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Nucleic Acids Research 2005 33(1):213-224; doi:10.1093/nar/gki160
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Published online 12 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; 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 permissions, please contact journals.permissions{at}oupjournals.org.

Article

i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats

Narcisse Esmaili and Jean Louis Leroy*

Laboratoire de RMN à Haut Champ, Institut de Chimie des Substances Naturelles Gif-sur-Yvette, F-91198, France

*To whom correspondence should be addressed. Tel: +33 169 823630; Fax: +33 169 823784; Email: Jean-Louis.Leroy{at}icsn.cnrs-gif.fr

Received September 17, 2004. Revised December 10, 2004. Accepted December 10, 2004.

Using NMR methods, we have resolved the i-motif structures formed by d(AACCCC) and by d(CCCCAA), two versions of the DNA sequence repeated in the telomeric regions of the C-rich strand of tetrahymena chromosomes. Both oligonucleotides form fully symmetrical i-motif tetramers built by intercalation of two hemiprotonated duplexes containing four C•C+ pairs. The structures are extremely stable. In the tetramer of d(AACCCC), the outermost C•C+ pairs are formed by the cytidines of the 5' ends of the cytidine tracts. A2 forms an A2•A2 (H6trans–N7) pair stacked to C3•C3+ and cross-strand stacked to A1. At 0°C, the lifetimes of the hemiprotonated pairs range from 1 ms for the outermost pair to ~1 h for the innermost pairs. The tetramer of d(CCCCAA) adopts two distinct intercalation topologies in slow conformational exchange. One, whose outermost C•C+ pairs are built by the cytidines of the 5' end and the other by those of the 3' end. In both topologies, the adenosine bases are fairly well stacked to the adjacent C•C+ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other.


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