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Nucleic Acids Research 2005 33(17):5471-5481; doi:10.1093/nar/gki843
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Published online 4 October 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

Structure, internal motions and association–dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC)

Muriel Canalia and Jean Louis Leroy*

Laboratoire de RMN à Haut Champ., Institut de Chimie des Substances Naturelles Gif-sur-Yvette 91128, France

*To whom correspondence should be addressed. Tel: +33 1 69 82 36 30; Fax: +33 1 69 82 37 84; Email: Jean-Louis.Leroy{at}icsn.cnrs-gif.fr

Received July 18, 2005. Revised August 31, 2005. Accepted August 31, 2005.

At slightly acidic pH, the association of two d(5mCCTCACTCC) strands results in the formation of an i-motif dimer. Using NMR methods, we investigated the structure of [d(5mCCTCACTCC)]2, the internal motion of the base pairs stacked in the i-motif core, the dimer formation and dissociation kinetics versus pH. The excellent resolution of the 1H and 31P spectra provided the determination of dihedral angles, which together with a large set of distance restraints, improve substantially the definition of the sugar-phosphate backbone by comparison with previous NMR studies of i-motif structures. [d(5mCCTCACTCC)]2 is built by intercalation of two symmetrical hairpins held together by six symmetrical C•C+ pairs and by pair T7•T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The base pair intercalation order is C9•C9+/5mC1•5mC1+/C8•C8+/C2•C2+/T7.T7/C6•C6+/C4•C4+. The T3 bases are flipped out in the wide grooves. The core of the structure includes four long-lived pairs whose lifetimes at 15°C range from 100 s (C8•C8+) to 0.18 s (T7•T7). The formation rate and the lifetime of [d(5mCCTCACTCC)]2 were measured between pH 6.8 and 4.8. The dimer formation rate is three to four magnitude orders slower than that of a B-DNA duplex. It depends on pH, as it must occur for a bimolecular process involving non cooperative association of neutral and protonated residues. In the range of pH investigated, the dimer lifetime, 500 s at 0°C, pH 6.8, varies approximately as 10–pH.

PDB ID nos 190D and 1BNA


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