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Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11555-60.

RNA folding causes secondary structure rearrangement.

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  • 1Department of Chemistry, University of California, Berkeley, and Structural Biology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460, USA.


The secondary structure of the P5abc subdomain (a 56-nt RNA) of the Tetrahymena thermophila group I intron ribozyme has been determined by NMR. Its base pairing in aqueous solution in the absence of magnesium ions is significantly different from the RNA in a crystal but is consistent with thermodynamic predictions. On addition of magnesium ions, the RNA folds into a tertiary structure with greatly changed base pairing consistent with the crystal structure: three Watson-Crick base pairs, three G.U base pairs, and an extra-stable tetraloop are lost. The common assumption that RNA folds by first forming secondary structure and then forming tertiary interactions from the unpaired bases is not always correct.

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