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Kinetic intermediates trapped by native interactions in RNA folding

D K Treiber1, M S Rook, P P Zarrinkar

  • 1Department of Molecular Biology, MB33, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Science (New York, N.Y.)
|April 16, 1998
PubMed
Summary

Tetrahymena ribozyme folding involves kinetic traps. Mutations disrupting native interactions accelerate P3-P7 domain formation by destabilizing these traps, revealing native structures as folding barriers.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA Biology

Background:

  • Magnesium ion (Mg2+) is crucial for the correct folding of the Tetrahymena ribozyme.
  • A specific kinetic intermediate forms where the P4-P6 domain is folded, but the P3-P7 domain remains unfolded.

Purpose of the Study:

  • To investigate the kinetic barriers hindering the formation of the P3-P7 domain in Tetrahymena ribozyme folding.
  • To identify mutations that enhance the folding rate of the P3-P7 domain.

Main Methods:

  • Utilized in vitro selection to isolate mutant RNA molecules with accelerated P3-P7 domain folding rates.
  • Analyzed the impact of critical mutations on native tertiary interactions within the P4-P6 domain.

Main Results:

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  • Identified specific mutations that disrupt native tertiary interactions in the P4-P6 domain.
  • These mutations significantly increased the rate of P3-P7 domain formation.
  • Destabilization of a kinetically trapped intermediate was identified as the mechanism for accelerated folding.

Conclusions:

  • Kinetic traps, stabilized by native RNA interactions, can pose significant barriers to RNA folding.
  • Native tertiary interactions, not just mispaired nonnative structures, can stabilize rate-limiting kinetic intermediates.