title: Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET.
abstract: Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. Here we investigate one such feature, the specific interaction of monovalent cations with a structured RNA, the P4-P6 domain of the Tetrahymena ribozyme. We employ single molecule FRET (smFRET) approaches as these allow determination of folding equilibrium and rate constants over a wide range of stabilities and thus allow direct comparisons without the need for extrapolation. These experiments provide additional evidence for specific binding of monovalent cations, Na+ and K+, to the RNA tetraloop-tetraloop receptor (TL-TLR) tertiary motif. These ions facilitate both folding and unfolding, consistent with an ability to help order the TLR for binding and further stabilize the tertiary contact subsequent to attainment of the folding transition state.
authors: *Department of Biochemistry, Stanford University, Stanford, CA 94305, U.S.A.
authors: Namita
authors: N
authors: Bisaria
authors: *Department of Biochemistry, Stanford University, Stanford, CA 94305, U.S.A.
authors: Daniel
authors: D
authors: Herschlag
mesh_terms: D001665:Binding Sites; D002414:Cations, Monovalent / Q000737:chemistry / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding / Q000235:genetics*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D012964:Sodium / Q000737:chemistry; D013768:Tetrahymena / Q000201:enzymology; D013816:Thermodynamics
chemical_list: D002414:Cations, Monovalent; D016337:RNA, Catalytic; D012313:RNA; D012964:Sodium; D008274:Magnesium