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Kinetic intermediates in RNA folding

P P Zarrinkar1, J R Williamson

  • 1Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.

Science (New York, N.Y.)
|August 12, 1994
PubMed
Summary

Investigating the Tetrahymena ribozyme

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Area of Science:

  • Molecular biology
  • Biochemistry
  • RNA structure and function

Background:

  • The folding pathways of large, highly structured RNA molecules remain largely unexplored.
  • Understanding RNA folding is crucial for elucidating biological function and developing novel therapeutics.

Purpose of the Study:

  • To investigate the Mg(2+)-induced folding pathway of the Tetrahymena ribozyme.
  • To elucidate the kinetics and identify intermediates in the RNA folding process.

Main Methods:

  • Utilized hybridization of complementary oligodeoxynucleotide probes to study RNA folding kinetics.
  • Analyzed Mg(2+)-dependent and Mg(2+)-independent folding steps.

Main Results:

  • The Tetrahymena ribozyme folds via a complex mechanism involving distinct Mg(2+)-dependent and Mg(2+)-independent steps.
  • A hierarchical folding model was proposed, with the P4-P6 domain forming before the P3-P7 domain.
  • The formation of the P3-P7 domain was identified as the overall rate-limiting step, with a rate constant of 0.72 ± 0.14 min⁻¹.

Conclusions:

  • The folding mechanism of large RNAs shares similarities with multidomain protein folding.
  • Independently stable substructures form first and then associate to achieve the final RNA conformation.

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