title: Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer.
abstract: Adaptive binding, the ability of molecules to fold themselves around the structure of a ligand and thereby incorporating it into their three-dimensional fold, is a key feature of most RNA aptamers. The malachite green aptamer (MGA) has been shown to bind several closely related triphenyl dyes with planar and nonplanar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the adaptive nature of RNA-ligand interaction. The results of these studies reveal that binding of one ligand can reduce the ability of the aptamer pocket to adapt to another ligand, even if this second ligand has a significantly higher affinity to the free aptamer. A similar effect is observed in the presence of Mg(2+) ions which stabilize the binding pocket in a more ligand bound-like conformation.
authors.affiliation: Department of Chemistry, University of Waterloo , 200 University Ave West, Waterloo, ON N2L3G1, Canada.
authors.forename: Jason B
authors.initials: JB
authors.lastname: Da Costa
authors.forename: Aurelia I
authors.initials: AI
authors.lastname: Andreiev
authors.forename: Thorsten
authors.initials: T
authors.lastname: Dieckmann
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D002151:Calorimetry; D005840:Gentian Violet / Q000737:chemistry; D006575:Heterocyclic Compounds, 3-Ring / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D008274:Magnesium / Q000494:pharmacology; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D011754:Pyronine / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012235:Rhodamines; D012394:Rosaniline Dyes / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D052157:Aptamers, Nucleotide; D006575:Heterocyclic Compounds, 3-Ring; D008024:Ligands; D012235:Rhodamines; D012394:Rosaniline Dyes; C584549:malachite green RNA aptamer; C412715:tetramethylrosamine; C005095:malachite green; D012313:RNA; D008274:Magnesium; D005840:Gentian Violet; D011754:Pyronine