The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G4T4G4)

Abstract

The DNA sequence d(G4T4G4) [Oxy-1.5] consists of 1.5 units of the repeat in telomeres of Oxytricha nova and has been shown by NMR and X-ray crystallographic analysis to form a dimeric quadruplex structure with four guanine-quartets. However, the structure reported in the X-ray study has a fundamentally different conformation and folding topology compared to the solution structure. In order to elucidate the possible role of different counterions in this discrepancy and to investigate the conformational effects and dynamics of ion binding to G-quadruplex DNA, we compare results from further experiments using a variety of counterions, namely K+, Na+ and NH4+. A detailed structure determination of Oxy-1.5 in solution in the presence of K+ shows the same folding topology as previously reported with the same molecule in the presence of Na+. Both conformations are symmetric dimeric quadruplexes with T4 loops which span the diagonal of the end quartets. The stack of quartets shows only small differences in the presence of K+ versus Na+ counterions, but the T4 loops adopt notably distinguishable conformations. Dynamic NMR analysis of the spectra of Oxy-1.5 in mixed Na+/K+ solution reveals that there are at least three K+ binding sites. Additional experiments in the presence of NH4+ reveal the same topology and loop conformation as in the K+ form and allow the direct localization of three central ions in the stack of quartets and further show that there are no specific NH4+ binding sites in the T4 loop. The location of bound NH4+ with respect to the expected coordination sites for Na+ binding provides a rationale for the difference observed for the structure of the T4 loop in the Na+ form, with respect to that observed for the K+ and NH4+ forms.