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Nucleic Acids Research Advance Access originally published online on May 11, 2009
Nucleic Acids Research 2009 37(12):4127-4134; doi:10.1093/nar/gkp340
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Nucleic Acids Research, 2009, Vol. 37, No. 12 4127-4134
© 2009 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.

Chemistry and Synthetic Biology

The formation pathway of i-motif tetramers

Jean-Louis Leroy*

Laboratoire de Chimie et Biologie Structurale, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette. 91190, 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 April 2, 2009. Revised April 20, 2009. Accepted April 21, 2009.

The i-motif is a four-stranded structure formed by two intercalated parallel duplexes containing hemiprotonated C•C+ pairs. In order to describe the sequence of reactions by which four C-rich strands associate, we measured the formation and dissociation rates of three [TCn]4 tetramers (n = 3, 4 and 5), their dissociation constant and the reaction order for tetramer formation by NMR. We find that TCn association results in the formation of several tetramers differing by the number of intercalated C•C+ pairs. The formation rates of the fully and partially intercalated species are comparable but their lifetimes increase strongly with the number of intercalated C•C+ pairs, and for this reason the single tetramer detected at equilibrium is that with optimal intercalation. The tetramer half formation times vary as the power –2 of the oligonucleotide concentration indicating that the reaction order for i-motif formation is 3. This observation is inconsistent with a model supposing association of two preformed duplex and suggests that quadruplex formation proceeds via sequential strand association into duplex and triplex intermediate species and that triplex formation is rate limiting.


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