Cation localization and movement within DNA thrombin binding aptamer in solution.

The thrombin binding aptamer, 15-mer oligonucleotide d[G(2)T(2)G(2)TGTG(2)T(2)G(2)], was folded into the well known antiparallel unimolecular G-quadruplex in the presence of (15)NH(4)(+) ions. Although the formed G-quadruplex is thermodynamically less stable than in the presence of K(+) ions, the loop conformations and folding topology are the same. On the other hand, titration of Na(+) ions into an aqueous solution of TBA resulted in the formation of one major and several minor species of G-quadruplexes. Solution-state NMR was used to localize (15)NH(4)(+) ions between the two G-quartets within the core of the structure, and to determine the equilibrium binding constant, which equals 190 M(-1). No other potential cation binding sites were resolved on the time-scale of NMR spectrometer. Exchange of (15)NH(4)(+) ions between the inner binding site and bulk solution is characterized by the exchange rate constant of 1.0 s(-1) at 15 degrees C. T4 and T13 form a noncanonical base pair, which greatly affects access of bulk ions into the cation binding site in the G-quadruplex core. G2 and G11 exhibit out of plane bending towards the two TT loops away from the bound (15)NH(4)(+) ions, which in turn exposes them to more efficient chemical exchange processes with bulk ions and water.