Interactions of polyelectrolytes with simple electrolytes. II. Donnan equilibria obtained with DNA in solutions of 1-1 electrolytes

Strauss, Ulrich P.; Helfgott, C.; Pink, H.

doi:10.1021/j100867a024

Cited by 108 publications

(89 citation statements)

References 2 publications

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“…These results, together with other studies in the literature (1)(2)(3)(4)(5)(6)(7)(8)(9), suggest that all, or nearly all, monovalent cations bind to randomsequence dsDNA in aqueous solutions. The apparent K D observed for the binding of Tris + to ds26 is somewhat smaller than observed for the binding of other cations, suggesting that Tris-DNA complexes are stabilized by the formation of hydrogen bonds with the DNA bases (45), as well as by electrostatic interactions with the phosphate residues.…”

Section: Discussionsupporting

confidence: 81%

“…To take both effects into account, the mobility profiles can be analyzed with Eq. (3): (3) where μ M is the mobility observed for the analyte-ligand complex at any given concentration [M + ] of the test ion, μ o is the mobility observed when [M + ] = 0 (i.e., when the solution contains only a tetraalkylammonium ion as the cation), Δμ span is the span of the titration, (i.e., the difference in mobility that would be observed upon saturation of the binding site, if there were no conductivity effect), K D is the apparent dissociation constant characterizing the binding of the test ion to the analyte, and c is the slope of the line describing the conductivity effect. Binding, as used here, refers to the formation of a saturable complex between analyte and ligand, assuming the binding to be non-cooperative.…”

Section: Validation Of the Ri Methods Using The Adenosine Nucleotides mentioning

confidence: 99%

“…The cations used in the conductivity experiments described below included the alkali metal ions Li + , Na + , K + and Rb + ; the partially substituted ammonium ions MeNH 3 …”

Section: Buffersmentioning

confidence: 99%

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Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

2007

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A variation of affinity capillary electrophoresis, called the Replacement Ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion, and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The binding of monovalent cations to DNA and other polynucleotides has been studied for many years. Early free boundary electrophoresis and conductivity studies (1-3) showed that the affinity of cations for calf thymus DNA decreases in the order Li + > Na + > K + ≫ tetramethylammonium (TMA + ). Competitive dialysis measurements (4) showed that Li + , Na + , K + , Cs + and tetrabutylammonium (TBA + ) ions bind to double-stranded (ds) DNA in a sequence-independent manner, while TMA + and tetraethylammonium (TEA + ) ions are

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Section: Discussionsupporting

confidence: 81%

Section: Validation Of the Ri Methods Using The Adenosine Nucleotides mentioning

confidence: 99%

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Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

2007

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“…Ion counting via dialysis can provide a quantitative measure of the ionic atmosphere around the solute, but it provides only a total (excess) number, and not any information the shape of the ion cloud. 11,12 The q = 0 limit of small-angle X-ray scattering (SAXS) can provide similar excess counts for both water and ions. 13 Anomalous small angle X-ray scattering (ASAXS) data in principle yield additional information about the extent of perturbations of the ion/water environment, [14][15][16][17] but the ASAXS signal is known to be intertwined with all components in the system, complicating the analysis.…”

Section: Introductionmentioning

confidence: 99%

Extracting water and ion distributions from solution x-ray scattering experiments

Nguyên

Pabit

Pollack

et al. 2016

The Journal of Chemical Physics

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Small-angle X-ray scattering measurements can provide valuable information about the solvent environment around biomolecules, but it can be difficult to extract solvent-specific information from observed intensity profiles. Intensities are proportional to the square of scattering amplitudes, which are complex quantities. Amplitudes in the forward direction are real, and the contribution from a solute of known structure (and from the waters it excludes) can be estimated from theory; hence, the amplitude arising from the solvent environment can be computed by difference. We have found that this "square root subtraction scheme" can be extended to non-zero q values, out to 0.1 Å −1 for the systems considered here, since the phases arising from the solute and from the water environment are nearly identical in this angle range. This allows us to extract aspects of the water and ion distributions (beyond their total numbers), by combining experimental data for the complete system with calculations for the solutes. We use this approach to test molecular dynamics and integral-equation (3D-RISM (three-dimensional reference interaction site model)) models for solvent structure around myoglobin, lysozyme, and a 25 base-pair duplex DNA. Comparisons can be made both in Fourier space and in terms of the distribution of interatomic distances in real space. Generally, computed solvent distributions arising from the MD simulations fit experimental data better than those from 3D-RISM, even though the total small-angle X-ray scattering patterns are very similar; this illustrates the potential power of this sort of analysis to guide the development of computational models. Published by AIP Publishing. [http://dx

