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Structural specificity conferred by a group I RNA peripheral element.

Travis H Johnson1, Pilar Tijerina, Amanda B Chadee

  • 1Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA.

Proceedings of the National Academy of Sciences of the United States of America
|July 13, 2005
PubMed
Summary
This summary is machine-generated.

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Peripheral RNA structures, like P5abc, are crucial for stabilizing native RNA conformations. This study shows P5abc binds native RNA 50,000 times more tightly than misfolded forms, ensuring structural specificity.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • Structured RNAs, like proteins, must achieve a stable native conformation.
  • Unlike proteins, RNA's local structures are highly stable, making stabilization of native states against misfolded intermediates a key challenge.
  • Peripheral structural elements in RNAs are known to stabilize overall structure, but their role in stabilizing native states against alternative folds is less understood.

Purpose of the Study:

  • To investigate whether peripheral RNA structural elements specifically stabilize native conformations relative to alternative folds.
  • To quantify the contribution of the P5abc peripheral element to the thermodynamic stability of the native state of group I intron RNA.

Main Methods:

  • Utilized a two-piece version of the Tetrahymena group I intron RNA.

Related Experiment Videos

  • Measured binding affinities of the P5abc element to both native and misfolded conformations of the RNA.
  • Assessed RNA activity through measurements to compare the thermodynamic preference for the native state with and without the P5abc element.

    • Main Results:

    • The P5abc peripheral element binds the native conformation of the group I intron RNA 50,000 times more tightly than a long-lived misfolded conformation.
    • P5abc stabilizes the native conformation by approximately 6 kcal/mol relative to the misfolded conformation.
    • Without P5abc, the native conformation is only marginally preferred over the misfolded conformation (<0.5 kcal/mol).

    Conclusions:

    • Peripheral structural elements, exemplified by P5abc, play a critical role in conferring "structural specificity" by significantly stabilizing native RNA conformations.
    • This stabilization is achieved by preferentially binding the native state over misfolded intermediates, a function likely general to RNA peripheral domains.
    • The findings highlight the importance of peripheral structures in ensuring the thermodynamic fidelity of RNA folding.