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Nucleic Acids Research Advance Access published online on April 4, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm138
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© 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.

Structural Biology

NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

Peter Podbevsek1, Nicholas V. Hud2 and Janez Plavec1,*

1Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia and 2School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA

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

Received January 25, 2007. Revised February 21, 2007. Accepted February 22, 2007.

d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15Formula ions. NMR spectroscopy confirmed that its topology is the same as the solution state structure determined earlier by Wang and Patel (J. Mol. Biol., 1995; 251: 76–94) in the presence of Na+ ions. The d[G4(T4G4)3] G-quadruplex exhibits four G-quartets with three 15Formula-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15Formula ions as a NMR probe clearly demonstrates that there is no unidirectional 15Formula ion movement through the central cavity of the G-quadruplex. 15Formula ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15Formula ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15Formula ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15Formula ions from the interior of the G-quadruplex to bulk solution is faster than exchange within the G-quadruplex. The structural details of the G-quadruplex define stiffness of individual G-quartets that intimately affects 15Formula ion movement. The stiffness of G-quartets and steric hindrance imposed by thymine residues in the loops contribute to the 5-fold difference in the exchange rate constants through the outer G-quartets.


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