title: Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.
abstract: Counterions are required for RNA folding, and divalent metal ions such as Mg(2+) are often critical. To dissect the role of counterions, we have compared global and local folding of wild-type and mutant variants of P4-P6 RNA derived from the Tetrahymena group I ribozyme in monovalent and in divalent metal ions. A remarkably simple picture of the folding thermodynamics emerges. The equilibrium folding pathway in monovalent ions displays two phases. In the first phase, RNA molecules that are initially in an extended conformation enforced by charge-charge repulsion are relaxed by electrostatic screening to a state with increased flexibility but without formation of long-range tertiary contacts. At higher concentrations of monovalent ions, a state that is nearly identical to the native folded state in the presence of Mg(2+) is formed, with tertiary contacts that involve base and backbone interactions but without the subset of interactions that involve specific divalent metal ion-binding sites. The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA.
authors.affiliation: Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA.
authors.forename: Keiji
authors.initials: K
authors.lastname: Takamoto
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Qin
authors.initials: Q
authors.lastname: He
authors.forename: Sebastian
authors.initials: S
authors.lastname: Doniach
authors.forename: Michael
authors.initials: M
authors.lastname: Brenowitz
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
authors.forename: Mark R
authors.initials: MR
authors.lastname: Chance
mesh_terms: D000818:Animals; D002414:Cations, Monovalent / Q000378:metabolism*; D008274:Magnesium / Q000378:metabolism; D009154:Mutation; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012964:Sodium; D055672:Static Electricity; D013768:Tetrahymena / Q000235:genetics / Q000378:metabolism
chemical_list: D002414:Cations, Monovalent; D016337:RNA, Catalytic; D012964:Sodium; D008274:Magnesium