Journal Article

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

Peter Podbevšek, Nicholas V. Hud and Janez Plavec

in Nucleic Acids Research

Volume 35, issue 8, pages 2554-2563
Published in print April 2007 | ISSN: 0305-1048
Published online April 2007 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gkm138
NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution

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d[G4(T4G4)3] has been folded into a unimolecular G-quadruplex in the presence of 15[math] 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[math]-ion-binding sites (O1, I and O2). Quantitative analysis utilizing 15[math] ions as a NMR probe clearly demonstrates that there is no unidirectional 15[math] ion movement through the central cavity of the G-quadruplex. 15[math] ions move back and forth between the binding sites within the G-quadruplex and exchange with ions in bulk solution. 15[math] ion movement is controlled by the thermodynamic preferences of individual binding sites, steric restraints of the G-quartets for 15[math] ion passage and diagonal versus edge-type arrangement of the T4 loops. The movement of 15[math] 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[math] 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.

Journal Article.  7309 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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