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Nucleic Acids Research 2005 33(22):6961-6971; doi:10.1093/nar/gki1004
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Published online 23 December 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

Solution structure of {psi}32-modified anticodon stem–loop of Escherichia coli tRNAPhe

Javier Cabello-Villegas and Edward P. Nikonowicz*

Department of Biochemistry and Cell Biology, Rice University Houston, TX 77251-1892, USA

*To whom correspondence should be addressed. Tel: +1 713 348 4912; Fax +1 713 348 5154; Email: edn{at}bioc.rice.edu

Received September 13, 2005. Revised November 17, 2005. Accepted November 17, 2005.

Nucleoside base modifications can alter the structures and dynamics of RNA molecules and are important in tRNAs for maintaining translational fidelity and efficiency. The unmodified anticodon stem–loop from Escherichia coli tRNAPhe forms a trinucleotide loop in solution, but Mg2+ and dimethylallyl modification of A37 N6 destabilize the loop-proximal base pairs and increase the mobility of the loop nucleotides. The anticodon arm has three additional modifications, {psi}32, {psi}39, and A37 C2-thiomethyl. We have used NMR spectroscopy to investigate the structural and dynamical effects of {psi}32 on the anticodon stem-loop from E.coli tRNAPhe. The {psi}32 modification does not significantly alter the structure of the anticodon stem–loop relative to the unmodified parent molecule. The stem of the RNA molecule includes base pairs {psi}32-A38 and U33–A37 and the base of {psi}32 stacks between U33 and A31. The glycosidic bond of {psi}32 is in the anti configuration and is paired with A38 in a Watson–Crick geometry, unlike residue 32 in most crystal structures of tRNA. The {psi}32 modification increases the melting temperature of the stem by ~3.5°C, although the {psi}32 and U33 imino resonances are exchange broadened. The results suggest that {psi}32 functions to preserve the stem integrity in the presence of additional loop modifications or after reorganization of the loop into a translationally functional conformation.

Present address: Javier Cabello-Villegas, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045, USA


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