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Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
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Ion-mediated nucleic acid helix-helix interactions.

Zhi-Jie Tan1, Shi-Jie Chen

  • 1Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA.

Biophysical Journal
|May 2, 2006
PubMed
Summary

The tightly bound ion (TBI) model reveals salt ions mediate attraction between nucleic acid helices, unlike repulsion predicted by other theories. This ion-mediated attraction is crucial for nucleic acid folding and stability.

Area of Science:

  • Biophysics
  • Physical Chemistry
  • Computational Biology

Background:

  • Salt ions play a critical role in the folding and structural stability of nucleic acids.
  • Understanding ion-nucleic acid interactions is essential for comprehending biological processes.
  • Existing theories like Poisson-Boltzmann may not fully capture ion-nucleic acid correlations.

Purpose of the Study:

  • To investigate the electrostatic free-energy landscape of two parallel nucleic acid helices in salt solutions.
  • To explore the role of ion-nucleic acid correlations and fluctuations using the TBI model.
  • To compare TBI predictions with mean-field theories and experimental data.

Main Methods:

  • Utilized the tightly bound ion (TBI) model, accounting for ion correlations and fluctuations.

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  • Applied the TBI model to realistic atomic structures of nucleic acid helices.
  • Analyzed electrostatic interactions in monovalent and divalent salt solutions.

    • Main Results:

    • TBI model predicts an effective attraction between helices in divalent salt, contrasting with Poisson-Boltzmann repulsion.
    • Helices are stabilized at an interhelix distance of 26-36 Å with an attractive force up to -0.37 k(B)T/bp.
    • Attraction strength and stable distance depend significantly on salt concentration, ion size, and solvent dielectric constant.

    Conclusions:

    • The TBI model provides a more accurate description of ion-mediated interactions between nucleic acid helices.
    • Ion-mediated attraction is a key factor in nucleic acid helix stabilization.
    • Theoretical findings align with experimental osmotic pressure measurements and computer simulations.