title: Correlating structural dynamics and function in single ribozyme molecules.
abstract: We have studied the correlation between structural dynamics and function of the hairpin ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked (inactive) conformations. Using single-molecule fluorescence methods, we found complex structural dynamics with four docked states of distinct stabilities and a strong memory effect where each molecule rarely switches between different docked states. We also found substrate cleavage to be rate-limited by a combination of conformational transitions and reversible chemistry equilibrium. The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA.
authors.affiliation: Department of Physics, Stanford University, Stanford, CA 94305, USA.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhuang
authors.forename: Harold
authors.initials: H
authors.lastname: Kim
authors.forename: Miguel J B
authors.initials: MJ
authors.lastname: Pereira
authors.forename: Hazen P
authors.initials: HP
authors.lastname: Babcock
authors.forename: Nils G
authors.initials: NG
authors.lastname: Walter
authors.forename: Steven
authors.initials: S
authors.lastname: Chu
mesh_terms: D002232:Carbocyanines / Q000378:metabolism; D002384:Catalysis; D004800:Enzymes, Immobilized; D005453:Fluorescence; D006860:Hydrogen Bonding; D007700:Kinetics; D017860:Nepovirus / Q000235:genetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D019244:RNA, Satellite; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D002232:Carbocyanines; D004800:Enzymes, Immobilized; D016337:RNA, Catalytic; D019244:RNA, Satellite; D012367:RNA, Viral; C089187:cyanine dye 3; C085321:cyanine dye 5