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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Xue, Y; Gracia, B; Herschlag, D; Russell, R; Al-Hashimi, HM

Published Date

  • June 13, 2016

Published In

Volume / Issue

  • 7 /

Start / End Page

  • ncomms11768 -

PubMed ID

  • 27292179

Pubmed Central ID

  • PMC4909931

Electronic International Standard Serial Number (EISSN)

  • 2041-1723

Digital Object Identifier (DOI)

  • 10.1038/ncomms11768


  • eng

Conference Location

  • England