ArticleBiochemistry2004
Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme.
Article in Biochemistry, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.Journal of the American Chemical Society · 2018Article
- Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.Nucleic acids research · 2018Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices.Biophysical journal · 2013Article
- Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry.Nucleic acids research · 2012Article
- Visualizing large RNA molecules in solution.RNA (New York, N.Y.) · 2012Article
- Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.Biochemistry · 2011Article
- Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction.Biochemistry · 2009Article
- Isothermal titration calorimetry of RNA.Methods (San Diego, Calif.) · 2009Review
- Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry.Methods in enzymology · 2009Article
- Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry.Biophysical journal · 2009Article
- Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.Journal of molecular biology · 2008Article
- Discrete state model and accurate estimation of loop entropy of RNA secondary structures.The Journal of chemical physics · 2008Article
- Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme.RNA (New York, N.Y.) · 2007Article
- Heat capacity changes associated with nucleic acid folding.Biopolymers · 2006Review
- Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length.Biophysical journal · 2006Article
- A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.Nucleic acids research · 2006Article
- Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs.Nature structural & molecular biology · 2004Article
- Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures.RNA (New York, N.Y.) · 2004Article
- Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation.Nucleic acids research · 2004Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Helical junctions are extremely common motifs in naturally occurring RNAs, but little is known about the thermodynamics that drive their folding. Studies of junction folding face several challenges: non-two-state folding behavior, superposition of secondary and tertiary structural energetics, and drastically opposing enthalpic and entropic contributions to folding. Here we describe a thermodynamic dissection of the folding of the hammerhead ribozyme, a three-way RNA helical junction, by using isothermal titration calorimetry of bimolecular RNA constructs. By using this method, we show that tertiary folding of the hammerhead core occurs with a highly unfavorable enthalpy change, and is therefore entropically driven. Furthermore, the enthalpies and heat capacities of core folding are the same whether supported by monovalent or divalent ions. These properties appear to be general to the core sequence of bimolecular hammerhead constructs. We present a model for the ion-induced folding of the hammerhead core that is similar to those advanced for the folding of much larger RNAs, involving ion-induced collapse to a structured, non-native state accompanied by rearrangement of core residues to produce the native fold. In agreement with previous enzymological and structural studies, our thermodynamic data suggest that the hammerhead structure is stabilized in vitro predominantly by diffusely bound ions. Our approach addresses several significant challenges that accompany the study of junction folding, and should prove useful in defining the thermodynamic determinants of stability in these important RNA motifs.
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