Thermodynamics and Kinetics of Adaptive Binding in the Malachite Green RNA Aptamer

Jason B. Da Costa, Aurelia I. Andreiev, Thorsten Dieckmann
2013 Biochemistry  
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 tri-phenyl dyes with planar and non-planar structures in this manner. Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics have been conducted with the aim of understanding the
more » ... derstanding 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.
doi:10.1021/bi400549s pmid:23984874 fatcat:dhwkyzwwybg6vpenhf462erv4u