ArticleBiochemistry2009
Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- New opportunities for designing effective small interfering RNAs.Scientific reports · 2019Article
- Local-to-global signal transduction at the core of a MnNature communications · 2019Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Cellobiohydrolase 1 from Trichoderma reesei degrades cellulose in single cellobiose steps.Nature communications · 2015Article
- Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Exploring the electrostatic energy landscape for tetraloop-receptor docking.Physical chemistry chemical physics : PCCP · 2014Article
- Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA pseudoknot: temperature-/urea-dependent folding kinetics and thermodynamics.The journal of physical chemistry. B · 2014Article
- Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics.Biophysical journal · 2014Article
- Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices.Biophysical journal · 2013Article
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
- Thermodynamic origins of monovalent facilitated RNA folding.Biochemistry · 2012Article
- Article
- Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex.Biophysical journal · 2012Article
- Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry.Nucleic acids research · 2012Article
- Entropic origin of Mg2+-facilitated RNA folding.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme.Structure (London, England : 1993) · 2010Article
- Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.RNA (New York, N.Y.) · 2010Article
- Analysis of complex single-molecule FRET time trajectories.Methods in enzymology · 2010Article
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5 authors.
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Abstract
RNA folding thermodynamics are crucial for structure prediction, which requires characterization of both enthalpic and entropic contributions of tertiary motifs to conformational stability. We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop-receptor docking interaction, exploiting immobilized and freely diffusing single-molecule fluorescence resonance energy transfer (smFRET) methods. The equilibrium constant for intramolecular docking is obtained as a function of temperature (T = 21-47 degrees C), from which a van't Hoff analysis yields the enthalpy (DeltaH degrees) and entropy (DeltaS degrees) of docking. Tetraloop-receptor docking is significantly exothermic and entropically unfavorable in 1 mM MgCl(2) and 100 mM NaCl, with excellent agreement between immobilized (DeltaH degrees = -17.4 +/- 1.6 kcal/mol, and DeltaS degrees = -56.2 +/- 5.4 cal mol(-1) K(-1)) and freely diffusing (DeltaH degrees = -17.2 +/- 1.6 kcal/mol, and DeltaS degrees = -55.9 +/- 5.2 cal mol(-1) K(-1)) species. Kinetic heterogeneity in the tetraloop-receptor construct is unaffected over the temperature range investigated, indicating a large energy barrier for interconversion between the actively docking and nondocking subpopulations. Formation of the tetraloop-receptor interaction can account for approximately 60% of the DeltaH degrees and DeltaS degrees of P4-P6 domain folding in the Tetrahymena ribozyme, suggesting that it may act as a thermodynamic clamp for the domain. Comparison of the isolated tetraloop-receptor and other tertiary folding thermodynamics supports a theme that enthalpy- versus entropy-driven folding is determined by the number of hydrogen bonding and base stacking interactions.
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