Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding

Robb Welty, Kathleen B. Hall

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


The tertiary structure of the GTPase center (GAC) of 23S ribosomal RNA (rRNA) as seen in cocrystals is extremely compact. It is stabilized by long-range hydrogen bonds and nucleobase stacking and by a triloop that forms within its three-way junction. Its folding pathway from secondary structure to tertiary structure has not been previously observed, but it was shown to require Mg2 + ions in equilibrium experiments. The fluorescent nucleotide 2-aminopurine was substituted at selected sites within the 60-nt GAC. Fluorescence intensity changes upon addition of MgCl2 were monitored over a time-course from 1 ms to 100 s as the RNA folds. The folding pathway is revealed here to be hierarchical through several intermediates. Observation of the nucleobases during folding provides a new perspective on the process and the pathway, revealing the dynamics of nucleobase conformational exchange during the folding transitions.

Original languageEnglish
Pages (from-to)4490-4502
Number of pages13
JournalJournal of Molecular Biology
Issue number22
StatePublished - Nov 6 2016


  • 2-aminopurine fluorescence
  • GTPase center RNA
  • RNA folding kinetics
  • stopped-flow fluorescence


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