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Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Publication ,  Journal Article
Xue, Y; Gracia, B; Herschlag, D; Russell, R; Al-Hashimi, HM
Published in: Nat Commun
June 13, 2016

Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg(2+) or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways.

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Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

June 13, 2016

Volume

7

Start / End Page

ncomms11768

Location

England

Related Subject Headings

  • Thermodynamics
  • Tetrahymena
  • RNA Folding
  • RNA
  • Nucleic Acid Conformation
  • Mutation
  • Magnetic Resonance Spectroscopy
  • Magnesium
  • Base Sequence
 

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Xue, Y., Gracia, B., Herschlag, D., Russell, R., & Al-Hashimi, H. M. (2016). Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun, 7, ncomms11768. https://doi.org/10.1038/ncomms11768
Xue, Yi, Brant Gracia, Daniel Herschlag, Rick Russell, and Hashim M. Al-Hashimi. “Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.Nat Commun 7 (June 13, 2016): ncomms11768. https://doi.org/10.1038/ncomms11768.
Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun. 2016 Jun 13;7:ncomms11768.
Xue, Yi, et al. “Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.Nat Commun, vol. 7, June 2016, p. ncomms11768. Pubmed, doi:10.1038/ncomms11768.
Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun. 2016 Jun 13;7:ncomms11768.

Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

June 13, 2016

Volume

7

Start / End Page

ncomms11768

Location

England

Related Subject Headings

  • Thermodynamics
  • Tetrahymena
  • RNA Folding
  • RNA
  • Nucleic Acid Conformation
  • Mutation
  • Magnetic Resonance Spectroscopy
  • Magnesium
  • Base Sequence