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Nucleic Acids Research 2005 33(11):3691-3697; doi:10.1093/nar/gki690
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Published online 28 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Identification of mixed di-cation forms of G-quadruplex in solution

Primoz Sket, Martin Crnugelj and Janez Plavec*

Slovenian NMR Center, National Institute of Chemistry Hajdrihova 19, PO Box 660, SI-1001 Ljubljana, Slovenia

*To whom correspondence should be addressed. Tel: +386 1 47 60 353; Fax: +386 1 47 60 300; Email: janez.plavec{at}ki.si

Received May 17, 2005. Revised June 15, 2005. Accepted June 15, 2005.

Multinuclear NMR study has demonstrated that G-quadruplex adopted by d(G3T4G4) exhibits two cation binding sites between three of its G-quartets. Titration of tighter binding K+ ions into the solution of d(G3T4G4)2 folded in the presence of ions uncovered a mixed mono-K+-mono- form that represents intermediate in the conversion of into di-K+ form. Analogously, ions were found to replace Na+ ions inside d(G3T4G4)2 quadruplex. The preference of over Na+ ions for the two binding sites is considerably smaller than the preference of K+ over ions. The two cation binding sites within the G-quadruplex core differ to such a degree that ions bound to the site, which is closer to the edge-type loop, are always replaced first during titration by K+ ions. The second binding site is not taken up by K+ ion until K+ ion already resides at the first binding site. Quantitative analysis of concentrations of the three di-cation forms, which are in slow exchange on the NMR time scale, at 12 K+ ion concentrations afforded equilibrium binding constants. K+ ion binding to sites U and L within d(G3T4G4)2 is more favorable with respect to ions by Gibbs free energies of approximately –24 and –18 kJ mol–1 which includes differences in cation dehydration energies, respectively.


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