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

Michael P. Latham, Grant R. Zimmermann, Arthur Pardi

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish
Pages (from-to)5052-5053
Number of pages2
JournalJournal of the American Chemical Society
Volume131
Issue number14
DOIs
StatePublished - Apr 15 2009

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