The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: a thermodynamic analysis by 1H NMR

Biochemistry
N V HudJ Feigon

Abstract

We have studied the competition between Na+ and K+ for coordination by G quartets using the oligonucleotide d(G3T4G3) as a model system. d(G3T4G3) forms a dimeric foldback structure containing three G quartets in the presence of either NaCl or KCl. Proton chemical shifts, which are particular to the species of coordinated ion, have been used to monitor the conversion between the sodium and potassium forms under equilibrium conditions. Analysis of titration experiments indicates that at least two K+ are coordinated by the three quartets of the dimeric molecule, and perfect fits of the data are obtained for two Na+ being displaced by two K+. Our results also indicate that the conversion of [d(G3T4G3)]2 from the sodium to the potassium form is associated with a net free energy change (delta G degrees) of -1.7 +/- 0.15 kcal/mol. It has long been suggested that the greater thermal stability of DNA quadruplex structures in the presence of K+ is primarily a result of the optimal fit of this ion in the coordination sites formed by G quartets. However, a consideration of the relatively small change in free energy associated with the conversion from the sodium to the potassium form and the relatively large difference between the free ene...Continue Reading

References

Nov 1, 1992·Journal of Biomolecular NMR·M PiottoV Sklenár
Dec 1, 1990·Journal of Biomolecular Structure & Dynamics·W GuschlbauerD Thiele
Oct 15, 1995·European Journal of Biochemistry·M A KeniryR H Shafer
Aug 4, 1995·Journal of Molecular Biology·Y Wang, D J Patel
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·J R Williamson
Aug 2, 1994·Proceedings of the National Academy of Sciences of the United States of America·R GiraldoD Rhodes
Jan 26, 1996·Journal of Molecular Biology·H Deng, W H Braunlin
Mar 1, 1962·Biophysical Journal·G EISENMAN

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Citations

Nov 13, 2008·Cytotechnology·Lionel GuittatJean-Louis Mergny
Jun 19, 2007·Journal of the American Society for Mass Spectrometry·Xinhua GuoZhan Yu
Jun 11, 2002·Journal of Molecular Biology·Graeme L ConnDavid E Draper
Jun 25, 2002·Journal of Molecular Biology·Shozeb HaiderStephen Neidle
Jan 28, 2003·Journal of Molecular Biology·Shozeb M HaiderStephen Neidle
Feb 6, 2003·International Journal of Biological Macromolecules·Luigi PetracconeConcetta Giancola
Mar 31, 2000·Pharmacology & Therapeutics·L H HurleyD D Von Hoff
Dec 3, 2010·Journal of the American Chemical Society·Pere MiróCarles Bo
Jan 14, 2012·Journal of the American Chemical Society·Melissa A MullenPhilip C Bevilacqua
Sep 1, 2012·Journal of the American Chemical Society·Haiqing YuNaoki Sugimoto
Nov 2, 2012·Journal of the American Chemical Society·Amy Y Q Zhang, Shankar Balasubramanian
Nov 26, 2013·Journal of the American Chemical Society·Chuanqi ZhaoXiaogang Qu
Nov 10, 1998·Nature Structural Biology·D E Draper, V K Misra
Oct 13, 2006·Organic & Biomolecular Chemistry·Patrizia AlbertiJean-Louis Mergny
Aug 10, 2006·Chemical Communications : Chem Comm·Abd-Elgawad Radi, Ciara K O'Sullivan
May 4, 2001·Journal of Biomolecular Structure & Dynamics·S Chowdhury, M Bansal
Oct 12, 2004·Journal of Biomolecular Structure & Dynamics·J A Mondragon-SanchezE Taillandier
Jan 8, 2011·Supramolecular Chemistry·Mariana Martín-HidalgoJosé M Rivera
Apr 25, 2007·Nucleosides, Nucleotides & Nucleic Acids·Narayana NageshMedicharla V Jagannadham
Dec 11, 2007·Nucleosides, Nucleotides & Nucleic Acids·Peter PodbevsekJanez Plavec
Apr 11, 2000·Nucleic Acids Research·V M Marathias, P H Bolton
Feb 13, 2003·Nucleic Acids Research·Daisuke MiyoshiNaoki Sugimoto
Apr 12, 2003·Nucleic Acids Research·Virna DapićPaula J Bates
Jun 30, 2005·Nucleic Acids Research·Primoz SketJanez Plavec
Nov 30, 2007·Nucleic Acids Research·Caroline Bardin, Jean Louis Leroy
Aug 23, 2008·Nucleic Acids Research·Andrew N LaneJohn O Trent
Sep 24, 2010·Nucleic Acids Research·Melissa A MullenPhilip C Bevilacqua
May 19, 2011·Nucleic Acids Research·Banabihari GiriJames P Vaughn
Jul 1, 2011·Nucleic Acids Research·Irene Russo KraussFilomena Sica
Oct 25, 2011·Nucleic Acids Research·Eun-Ang RaiberShankar Balasubramanian
Jan 1, 2013·Nucleic Acids Research·Brighton SamatangaFrédéric H-T Allain
Sep 9, 2008·Biochemistry. Biokhimii︠a︡·Bo ChenXiaochuan Liu
Jun 19, 2001·Biological Chemistry·T Simonsson

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