Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex

Abstract

Guanine quartets are readily formed by guanine nucleotides and guanine-rich oligonucleotides in the presence of certain monovalent and divalent cations. The quadruplexes composed of these quartets are of interest for their potential roles in vivo, their relatively frequent appearance in oligonucleotides derived from in vitro selection, and their inhibition of template directed RNA polymerization under proposed prebiotic conditions. The requirement of cation coordination for the stabilization of G quartets makes understanding cation-quadruplex interactions an essential step towards a complete understanding of G quadruplex formation. We have used 15NH4+ as a probe of cation coordination by the four G quartets of the DNA bimolecular quadruplex [d(G4T4G4)]2, formed from oligonucleotides with the repeat sequence found in Oxytricha nova telomeres. 1H and 15N heteronuclear NMR spectroscopy has allowed the direct localization of monovalent cation binding sites in the solution state and the analysis of cation movement between the binding sites. These experiments show that [d(G4T4G4)]2 coordinates three ammonium ions, one in each of two symmetry related sites and one on the axis of symmetry of the dimeric molecule. The NH4+ move along the central axis of the quadruplex between these sites and the solution, reminiscent of an ion channel. The residence time of the central ion is determined to be 250 ms. The 15NH4+ is shown to be a valuable probe of monovalent cation binding sites and dynamics.