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G S Manning

Publications and source records attributed to G S Manning.

18 recordsLinked to original sources
PubMed1992

Theory of delocalized ionic binding to polynucleotides: structural and excluded-volume effects.

A previously developed theory for the delocalized binding of ions to polyelectrolytes was restricted to point ions and a structurally rigid polyelectrolyte. For the binding of substances like oligolysines and polyamines to DNA, the restriction to point ions would appear not to be realistic. For the binding of ions to flexible chains like single-stranded polynucleotides, the restriction to a rigid polyelectrolyte may not be realistic. In this article, we assess the effect of relaxation of these two restrictions. Excluded volume among bound ions is modeled by a hard-rod potential in the context of the theory of a one-dimensional fluid. The possibility that a flexible chain folds in some manner in the immediate vicinity of a bound ion is modeled by allowing the mean spacing between charged groups on the polymer to become smaller as the number of bound ions increases. We compare our results with recent data on the binding of a series of oligolysines to single-stranded polynucleotides, which conflict with the predictions of the original theory of delocalized binding of point ions to rigid polyelectrolytes. Inclusion of excluded volume among bound ions does not significantly improve agreement with the data. Substantial improvement in the level of agreement is obtained when the polyion chain is assumed to be flexible. One of our conclusions is that the excluded-site description of anticooperativity, which was designed for the binding of ligands to discrete sites on a polymer chain, and which does not include the effect of ionic forces, should not be used in cases of delocalized binding of ions.

Binding Sites↗
PubMed1991

The elastic resilience of DNA can induce all-or-none structural transitions in the nucleosome core particle.

DNA on the surface of the histone octamer in the native nucleosome core particle is modeled as a circumferentially wound elastic line on the surface of a cylinder. In a model for the radial transition, the line is allowed to straighten, and thus lose energy, by swinging off the surface, but it is impeded in such an excursion by a radial force field representing the attractive interaction between DNA and histone octamer. In a model for the axial transition, the line may straighten by becoming more parallel to a generator of the cylinder while remaining on the surface. In this mode of straightening, dimer-tetramer or tetramer-tetramer interfaces are disrupted, and the resulting energy gain impedes the transition. Both radial and axial transitions are predicted to occur in all-or-none fashion. We propose that these models are related to the abrupt transitions actually observed in the nucleosome core particle.

DNA↗
PubMed1990

Approach to the limit of counterion condensation.

According to counterion condensation theory, one of the contributions to the polyelectrolyte free energy is a pairwise sum of Debye-Hückel potentials between polymer charges that are reduced by condensed counterions. When the polyion model is taken as an infinitely long and uniformly spaced line of charges, a simple closed expression for the summation, combined with entropy-derived mixing contributions, leads to the central result of the theory, a condensed fraction of counterions dependent only on the linear charge density of the polyion and the valence of the counterion, stable against increases of salt up to concentrations in excess of 0.1 M. Here we evaluate the sum numerically for B-DNA models other than the infinite line of B-DNA charges. For a finite-length line there are end effects at low salt. The condensation limit is reached as a flat plateau by increasing the salt concentration. At a fixed salt concentration the condensation limit is reached by increasing the length of the line. At moderate salt even very short B-DNA line-model oligomers have condensed fractions not far from the infinite polymer limit. For a long double-helical array with charge coordinates at the phosphates of B-DNA, the limiting condensed fraction appears to be approached at low salt. In contrast to the results for the line of charges, however, the computed condensed fraction varies strongly with salt in the range of experimentally typical concentrations. Salt invariance is restored, in agreement with both the line model and experimental data, when dielectric saturation is considered by means of a distance-dependent dielectric function. For sufficiently long B-DNA line and helical models, as typical salt concentrations, the counterion binding fraction approaches the polymer limit as a linear function of 1/P, where P is the number of phosphate groups of B-DNA.

Animals↗
PubMed1990

A numerical counterion condensation analysis of the B-Z transition of DNA.

