ArticleBiochemistry2006
Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
- Destabilization of Structured RNAs by OPC and TIP4PD Water Models.Journal of chemical theory and computation · 2026Article
- Combining UV-Vis Absorption and FRET Melting Curves to Screen the Thermodynamic Stability and Folding Pathways of Nucleic Acids In Vitro.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2018Article
- Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.Journal of the American Chemical Society · 2017Article
- Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch.Cell reports · 2016Article
- 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
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
- Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix.Biochemistry · 2012Article
- Thermodynamic origins of monovalent facilitated RNA folding.Biochemistry · 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
- Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient.Biochemistry · 2010Article
- Real-Time Infrared Overtone Laser Control of Temperature in Picoliter H(2)O Samples: "Nanobathtubs" for Single Molecule Microscopy.The journal of physical chemistry letters · 2010Article
- Compact intermediates in RNA folding.Annual review of biophysics · 2010Review
- The influence of monovalent cation size on the stability of RNA tertiary structures.Journal of molecular biology · 2009Article
- Single-Molecule Fluorescence Studies of RNA: A Decade's Progress.Chemical physics letters · 2009Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The GAAA tetraloop-receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a single-stranded A(7) linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking {[Co(NH(3))(6)(3+)] << [Ca(2+)], [Mg(2+)], [Mn(2+)] << [Na(+)], [K(+)]}. Analysis of metal ion cooperativity yielded Hill coefficients of approximately 2 for Na(+)- or K(+)-dependent docking versus approximately 1 for the divalent ions and Co(NH(3))(6)(3+). Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloop-receptor docking. RNA constructs with U(7) and A(14) single-stranded linkers were investigated by single-molecule and ensemble FRET techniques to determine how linker length and composition affect docking. These studies showed that the single-stranded region functions primarily as a flexible tether. Inhibition of docking by oligonucleotides complementary to the linker was also investigated. The influence of flexible versus rigid linkers on GAAA tetraloop-receptor docking is discussed.
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