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Nucleic Acids Research 2005 33(17):5482-5493; doi:10.1093/nar/gki861
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Published online 25 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

A diminutive and specific RNA binding site for L-tryptophan

Irene Majerfeld and Michael Yarus*

Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309-0347, USA

*To whom correspondence should be addressed. Tel: +1 303 492 8376; Fax: +1 303 492 7744; Email: yarus{at}buffmail.colorado.edu

Received July 20, 2005. Revised September 7, 2005. Accepted September 7, 2005.

Selection for amino acid affinity by elution of RNAs from tryptophan–Sepharose using free L-tryptophan evokes one sequence predominantly (KD = 12 µM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in randomized tracts of 70, 60, 40, 20 and 17 nt show that this internal loop is the simplest sequence that can meet the column affinity selection. From sequence variation in ~50 independent isolates, only 26 bits of information are required to describe this loop (equivalent to only 13 fully conserved nucleotides). Thus, it is among the simplest amino acid binding sites known, as well as selective among hydrophobic side chains. Among site sequences defined as essential to affinity by conservation, protection and modification-interference, there is a recurring CCA sequence (a tryptophan anticodon triplet) which apparently forms one side of the binding site. Such conserved juxtaposition of tryptophan with a cognate coding triplet supports a stereochemical origin for the genetic code.


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