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

Michael Latham, Grant R. Zimmermann, Arthur Pardi

Research output: Contribution to journalArticle

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 (1)H-(1)H 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) approximately 3.0 mM at 15 degrees C) show slow exchange on the NMR chemical shift time scal
Original languageEnglish
Pages (from-to)5052–5053
JournalJournal of the American Chemical Society
StatePublished - 2009

Fingerprint Dive into the research topics of 'NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer'. Together they form a unique fingerprint.

Cite this