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“…Salt-nucleic acid preferential interaction coefficients, which characterize the net thermodynamic consequences of cation accumulation and anion exclusion in the vicinity of a nucleic acid polyion, have been measured by dialysis (22). Differences between preferential interaction coefficients of reactant(s) and product(s) of a nucleic acid process are the fundamental thermodynamic determinant of the strong dependence of the thermodynamics of that process on [ (31).…”

mentioning

confidence: 99%

Asymptotic solution of the cylindrical nonlinear Poisson–Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient

Shkel

Tsodikov

Record

2002

Proc. Natl. Acad. Sci. U.S.A.

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The analytic solution to the nonlinear Poisson-Boltzmann equation describing the ion distributions surrounding a nucleic acid or other cylindrical polyions as a function of polyion structural quantities and salt concentration ([salt]) has been sought for more than 80 years to predict the effect of these quantities on the thermodynamics of polyion processes. Here we report an accurate asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low to moderate concentration of a symmetrical electrolyte (<0.1 M 1:1 salt). The approximate solution for the potential is derived as an asymptotic series in the small parameter ؊1 , where ϵ ؊1 ͞a, the ratio of the Debye length ( ؊1 ) to the polyion radius (a). From the potential at the polyion surface, we obtain the coulombic contribution to the salt-polyelectrolyte preferential interaction (Donnan) coefficient (⌫ u coul ) per polyion charge at any reduced axial charge density . ⌫ u coul is the sum of the previously recognized low-salt limiting value and a salt-dependent contribution, analytically derived here in the range of low-salt concentra- T he cylindrical nonlinear Poisson-Boltzmann (NLPB or PB) equation is widely used for calculating electrostatic potential around rod-like charged objects surrounded by mobile ions both in the theory of polyelectrolyte solutions (1, 2), in applications in plasma physics (3) and in colloid and surface sciences (4). In particular, the surface coulombic potential (and͞or its distance dependence) of a charged polyion in an electrolyte solution is required for calculations of such thermodynamic properties as electrostatic free energy (5, 6), polyion-ligand binding constant (7,8), and especially the fundamental thermodynamic quantity ⌫ u coul , the coulombic contribution to the preferential interaction coefficient (equivalent to the experimentally observable Donnan coefficient). This coefficient is required for interpretation of thermodynamic experiments on salt-polyion interactions and on effects of salt concentration ([salt], C b ) on polyion processes (1, 9). Numerical calculations of NLPB solution for the model of a long periodically charged polyion as an infinite charged cylinder characterized by only two structural quantities, reduced charge density § and radius a, are known to successfully describe experimentally measured thermodynamic properties of polyelectrolyte solutions (1). Monte Carlo simulations confirm the accuracy of the cylindrical PB equation in the presence of added univalent salt up to 0.1 M (10, 11). However, despite numerous studies devoted to solving the NLPB equation (2, 3), no sufficiently accurate analytic solution for the cylindrical NLPB equation was known at low-to moderate-salt concentration.Solution of cylindrical NLPB equation is more challenging at low-salt (LS) concentration than at high [salt], where several useful accurate approximations for the potential, electrostatic free energy and preferential interaction coefficient are known (4,(12)(13)(14). In the absence of added salt, the ...

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Interactions of polyelectrolytes with simple electrolytes. II. Donnan equilibria obtained with DNA in solutions of 1-1 electrolytes

Cited by 108 publications

References 2 publications

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

Extracting water and ion distributions from solution x-ray scattering experiments

Asymptotic solution of the cylindrical nonlinear Poisson–Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient

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