Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding. Issue 22 (6th November 2016)

• Record Type: Journal Article
• Authors: Welty, Robb; Hall, Kathleen B.
• Is Part Of: Journal of molecular biology. Volume 428:Issue 22(2016:Nov. 06)
• Page Start: 4490
• Page End: 4502
• Publication Date: 2016-11-06
• Subjects: GAC GTPase center -- 2AP 2-aminopurine -- SAXS small angle X-ray scattering -- rRNA ribosomal RNA; GTPase center RNA -- 2-aminopurine fluorescence -- RNA folding kinetics -- stopped-flow fluorescence; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2016.09.015
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: 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 Mg 2 + 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. Graphical Abstract: Highlights: Mg 2 + -dependent RNA folding pathways reveal how tertiary structures utilize ions. GAC tertiary folding pathway has four intermediates; two require Mg 2 + . GAC folding kinetics range from milliseconds (local) to seconds (global). Fluorescent bases reveal transient conformational changes before global folding.