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Nucleic Acids Research Advance Access originally published online on November 27, 2007
Nucleic Acids Research 2008 36(2):477-488; doi:10.1093/nar/gkm1050
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Nucleic Acids Research, 2008, Vol. 36, No. 2 477-488
© 2007 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

The formation pathway of tetramolecular G-quadruplexes

Caroline Bardin and 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 3784; Email: Jean-Louis.Leroy{at}icsn.cnrs-gif.fr

Received July 24, 2007. Revised October 31, 2007. Accepted November 6, 2007.

Oligonucleotides containing guanosine stretches associate into tetrameric structures stabilized by monovalent ions. In order to describe the sequence of reactions leading to association of four identical strands, we measured by NMR the formation and dissociation rates of (TGnT)4 quadruplexes (n = 3–6), their dissociation constants and the reaction orders for quadruplex formation. The quadruplex formation rates increase with the salt concentration but weakly depend on the nature (K+, Na+ or Li+) of the counter ions. The activation energies for quadruplex formation are negative. The quadruplex lifetimes strongly increase with the G-tract length and are much more longer in K+ solution than in Na+ or Li+ solutions. The reaction order for quadruplex formation is 3 in 0.125 M KCl and 4 in LiCl solutions. The kinetics measurements suggest that quadruplex formation proceeds step by step via sequential strand association into duplex and triplex intermediate species. Triplex formation is rate limiting in 0.125 M KCl solution. In LiCl, each step of the association process depends on the strand concentration. Parallel reactions to formation of the fully matched canonical quadruplex may result in kinetically trapped mismatched quadruplexes making the canonical quadruplex practically inaccessible in particular at low temperature in KCl solution.


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