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

Guanine quarters are readily formed by guanine nucleotides and guanine-rich oligonucleotides in the presence of certain monovalent and divalent cation s. The quadruplexes composed of these quartets are of interest for their po tential roles in vivo, their relatively frequent appearance in oligonucleot ides derived from in vitro selection, and their inhibition of template dire cted RNA polymerization under proposed prebiotic conditions. The requiremen t of cation coordination for the stabilization of G quartets makes understa nding cation-quadruplex interactions an essential step towards a complete u nderstanding of G quadruplex formation. We have used (NH4+)-N-15 as a probe of cation coordination by the four G quarters of the DNA bimolecular quadr uplex [d(G(4)T(4)G(4))](2), formed from oligonucleotides with the repeat se quence found in Oxytricha nova telomeres. H-1 and N-15 heteronuclear NMR sp ectroscopy has allowed the direct localization of monovalent cation binding sites in the solution state and the analysis of cation movement between th e binding sites. These experiments show that [d(G(4)T(4)G(4))](2) coordinat es three ammonium ions, one in each of two symmetry related sites and one o n the axis of symmetry of the dimeric molecule. The NH4+ move along the cen tral axis of the quadruplex between these sites and the solution, reminisce nt of an ion channel. The residence time of the central ion is determined t o be 250 ms. The (NH4+)-N-15 is shown to be a valuable probe of monovalent cation binding sites and dynamics. (C) 1999 Academic Press.