ArticleNucleic acids research2007
Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 58 citations in OpenAlex.
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- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Molecular basis of facilitated target search and sequence discrimination of TALE homeodomain transcription factor Meis1.Nature communications · 2024Article
- Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.iScience · 2022Article
- Base-Pair Opening Dynamics Study of Fluoride Riboswitch in theInternational journal of molecular sciences · 2021Article
- Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.Biophysical journal · 2020Article
- Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs.RNA biology · 2020Article
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- Base-pair Opening Dynamics of Nucleic Acids in Relation to Their Biological Function.Computational and structural biotechnology journal · 2019Review
- Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets.ACS omega · 2017Article
- Comparison of the free and ligand-bound imino hydrogen exchange rates for the cocaine-binding aptamer.Journal of biomolecular NMR · 2017Article
- Base-pair opening dynamics of primary miR156a using NMR elucidates structural determinants important for its processing level and leaf number phenotype in Arabidopsis.Nucleic acids research · 2017Article
- Structural features of influenza A virus panhandle RNA enabling the activation of RIG-I independently of 5'-triphosphate.Nucleic acids research · 2016Article
- Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B-Z transition.Nucleic acids research · 2016Article
- Individual basepair stability of DNA and RNA studied by NMR-detected solvent exchange.Biophysical journal · 2012Article
- Base pair opening kinetics study of the aegPNA:DNA hydrid duplex containing a site-specific GNA-like chiral PNA monomer.Nucleic acids research · 2011Article
- On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics.Nucleic acids research · 2011Article
- Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution.Nucleic acids research · 2010Article
- A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics.Journal of the American Chemical Society · 2009Article
- Kinetic barriers and the role of topology in protein and RNA folding.Protein science : a publication of the Protein Society · 2008Review
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
The thermodynamics and kinetics for base-pair opening of the P1 duplex of the Tetrahymena group I ribozyme were studied by NMR hydrogen exchange experiments. The apparent equilibrium constants for base pair opening were measured for most of the imino protons in the P1 duplex using the base catalysts NH3, HPO4(2-) or TRIS. These equilibrium constants were also measured for several modified P1 duplexes, and the C-2.G23 base pair was the most stable base pair in all the duplexes. The conserved U-1*G22 base pair is required for activity of the ribozyme and the data here show that this wobble base pair destabilizes neighboring base pairs on only one side of the wobble. A 2'-OMe modification on the U-3 residue stabilized its own base pair but had little effect on the neighboring base pairs. Three base pairs, U-1*G22, C-2*G23 and A2*U21 showed unusual equilibrium constants for opening and possible implications of the opening thermodynamics of these base pairs on the undocking rates of the P1 helix with catalytic core are discussed.
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