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Ion counting from explicit-solvent simulations and 3D-RISM.

George M Giambaşu1, Tyler Luchko1, Daniel Herschlag2

  • 1Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, New Jersey.

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|February 25, 2014
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Summary
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Ion counting experiments reveal the ionic atmosphere around DNA. Molecular dynamics (MD) and 3D-RISM simulations accurately predict ion distributions near physiological conditions, outperforming nonlinear Poisson-Boltzmann calculations at higher concentrations.

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Area of Science:

  • Biophysics
  • Physical Chemistry
  • Computational Biology

Background:

  • The atomic-level understanding of the ionic atmosphere surrounding nucleic acids is incomplete.
  • Ion counting (IC) experiments offer quantitative data crucial for validating theoretical models of ionic atmospheres.
  • Nucleic acids' structure and stability are significantly influenced by their surrounding ion and water layers.

Purpose of the Study:

  • To quantitatively assess and compare different theoretical methods for modeling the ionic atmosphere around DNA.
  • To validate computational models against experimental ion counting data.
  • To elucidate the distribution and behavior of ions and water molecules around DNA at various concentrations.

Main Methods:

  • Replication of ion counting experiments for duplex DNA in NaCl(aq) using molecular dynamics (MD) simulations.
  • Application of the three-dimensional reference interaction site model (3D-RISM) to model ion distributions.
  • Utilizing nonlinear Poisson-Boltzmann (NLPB) calculations for comparison.
  • Comparison of simulation results with experimental atomic emission spectroscopy measurements.

Main Results:

  • MD simulations and 3D-RISM show good agreement with experimental results near physiological ion concentrations.
  • At concentrations above 0.7 M, MD and 3D-RISM underestimate condensed cations and overestimate excluded anions.
  • The ionic and water atmosphere extends 20-25 Å from the DNA surface, exhibiting layered density profiles.
  • 3D-RISM results closely mirror MD simulations but indicate tighter phosphate binding and less groove binding of Na+.
  • NLPB calculations consistently underestimate condensed cations and produce qualitatively different, structureless ion distributions.

Conclusions:

  • MD simulation and 3D-RISM show promise for quantitatively characterizing the ion atmosphere around nucleic acids.
  • These methods can provide valuable insights into how the ionic environment affects nucleic acid structure and stability.
  • NLPB calculations are less suitable for accurately describing the detailed ion distributions around DNA compared to MD and 3D-RISM.