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Paper
Org. Biomol. Chem., 2009, 7, 4677 - 4684, DOI: 10.1039/b914783g
Cation localization and movement within DNA thrombin binding aptamer in solution
Marko Trajkovski, Primo
ket and Janez Plavec
The thrombin binding aptamer, 15-mer oligonucleotide d[G2T2G2TGTG2T2G2], was folded into the well known antiparallel unimolecular G-quadruplex in the presence of 15NH4+ 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 15NH4+ 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 15NH4+ ions between the inner binding site and bulk solution is characterized by the exchange rate constant of 1.0 s-1 at 15 °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 15NH4+ ions, which in turn exposes them to more efficient chemical exchange processes with bulk ions and water.
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