Nucleic Acids Research Advance Access first published online on September 25, 2006
This version published online on October 5, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl664
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© 2006 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.
Structural Biology |
Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
Department of Life and Environmental Sciences, Faculty of Engineering Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan 1 Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology 4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan 2 Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology 38 Nishigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
*To whom correspondence should be addressed. Tel/Fax: +81 47 478 0425; Email: gkawai{at}sea.it-chiba.ac.jp
Received June 7, 2006. Revised August 25, 2006. Accepted August 25, 2006.
The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3' conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U–U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3' conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U–U mismatch are required for efficient retrotransposition.
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