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Nucleic Acids Research, 2000, Vol. 28, No. 8 1778-1784
© 2000 Oxford University Press

The RNA-binding domain of ribosomal protein L11 recognizes an rRNA tertiary structure stabilized by both thiostrepton and magnesium ion

Lawrence B. Blyn*, Lisa M. Risen, Richard H. Griffey and David E. Draper1

Ibis Therapeutics, a Division of Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, CA 92008, USA and 1Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA

Antibiotics that inhibit ribosomal function may do so by one of several mechanisms, including the induction of incorrect RNA folding or prevention of protein and/or RNA conformational transitions. Thiostrepton, which binds to the ‘GTPase center’ of the large subunit, has been postulated to prevent conformational changes in either the L11 protein or rRNA to which it binds. Scintillation proximity assays designed to look at the binding of the L11 C-terminal RNA-binding domain to a 23S ribosomal RNA (rRNA) fragment, as well as the ability of thiostrepton to induce that binding, were used to demonstrate the role of Mg2+, L11 and thio­strepton in the formation and maintenance of the rRNA fragment tertiary structure. Experiments using these assays with both an Escherichia coli rRNA fragment and a thermostable variant of that RNA show that Mg2+, L11 and thiostrepton all induce the RNA to fold to an essentially identical tertiary structure.

* To whom correspondence should be addressed. Tel: +1 760 603 2579; Fax: +1 760 431 2768; Email: lblyn@isisph.com


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