NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer

The apparent on and off rate constants for binding of theophylline to its RNA aptamer in the absence of Mg ²⁺ were determined here by 2D ¹H- ¹H ZZ-exchange NMR spectroscopy. Analysis of the buildup rate of the exchange cross peaks for several base-paired imino protons in the RNA yielded an apparent k _on of 600 M ^-1 s ^-1. This small apparent k _on results because the free RNA exist as a dynamic equilibrium of inactive states rapidly interconverting with a low population of active species. The data found here indicate that the RNA aptamer employs a conformational selection mechanism for binding theophylline in the absence of Mg ²⁺. The kinetic data found here also explain a very unusual property of this RNA-theophylline system: slow exchange on the NMR chemical shift time scale for a weakly binding complex. To our knowledge, it is unprecedented to have such a weakly binding complex (K _d ≈ 3.0 mM at 15 °C) show slow exchange on the NMR chemical shift time scale, but the results clearly demonstrate that slow exchange and weak binding are readily rationalized by a small k _on. Comparisons with other ligand-receptor interactions are presented.