Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations

Pack, George R.; Wong, Linda; Lamm, Gene

doi:10.1002/(sici)1097-0282(199906)49:7<575::aid-bip4>3.0.co;2-j

Cited by 43 publications

(48 citation statements)

References 50 publications

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“…Consequently, the dependence of the effective interactions on a model parameter can systematically be studied and the trends can be compared to experiments. In this respect our model is superior to previous studies that describe the counterion screening by linear Debye-Hückel [39,42,4,43] or nonlinear Poisson-Boltzmann theory [26,4,[44][45][46][47][48][49][50][51] and even to recent approaches that include approximatively counterion correlations [52,53]. We also emphasize that one main goal of the paper is to incorporate the molecular shape and charge pattern explicitly which is modelled in many studies simply as a homogeneously charged cylinder [39,4,54,55].…”

Section: Introductionmentioning

confidence: 71%

Effective interaction between helical biomolecules

Allahyarov

Löwen

2000

Phys. Rev. E

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The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than 6Å it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.

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Section: Introductionmentioning

confidence: 71%

Effective interaction between helical biomolecules

Allahyarov

Löwen

2000

Phys. Rev. E

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“…Thus, a mechanism other than ion size is implicated. Theoretical studies suggest that spatial correlations of ions stabilize high cation densities close to the nucleic acid surface, resulting in a higher total cation association than predicted by PB 11,16,34 . The correlation effects are predicted to increase with ion valence and the charge density of the polyelectrolyte 16,17,51 .…”

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 90%

“…The predominant description of the ion atmosphere arises from theory 3,7,11,12 . The early treatments such as counterion condensation theory by Manning articulated the critical concept of the ion atmosphere and provided an excellent first-order estimation of ion association 7 .…”

Section: Introductionmentioning

confidence: 99%

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

et al. 2007

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The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na + in four-fold excess of Mg 2+ (20 vs. 5 mM), the ion atmosphere nevertheless has three-fold more Mg 2+ than Na + . Further, the dicationic polyamine putrescine 2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely-used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.

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“…88 It provides results which are in better agreement with experiment than the conventional PB model. Another simple criterion that can be used to define associative binding of counterions is, wðrÞez i \ ÀkT , see for example discussion in 89 and citations therein. The preferred binding 90 regions of magnesium to DNA are determined with the PB model by selectively decreasing the temperature in the Boltzmann expression for the magnesium concentration to values as low as 150 K. Such an approach was justified as the one allowing to qualitatively account for the correlation effects which are supposed to be stronger for divalent than monovalent ions.…”

Section: Site-bound Ionsmentioning

confidence: 99%

“…Indeed, earlier comparisons of the results of the NPBE and Monte-Carlo simulations for counterion condensation around DNA showed that the NPBE gives ionic distribu-tions which are too broad, and moreover, underestimate by 15-20% and 25-30% the surface concentrations of monovalent and divalent ions, respectively. 89 In the work of Misra and Draper, 91 which considers magnesium binding to RNA, the site binding is defined to occur in specific binding sites on the surface of the macromolecule, resulting in an overlap or integration of the first solvation shells of magnesium and phosphate groups. Such process is governed with the mass-action law with an association constant K. The site-bound ions are further divided into outersphere and inner-sphere site-bound ions, depending on whether a water molecule is mediating between magnesium and a phosphate group.…”

Section: Site-bound Ionsmentioning

confidence: 99%

Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications

2007

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This work is a review of the Poisson–Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding. The PB model is one of the mesoscopic theories that describes the electrostatic potential and equilibrium distribution of mobile ions around molecules in solution. It serves as a tool to characterize electrostatic properties of molecules, counterion association, electrostatic contributions to solvation, and molecular binding free energies. We focus on general formulations which can be applied to large molecules of arbitrary shape in all‐atomic representation, including highly charged biomolecules such as nucleic acids. These molecules present a challenge for theoretical description, because the conventional PB model may become insufficient in those cases. We discuss the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT, simple empirical extensions to this model accounting for finite size of ions, the modified PB theory including ionic correlations and fluctuations, the cell model, and supplementary methods allowing to incorporate site‐bound ions in the PB calculations. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 93–113, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations

Cited by 43 publications

References 50 publications

Effective interaction between helical biomolecules

Effective interaction between helical biomolecules

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications

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