RNA folding causes secondary structure rearrangement.
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.
Wu
M
M
Department of Chemistry, University of California, Berkeley, and Structural Biology Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460, USA.
Tinoco
I
I
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D008274:Magnesium / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics; D016808:Tetrahymena thermophila / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics
D016053:RNA, Protozoan; D012313:RNA; D008274:Magnesium