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Nucleic Acids Research, 2000, Vol. 28, No. 15 2935-2942
© 2000 Oxford University Press

Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions

J. A. Cowan*, Tsuyoshi Ohyama, Dongqing Wang and Kshama Natarajan

Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA

Aminoglycosides are an important class of antibiotic that selectively target RNA structural motifs. Recently we have demonstrated copper derivatives of amino­glycosides to be efficient cleavage agents for cognate RNA motifs. To fully develop their potential as phar­ma­ceutical agents it is necessary to understand both the structural mechanisms used by aminoglycosides to target RNA, and the relative contributions of hydrogen bonding and electrostatic interactions to recognition selectivity. Herein we report results from a calorimetric analysis of a stem–loop 23mer RNA aptamer complexed to the aminoglycoside neomycin B. Key thermodynamic parameters for complex formation have been determined by isothermal titration calorimetry, and from the metal-ion dependence of these binding parameters the relative contributions of electrostatics and hydrogen bonding toward binding affinity have been assessed. The principal mechanism for recognition and binding of neomycin B to the RNA major groove is mediated by hydrogen bonding.

* To whom correspondence should be addressed. Tel: +1 614 292 2703; Fax: +1 614 292 1685; Email: cowan@chemistry.ohio-state.edu


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