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Related Experiment Videos

Pathway modulation, circular permutation and rapid RNA folding under kinetic control.

T Pan1, X Fang, T Sosnick

  • 1Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA. taopan@midway.uchicago.edu

Journal of Molecular Biology
|February 20, 1999
PubMed
Summary
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Circularly permuted Bacillus subtilis RNase P ribozyme folds 15x faster by avoiding interdomain misfolding. This RNA folding pathway is highly malleable and kinetically controlled.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA structure and function

Background:

  • The ribozyme from Bacillus subtilis RNase P is crucial for tRNA processing.
  • Wild-type RNase P RNA folding is slow due to kinetically trapped misfolded structures.
  • Interactions between independently folding domains may contribute to misfolding.

Purpose of the Study:

  • To analyze and compare the thermodynamics and folding kinetics of a circularly permuted RNase P ribozyme construct with the wild-type.
  • To investigate the role of interdomain interactions in the kinetic trapping of wild-type RNase P RNA folding.
  • To determine if circular permutation can alleviate misfolding and accelerate folding.

Main Methods:

  • Circularly permuted construct creation by breaking a phosphodiester bond between domains.

Related Experiment Videos

  • Optical spectroscopy to monitor folding thermodynamics and kinetics.
  • Catalytic activity assays to assess functional folding.

    • Main Results:

    • The circularly permuted construct folds approximately 15-fold faster (t1/2 ≈ 9 seconds at 37°C) than the wild-type ribozyme.
    • In the circularly permuted construct, one domain folds significantly faster than the other, unlike the wild-type where domain folding is indistinguishable.
    • Interdomain interactions are identified as the major kinetic trap in wild-type RNase P RNA folding.
    • This kinetic trap is avoidable at 37°C in the permuted construct, but interdomain misfolding can still occur below 30°C or from specific intermediates.

    Conclusions:

    • The major kinetic trap in wild-type RNase P RNA folding involves interdomain interactions.
    • Circular permutation effectively bypasses this trap at physiological temperatures, leading to faster folding.
    • The folding pathway of this large RNA is highly adaptable and subject to kinetic control, influenced by temperature and magnesium ion concentration.