The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G(4)T(4)G(4))

The DNA sequence d(G(4)T(4)G(4)) [Oxy-1.5] consists of 1.5 units of the rep eat in telomeres of Oxytricha nova and has been shown by NMR and X-ray crys tallographic analysis to form a dimeric quadruplex structure with four guan ine-quartets, However, the structure reported in the X-ray study has a fund amentally different conformation and folding topology compared to the solut ion structure. In order to elucidate the possible role of different counter ions in this discrepancy and to investigate the conformational effects and dynamics of ion binding to G-quadruplex DNA, we compare results from furthe r experiments using a variety of counterions, namely K+, Na+ and NH4+. A de tailed structure determination of Oxy-1.5 in solution in the presence of K shows the same folding topology as previously reported with the same molec ule in the presence of Na+. Both conformations are symmetric dimeric quadru plexes with T-4 loops which span the diagonal of the end quartets, The stac k of quartets shows only small differences in the presence of K+ versus Na counterions, but the T-4 loops adopt notably distinguishable conformations . Dynamic NMR analysis of the spectra of Oxy-1.5 in mixed Na+/K+ solution r eveals that there are at least three KC binding sites. Additional experimen ts in the presence of NH4+ reveal the same topology and loop conformation a s 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+ bin ding sites in the T-4 loop, The location of bound NH4+ with respect to the expected coordination sites for Na+ binding provides a rationale for the di fference observed for the structure of the T-4 loop in the Nat form, with r espect to that observed for the K+ and NH4+ forms.