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Nucleic Acids Research Advance Access originally published online on January 7, 2009
Nucleic Acids Research 2009 37(4):1202-1210; doi:10.1093/nar/gkn1040
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Nucleic Acids Research, 2009, Vol. 37, No. 4 1202-1210
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Specificity of the ribosomal A site for aminoacyl-tRNAs

Taraka Dale1, Richard P. Fahlman2, Mikolaj Olejniczak3 and Olke C. Uhlenbeck4,*

1Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA, 2Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, 3Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland and 4Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA

*To whom correspondence should be addressed. Tel: +1 847 491 5139; Fax: +1 847 491 5444; Email: o-uhlenbeck{at}northwestern.edu

Received October 14, 2008. Revised December 12, 2008. Accepted December 14, 2008.

Although some experiments suggest that the ribosome displays specificity for the identity of the esterified amino acid of its aminoacyl-tRNA substrate, a study measuring dissociation rates of several misacylated tRNAs containing the GAC anticodon from the A site showed little indication for such specificity. In this article, an expanded set of misacylated tRNAs and two 2'-deoxynucleotide-substituted mRNAs are used to demonstrate the presence of a lower threshold in koff values for aa-tRNA binding to the A site. When a tRNA binds sufficiently well to reach this threshold, additional stabilizing effects due to the esterified amino acid or changes in tRNA sequence are not observed. However, specificity for different amino acid side chains and the tRNA body is observed when tRNA binding is sufficiently weaker than this threshold. We propose that uniform aa-tRNA binding to the A site may be a consequence of a conformational change in the ribosome, induced by the presence of the appropriate combination of contributions from the anticodon, amino acid and tRNA body.


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