Skip Navigation

Nucleic Acids Research 2005 33(2):745-754; doi:10.1093/nar/gki222
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3000K) Freely available
Right arrow Screen PDF (594K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sakamoto, T.
Right arrow Articles by Nakamura, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sakamoto, T.
Right arrow Articles by Nakamura, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 1 February 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}oupjournals.org.

Article

NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A

Taiichi Sakamoto, Akihiro Oguro, Gota Kawai1, Takashi Ohtsu and Yoshikazu Nakamura*

Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan 1 Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology Narashino-shi, Chiba 275-0016, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5307; Fax: +81 3 5449 5415; Email: nak{at}ims.u-tokyo.ac.jp

Received October 31, 2004. Revised January 1, 2005. Accepted January 14, 2005.

A high affinity RNA aptamer (APT58, 58 nt long) against mammalian initiation factor 4A (eIF4A) requires nearly its entire nucleotide sequence for efficient binding. Since splitting either APT58 or eIF4A into two domains diminishes the affinity for each other, it is suggested that multiple interactions or a global interaction between the two molecules accounts for the high affinity. To understand the structural basis of APT58's global recognition of eIF4A, we determined the solution structure of two essential nucleotide loops (AUCGCA and ACAUAGA) within the aptamer using NMR spectroscopy. The AUCGCA loop is stabilized by a U-turn motif and contains a non-canonical A:A base pair (the single hydrogen bond mismatch: Hoogsteen/Sugar-edge). On the other hand, the ACAUAGA loop is stabilized by an AUA tri-nucleotide loop motif and contains the other type of A:A base pair (single hydrogen bond mismatch: Watson–Crick/Watson–Crick). Considering the known structural and functional properties of APT58, we propose that the AUCGCA loop is directly involved in the interaction with eIF4A, while the flexibility of the ACAUAGA loop is important to support this interaction. The Watson–Crick edges of C7 and C9 in the AUCGCA loop may directly interact with eIF4A.

Present address: Taiichi Sakamoto, Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino-shi, Chiba 275-0016, Japan


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
Y. Bessho, R. Shibata, S.-i. Sekine, K. Murayama, K. Higashijima, C. Hori-Takemoto, M. Shirouzu, S. Kuramitsu, and S. Yokoyama
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA
PNAS, May 15, 2007; 104(20): 8293 - 8298.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.