Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories

Mills, Pamela; Anderson, Charles; Record, M. Thomas

doi:10.1021/j100265a012

Cited by 162 publications

(155 citation statements)

References 0 publications

Supporting

Mentioning

148

Contrasting

Order By: Relevance

“…The actual data are consistent with Manning's condensation parameter [82,83] θ 0 = λ/|q c |λ B = 0.71 particularly if the width δ is taken as one Bjerrum length. Our data are also in semiquantitative accordance with other computer simulations [38] and nuclear magnetic resonance (NMR) experiments which show that the condensed counterion fractions are in the range of 0.65 to 0.85 [84] or 0.53 to 0.57 [85,45]. , dp = 0.2Å), dot-dashed line-run B (dc = 2Å, dp = 2Å), dashed line-run C (dc = 2Å, dp = 6Å).…”

Section: Distance-resolved Forcessupporting

confidence: 91%

“…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: 70%

See 1 more Smart Citation

Effective interaction between helical biomolecules

Allahyarov

Löwen

2000

Phys. Rev. E

View full text Add to dashboard Cite

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.

show abstract

Section: Distance-resolved Forcessupporting

confidence: 91%

Section: Introductionmentioning

confidence: 70%

Effective interaction between helical biomolecules

Allahyarov

Löwen

2000

Phys. Rev. E

View full text Add to dashboard Cite

show abstract

“…None of the studies reported to date covers the range of salt concentrations we have explored, and except for two cases (16,17) the papers published were concerned exclusively with the B form of DNA modeled as an unstructured infinite charged cylinder (12)(13)(14)(15). For the Poisson-Boltzmann treatments based on realistic B DNA structural models similar to that presented here (16,17), quantitative results comparable, for example, to the cylindrically averaged distributions given in Fig.…”

Section: Methodsmentioning

confidence: 71%

“…The treatments have substantial differences in the structural modeling of DNA and the use of statistical approximations. If one pictures a DNA structure as an infinitely long uniformly charged cylinder, it is straightforward to compute the average cylindrically symmetric ionic distributions through the numerical solution of the Poisson-Boltzmann (10-12) and hypernetted chain equations (13,14) as well as by the Monte Carlo technique (14,15 (19)(20)(21)(22)(23)(24)(25). This method combined with force fields describing intramolecular interactions provides a general formalism for modeling biomolecules in simple electrolyte solutions (24,25).…”

mentioning

confidence: 99%

Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.

Klement

Soumpasis

Jovin

1991

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

View full text Add to dashboard Cite

We introduce an efficient computational methodology employing the potentials of mean force approach for estimating the detailed three-dimensional ionic distributions around arbitrarily complex charged biomolecular structures for all monovalent salt concentrations of practical interest (e.g., 0.1-5.0 M NaCl). Such distributions are required for specifying thermodynamic and structure-specific features of ion-mediated interactions of charged proteins, DNA and RNA, membranes, and macromolecular assemblies. As a first application, we present results for distributions around the B and Z, conformers of the DNA oligomer d(C-G)j8sd(C-G)js. The ionic microenvironment depends strongly on the DNA conformation, sequence, and bulk salt concentration.The computation of ionic distributions around highly charged biomolecules has been a subject ofcontinuous interest for the past 20 years due to the importance of the ionic environment for structural stability and transitions as well as for intermolecular.interactions and binding equilibria. For example, in the case of DNA, ionic effects play a central role in the extensively studied B -+ Z transition (for recent reviews, see refs. 1 and 2), at all levels of DNA structural organization (refs. 3 and 4 and references therein), and in ligand-DNA binding equilibria (5).The approaches proposed to date for computing ionic distributions around DNA vary widely with respect to (i) the structural modeling of the DNA-water-ions system, (ii) the statistical approximations employed, (iii) the computational complexity, (iv) the range of bulk ionic concentrations, and (v) the DNA conformations studied. If the water, ions, and DNA components are described microscopically, the only currently feasible way to determine ionic distributions is by large-scale computer simulations (i.e., Monte Carlo and molecular dynamics), as reported by Clementi and Corongiu (6-8) and more recently by van Gunsteren et al. (9). These calculations are extremely costly and can only be performed practically in the absence of added salt. For example, to simulate a 0.1 M NaCl electrolyte around DNA, one has to consider at least 50 anion-cation pairs and 25,000 water molecules in the central simulation box, an effort that is at present impossible.In previous studies water has been represented as a dielectric continuum and the ions have been considered either as hard or soft spheres or simply point particles. The treatments have substantial differences in the structural modeling of DNA and the use of statistical approximations. If one pictures a DNA structure as an infinitely long uniformly charged cylinder, it is straightforward to compute the average cylindrically symmetric ionic distributions through the numerical solution of the Poisson-Boltzmann (10-12) and hypernetted chain equations (13,14) This brief overview clearly shows that a general, fairly accurate, computationally efficient method to approximately solve the problem at hand for arbitrarily complex biomolecular structures over a wide range of bulk ionic ...

show abstract

“…[19,20] More systematic studies, with varying salt concentrations and/or ion type, have been carried out later. [21][22][23][24][25][26][27] The primary objective of these earlier computer simulation studies was to evaluate the applicability of analytical theories describing ionic distributions around DNA. In most of these works, the primitive model was used [i.e., the DNA was modeled as a hard body (cylinder) with a uniform distribution of surface charge, and the ions were represented as point charges or charged hard spheres].…”

Section: Evaluation Of Analytical Theoriesmentioning

confidence: 99%

Molecular Simulations of DNA Counterion Distributions

Lyubartsev¹

2004

Dekker Encyclopedia of Nanoscience and Nanotechnology, Second Edition - Six Volume Set (Print Version)

View full text Add to dashboard Cite

Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories

Cited by 162 publications

References 0 publications

Effective interaction between helical biomolecules

Effective interaction between helical biomolecules

Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA.

Molecular Simulations of DNA Counterion Distributions

Contact Info

Product

Resources

About