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Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.

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 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 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.

SUBMITTER: Welty R

PROVIDER: S-EPMC5085838 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.

Welty Robb R Hall Kathleen B KB

Journal of molecular biology 20160929 22

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<sup>2+</sup> ions in equilibrium experiments. The fluorescent nucleotide 2-aminopurine was substituted at selected si ...[more]

PMID: 27693721

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