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Is counterion delocalization responsible for collapse in RNA folding?
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
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.
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.
- 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.