title: The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme.
abstract: Large RNAs can collapse into compact conformations well before the stable formation of the tertiary contacts that define their final folds. This study identifies likely physical mechanisms driving these early compaction events in RNA folding. We have employed time-resolved small-angle X-ray scattering to monitor the fastest global shape changes of the Tetrahymena ribozyme under different ionic conditions and with RNA mutations that remove long-range tertiary contacts. A partial collapse in each of the folding time-courses occurs within tens of milliseconds with either monovalent or divalent cations. Combined with comparison to predictions from structural models, this observation suggests a relaxation of the RNA to a more compact but denatured conformational ensemble in response to enhanced electrostatic screening at higher ionic concentrations. Further, the results provide evidence against counterion-correlation-mediated attraction between RNA double helices, a recently proposed model for early collapse. A previous study revealed a second 100 ms phase of collapse to a globular state. Surprisingly, we find that progression to this second early folding intermediate requires RNA sequence motifs that eventually mediate native long-range tertiary interactions, even though these regions of the RNA were observed to be solvent-accessible in previous footprinting studies under similar conditions. These results help delineate an analogy between the early conformational changes in RNA folding and the "burst phase" changes and molten globule formation in protein folding.
authors.affiliation: Department of Physics, Stanford University, Stanford, CA 94305-4060, USA.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Kwok
authors.forename: Ian S
authors.initials: IS
authors.lastname: Millett
authors.forename: Yu
authors.initials: Y
authors.lastname: Bai
authors.forename: Thalia T
authors.initials: TT
authors.lastname: Mills
authors.forename: Jaby
authors.initials: J
authors.lastname: Jacob
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Maskel
authors.forename: Soenke
authors.initials: S
authors.lastname: Seifert
authors.forename: Simon G J
authors.initials: SG
authors.lastname: Mochrie
authors.forename: P
authors.initials: P
authors.lastname: Thiyagarajan
authors.forename: Sebastian
authors.initials: S
authors.lastname: Doniach
authors.forename: Lois
authors.initials: L
authors.lastname: Pollack
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
mesh_terms: D000818:Animals; D009690:Nucleic Acid Conformation; D017510:Protein Folding; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D016808:Tetrahymena thermophila / Q000201:enzymology / Q000235:genetics*
chemical_list: D016337:RNA, Catalytic; D012313:RNA