein residues. Close to the DNA, the net direct force is attractive. By weakening the direct repulsion between DNA phosphates and the negatively charged glutamate a...

We report further development of a pair potential for two identically charged rodlike polyions oriented in parallel. An attractive force mediated by condensed counterions of any valence, including univalent, is identified for separation distances between a Debye screening length and about a third of a Debye length. The characteristics of the potential are explored as a function of ionic strength, dielectric constant, counterion valence, and charge density of the polyions. The work required to assemble more than two polyions in parallel array is shown not to be pairwise additive. The free energy of assembling many parallel polyions in a hexagonally ordered cluster is calculated as a function of the number N of polyions in the cluster. The free energy has a minimum at a finite cluster size. Discrepancies between the theoretical structure of the stable cluster and experimental observations on polyelectrolyte clusters (with univalent counterions) are discussed, and it is tentatively concluded that the apparen...

We have computed the fraction of DNA phosphate charge neutralized by condensed counterions for parallel pairs of linear DNA segments, DNA circles, and representative closed-circular supercoiled DNA configurations ranging in length from 42 to 3000 base pairs. We find significant but small uptake of condensed counterions for the more compact structures relative to an isolated linear DNA segment.

It has been inferred from electric birefringence and electric dichroism data that the field-induced dipole moment on charged rodlike particles saturates at higher field strengths. We give theoretical justification for this interpretation of the data. We calculate the threshold field marking the onset of saturation and compare the result with measured values.

We develop formulas for the counterion−polyion and coion−polyion potentials of mean force in the context of counterion condensation theory. For separation distances on the scale of a Debye screening length, both potentials conform to Debye−Huckel screening behavior. Close to the polyion, in the region defining the layer of condensed counterions, the counterion potential is attractive and unscreened. A coion in this region acts like a charged group on the polyion; its potential is repulsive, and it augments the ability of the polymer to condense counterions. There is an interfacial region between condensed layer and diffuse cloud from which counterions are expelled back into the cloud but which accumulates coions. The associated radial distribution functions exhibit two peaks for the counterion and a single peak for the coion.

Complex formation between small carboxyl-terminated dendritic polymers and oppositely charged poly(dimethyldiallylammonium chloride) was monitored by turbidimetry, dynamic light scattering, viscometry and potentiometric titration. All techniques reveal a discontinuity at a well-defined pH, corresponding to the point of incipient complex formation. Conversion of this critical pH to a surface charge density σcrit leads to the observation that σcrit, to a first approximation, varies linearly with the Debye−Huckel parameter κ and that binding occurs more easily (i.e., at lower σcrit) for the larger dendrimer. A model is presented in which the distortion of the polyelectrolyte backbone in the complex is described in terms of the elastic resistance to bending around the contour of the spherical macroion, acting in opposition to attractive Coulombic forces. The elastic resistance is treated as a Hookean effect obtained from the measured persistence length. This simple theory produces the principal features of th...

A theory of attractive forces between identical highly charged polyions in a 1:1 supporting electrolyte, generated by the interaction of the layers of condensed counterions, is extended to a Z:Z‘ electrolyte and to rodlike polymer segments of any charge density. If the combined charge density of a polyion pair does not exceed the charge density critical for counterion condensation, then there is no attraction. But an attraction arises if the combined charge density does exceed the condensation threshold, even if the individual polymer charge densities lie below the critical value. The intensity of the attraction at a fixed ionic strength decreases with higher values of counterion valence. The effect of increased ionic strength is to decrease both the range and the intensity of the attractive force.

Using numerical counterion condensation theory, we compute the electrostatic component of the persistence length of DNA for three models. In the line model, the phosphate charges are represented as points uniformly distributed on a line of zero radius. In the helical model, the phosphates are given the three-dimensional coordinates deduced from X-ray fiber diffraction; the helical model is considered with and without the dielectric saturation effect. For each model, the free energy of bending smoothly to a specified radius of curvature is calculated. All models exhibit strong end effects for finite-length DNA. Our most reliable model is the helical model with dielectric saturation. Persistence lengths calculated for it are linearly correlated, to good numerical approximation, with the inverse concentration of salt. Comparison with experimental data suggests that real thermal bending fluctuations of DNA in solution may not be describable as the smooth length-invariant bending postulated by any of the models. 22 refs., 12 figs., 3 tabs.

P R E V I O U S CALCULATIONS of thermodynamic properties have been based on two sources of primary data: pressure-volume-temperature measurements made under static conditions in various types of equipment and JouleThomson data obtained from throttling calorimeters. Joule-Thomson coefficients have been generally accepted as more reliable than low pressure P-V-T data, and a t least one laboratory ( I I ) , which is the source of impressive contributions to the literature of thermodynamic properties, has used Joule-Thomson data extensively when calculating thermodynamic properties of hydrocarbons. In the past, because of a dearth of PV-T data in the low pressure and low temperature regions (less than 10 atm. and 1000 C.), Joule-Thomson measurements were the only source of extensive information. Recently, however, PV-T information has begun to appear in the literature, and it is now possible to evaluate the reliability of Joule-Thomson work which, of necessity, has been taken more or less for granted. A powerful consistency test for P-V-T data and JouleThomson coefficients involves second virial coefficients evaluated from the PV-T data and Joule-Thomson coefficients extrapolated to zero pressure. When compressibility factors are fitted to the equation