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Nucleic Acids Research 2006 34(8):2386-2397; doi:10.1093/nar/gkl098
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Published online 8 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes

Jean-Louis Mergny*, Anne De Cian, Samir Amrane and Mateus Webba da Silva1,2,*

Laboratoire de Biophysique, Muséum National d'Histoire Naturelle USM503, INSERM U565, CNRS UMR 5153 43 rue Cuvier, 75231 Paris cedex 05, France 1 School of Biomedical Sciences, University of Ulster Coleraine BT52 1SA, Northern Ireland, UK 2 Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, New York, NY 10021, USA

*To whom correspondence should be addressed. Jean-Louis Mergny: Tel: +33 1 40 79 36 89; Fax: +33 1 40 79 37 05; Email: faucon{at}mnhn.fr

*Correspondance may also be addressed to M. Webba da Silva. Tel: +44 28 7032 4009; Fax: +44 28 7032 4375; Email: mm.webba-da-silva{at}ulster.ac.uk

Received January 23, 2006. Revised February 22, 2006. Accepted March 7, 2006.

Repetitive 5'GGXGG DNA segments abound in, or near, regulatory regions of the genome and may form unusual structures called G-quadruplexes. Using NMR spectroscopy, we demonstrate that a family of 5'GCGGXGGY sequences adopts a folding topology containing double-chain reversals. The topology is composed of two bistranded quadruplex monomeric units linked by formation of G:C:G:C tetrads. We provide a complete thermodynamic and kinetic analysis of 13 different sequences using absorbance spectroscopy and DSC, and compare their kinetics with a canonical tetrameric parallel-stranded quadruplex formed by TG4T. We demonstrate large differences (up to 105-fold) in the association constants of these quadruplexes depending on primary sequence; the fastest samples exhibiting association rate equal or higher than the canonical TG4T quadruplex. In contrast, all sequences studied here unfold at a lower temperature than this quadruplex. Some sequences have thermodynamic stability comparable to the canonical TG4T tetramolecular quadruplex, but with faster association and dissociation. Sequence effects on the dissociation processes are discussed in light of structural data.


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