Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.
Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg(2+) or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways.
Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Yi
Y
Xue
Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
Brant
B
Gracia
Department of Biochemistry, Beckman Center, Stanford University, Stanford, California 94305, USA.|Department of Chemistry, Stanford University, Stanford, California 94305, USA.|Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA.|Chemistry, Engineering, and Medicine for Human Health (ChEM-H) Institute, Stanford University, Stanford, California 94305, USA.
Daniel
D
Herschlag
Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
Rick
R
Russell
Department of Biochemistry, Duke Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.|Department of Chemistry, Duke University, Durham, Stanford, North Carolina 27710, USA.
Hashim M
HM
Al-Hashimi
D001483:Base Sequence; D008274:Magnesium / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D059370:RNA Folding / Q000187:drug effects; D013768:Tetrahymena; D013816:Thermodynamics
D012313:RNA; D008274:Magnesium