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Related Experiment Videos

Excess counterion accumulation around branched nucleic acids

M C Olmsted1, P J Hagerman

  • 1Department of Biochemistry, Biophysics and Genetics, University of Colorado Health Sciences Center, Denver 80262.

Journal of Molecular Biology
|November 11, 1994
PubMed
Summary

Tertiary nucleic acid structures bind significantly more counterions than linear DNA. This excess counterion association influences ligand binding and structural stability.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Nucleic acids with tertiary structures, like those in tRNAs and ribosomal RNAs, exhibit high regional phosphate charge density.
  • The counterion requirements for the stability of these structures are known, but their specific counterion association levels are less understood.

Purpose of the Study:

  • To quantify the extent of counterion association in four-branch DNA junctions with high charge density.
  • To investigate the influence of this excess counterion association on ligand binding and structural stability.

Main Methods:

  • Defined "excess counterion association" using Donnan equilibrium dialysis.
  • Employed Grand canonical Monte Carlo computations with a primitive model for nucleic acids and 1:1 electrolyte.

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  • Calculated Donnan distribution coefficients to determine counterion association.

    • Main Results:

    • Four-branch DNA junctions associate with at least 24 excess counterions in the long branch limit.
    • This excess association is significantly higher than that of linear DNA.
    • The release of these counterions upon ligand binding can direct ligand interaction with the junction.

    Conclusions:

    • Excess counterion association is a critical factor in the stability of nucleic acid tertiary structures.
    • The binding and release of counterions near junctions can guide the binding of proteins and cationic ligands.
    • Understanding counterion dynamics is essential for predicting the behavior of complex nucleic acid architectures.