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Related Experiment Videos

Is counterion delocalization responsible for collapse in RNA folding?

V L Murthy1, G D Rose

  • 1Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 701 Wood Basic Sciences, Baltimore, Maryland 21205-2105, USA.

Biochemistry
|November 23, 2000
PubMed
Summary

DNA and RNA molecules unexpectedly pack together in crystals, with parallel arrangements being surprisingly common. Condensed counterions drive this entropy-driven RNA folding, similar to the hydrophobic effect in proteins.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Predicting nucleic acid secondary structures is established, but tertiary structure arrangement remains challenging.
  • Conventional models suggest charge repulsion disfavors helix interactions.

Purpose of the Study:

  • To investigate the packing arrangements of DNA, RNA, and DNA/RNA hybrid molecules in crystalline structures.
  • To explain the observed preferential packing of charged nucleic acid helices.

Main Methods:

  • Analysis of crystal packing in DNA, RNA, and DNA/RNA hybrid molecules.
  • Development of a novel model for RNA folding incorporating counterion effects.

Main Results:

  • Approximately 80% of analyzed cases show specific, preferential packing between secondary structure elements.

Related Experiment Videos

  • Three main packing categories identified: major groove interlocking, side-by-side parallel packing, and backbone-to-major groove interactions.
  • Parallel packing motifs, unexpectedly common (over 50% in A-form RNA), are explained by entropy gains from condensed cations.

    • Conclusions:

    • Specific packing arrangements, including parallel ones, are prevalent in nucleic acid crystals.
    • Condensed counterions play a crucial role in driving RNA folding through entropy, analogous to the hydrophobic effect in proteins.