We examine the salt dependence of the B-Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference delta G is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concentrations and polymer lengths. For the solvent we employ both a constant-dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance-dependent dielectric constant). Where comparison can be made, the results for the constant-dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low-salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZI and ZII are qualitatively similar throughout the entire salt range for the constant-dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic delta G, in the presence of dielectric saturation, bears comparison with the high-salt trend of the measured total delta G if "Z-DNA" is predominantly ZI, but not if it is predominantly ZII.

Animals↗
PubMed1978

Limiting laws and counterion condensation in polyelectrolyte solutions. V. Further development of the chemical model.

Counterion binding to polyelectrolyte chains is formulated as a chemical reaction Mz (free) leads to Mz (bound). Expressions for the chemical potentials of free and bound counterions are set equal to obtain the reaction equilibrium. The results are equivalent to those in the previous paper of this series. An additional result obtained here is that a polyion holds its bound counterion layer with a strength on the order of 100 kcal/(mole cooperative unit). The method is then applied to the calculation of the polarizability along the chain due to the bound (condensed) counterions.

Electrolytes↗
PubMed1977

Limiting laws and counterion condensation in polyelectrolyte solutions. IV. The approach to the limit and the extraordinary stability of the charge fraction.

The limiting laws for polyelectrolyte solutions developed in previous papers of this series have been amply confirmed by measurement. A surprising result of the accumulated data is that the limiting polyelectrolyte charge fraction (fraction of fixed charges uncompensated by condensed counterions in the limit of zero concentration), persists up to concentrations of 0.1 M or even higher. Here the theory is extended in a simple manner to finite concentrations, and the stability of the charge fraction is found to be firmly based on consequences of the long-range polyelectrolyte field. The associated counterions are assumed to translate freely in a region centered on the contour axis of the polyion. The numerical value of the free volume is determined self-consistently from the axial charge density of the polyelectrolyte and is used as the general framework within which specific binding effects are treated.

Calcium Chloride↗
PubMed1977

Theory of the delocalized binding of Mg(II) to DNA: preliminary analysis for low binding levels.

A simple theoretical equation for the binding of Mg2+ to DNA in the presence of excess 1:1 salt is derived from a model that does not specify discrete binding sites but rather allows the associated metal ions to move freely near the surface of the DNA polyion. Use of a numerical value for the free volume, determined uniquely, in a separate communication, by a free energy minimization, leads to predicted values for the Mg2+ binding constant that are in essential agreement with measured values taken from the literature.

Binding Sites↗
PubMed1977

A field-dissociation relation for polyelectrolytes with an application to field-induced conformational changes of polynucleotides.

An extension to polyelectrolyte solutions of Onsager's field-dissociation relation for weak electrolytes can be derived in a simple way. It is found that, except in the limit of zero ionic strength, a strong applied electric field prevents counterion condensation from proceeding to completion. The extent of incompleteness initially varies linearly with the applied field. The field-dissociation relation can easily be incorporated into the theory of ionic effects on the stability of ordered polynucleotide structures, whereupon a dependence of the stability on field strength emerges. An explicit calculation for a co-operative transition of the DNA melting type is presented, and it is concluded that for sufficiently low ionic strengths, a field of the order of 10 kV/cm may be able to induce melting by lowering the Tm by a few degrees. The threshold effect found experimentally by Pörschke, and particularly the observed linear dependence of the threshold field on the logarithm of the ionic strength, appears here as a simple consequence of the linear increase of the stabilization free energy with the logarithm of ionic strength.

Chemical Phenomena↗
PubMed1975

The relation between osmotic flow and tracer solvent diffusion for single-file transport.

It is demonstrated that a reasonably general model for single-file passage of solvent through an ultra-narrow pore implies the equality of tracer diffusion and osmotic flow. This result is not trival, but follows from the exactly compensating effects of solvent-solvent interaction on the paritioning of bulk solvent into the pore and on the diffusion rate within the pore. A previous calculation of Longuet-Higgins and Austin is seen to be valid only in the absence of interactions among solvent molecules in the pore.

Biological Transport↗