Nucleic Acids Research Advance Access originally published online on April 4, 2007
Nucleic Acids Research 2007 35(8):2554-2563; doi:10.1093/nar/gkm138
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Nucleic Acids Research, 2007, Vol. 35, No. 8 2554-2563
© 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
ek11Slovenian 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 15
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 15-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15 ions as a NMR probe clearly demonstrates that there is no unidirectional 15 ion movement through the central cavity of the G-quadruplex. 15 ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15 ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15 ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15 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 15 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.