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Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2

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. Dele...

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Autores principales: Nomura, Yusuke, Kajikawa, Masaki, Baba, Seiki, Nakazato, Shinta, Imai, Takayuki, Sakamoto, Taiichi, Okada, Norihiro, Kawai, Gota
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636434/
https://www.ncbi.nlm.nih.gov/pubmed/17000640
http://dx.doi.org/10.1093/nar/gkl664
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author Nomura, Yusuke
Kajikawa, Masaki
Baba, Seiki
Nakazato, Shinta
Imai, Takayuki
Sakamoto, Taiichi
Okada, Norihiro
Kawai, Gota
author_facet Nomura, Yusuke
Kajikawa, Masaki
Baba, Seiki
Nakazato, Shinta
Imai, Takayuki
Sakamoto, Taiichi
Okada, Norihiro
Kawai, Gota
author_sort Nomura, Yusuke
collection PubMed
description 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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spelling pubmed-16364342006-11-29 Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2 Nomura, Yusuke Kajikawa, Masaki Baba, Seiki Nakazato, Shinta Imai, Takayuki Sakamoto, Taiichi Okada, Norihiro Kawai, Gota Nucleic Acids Res Structural Biology 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. Oxford University Press 2006-10 2006-09-25 /pmc/articles/PMC1636434/ /pubmed/17000640 http://dx.doi.org/10.1093/nar/gkl664 Text en © 2006 The Author(s)
spellingShingle Structural Biology
Nomura, Yusuke
Kajikawa, Masaki
Baba, Seiki
Nakazato, Shinta
Imai, Takayuki
Sakamoto, Taiichi
Okada, Norihiro
Kawai, Gota
Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title_full Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title_fullStr Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title_full_unstemmed Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title_short Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2
title_sort solution structure and functional importance of a conserved rna hairpin of eel line unal2
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636434/
https://www.ncbi.nlm.nih.gov/pubmed/17000640
http://dx.doi.org/10.1093/nar/gkl664
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