Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.
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 MgCl2were monitored over a time-course from 1ms to 100s 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.
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: robb@wustl.edu.
Robb
R
Welty
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address: kathleenhal@gmail.com.
Kathleen B
KB
Hall
D002413:Cations, Divalent / Q000378:metabolism; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012338:RNA, Ribosomal, 23S / Q000737:chemistry* / Q000378:metabolism*
D002413:Cations, Divalent; D012338:RNA, Ribosomal, 23S; D008274:Magnesium
2-aminopurine fluorescence; GTPase center RNA; RNA folding kinetics; stopped-flow fluorescence
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