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| - Stacking and Not Solely Topology of T3 Loops Controls Rigidity and Ammonium Ion Movement within d(G4T3G4)2 G-Quadruplex
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| - A solution state NMR study has shown that d(G4T3G4) in the presence of 15NH4+ ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K+ ions [Neidle et al. J. Am. Chem. Soc.2006, 128, 5480]. In contrast, the presence of K+ ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base−base stack on the outer G-quartets and in this way stabilize a single structure in the presence of 15NH4+ ions. The use of heteronuclear NMR enabled us to localize three 15NH4+ ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no 15NH4+ ion movement within the G-quadruplex was detected at 25 °C. At 35 °C we were able to observe slow movement of 15NH4+ ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of 15NH4+ ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.
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| - Role of Loop Structure on Cation Mobility
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