Exploring the folding landscape of a structured RNA.
Structured RNAs achieve their active states by traversing complex, multidimensional energetic landscapes. Here we probe the folding landscape of the Tetrahymena ribozyme by using a powerful approach: the folding of single ribozyme molecules is followed beginning from distinct regions of the folding landscape. The experiments, combined with small-angle x-ray scattering results, show that the landscape contains discrete folding pathways. These pathways are separated by large free-energy barriers that prevent interconversion between them, indicating that the pathways lie in deep channels in the folding landscape. Chemical protection and mutagenesis experiments are then used to elucidate the structural features that determine which folding pathway is followed. Strikingly, a specific long-range tertiary contact can either help folding or hinder folding, depending on when it is formed during the process. Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape.
Russell
Rick
R
Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
Zhuang
Xiaowei
X
Babcock
Hazen P
HP
Millett
Ian S
IS
Doniach
Sebastian
S
Chu
Steven
S
Herschlag
Daniel
D
D000818:Animals; D004305:Dose-Response Relationship, Drug; D007700:Kinetics; D008274:Magnesium / Q000494:pharmacology; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D017510:Protein Folding; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry*; D012542:Scattering, Radiation; D012964:Sodium / Q000494:pharmacology; D013463:Sulfuric Acid Esters / Q000494:pharmacology; D013768:Tetrahymena / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors; D014965:X-Rays
D016337:RNA, Catalytic; D013463:Sulfuric Acid Esters; D012313:RNA; D012964:Sodium; D008274:Magnesium; C007482:dimethyl sulfate