Internal sodium ions and water molecules in guanine quadruplexes: Magnetic relaxation dispersion studies of [d(G₃T₄G ₃)]₂ and [d(G₄T₄G₄)] ₂

The structural stability of guanine quadruplexes depends critically on an unusual configuration of dehydrated Na⁺ or K⁺ ions, closely spaced along the central axis of the quadruplex. Crystallography and NMR spectroscopy indicate that these internal ions can be located between the G-quartet planes as well as in the thymine loops, but the precise ion coordination has been firmly established in only a few cases. Here, we examine the bimolecular diagonal-looped foldback quadruplexes [d(G₃T ₄G₃)]₂ (Q3) and [d(G₄T ₄G₄)]₂ (Q4) by ²H, ¹⁷O, and ²³Na magnetic relaxation dispersion (MRD). The MRD data indicate that both quadruplexes contain Na⁺ ions between the T₄ loops and the terminal G-quartets and that these ions have one water ligand. These ions exchange with external ions on a time scale of 10-60 μs at 27 °C, while their highly ordered water ligands have residence times in the range 10^-8-10^-6 s. The MRD data indicate that Q4 contains three Na⁺ ions in the stem sites, in agreement with previous solid-state ²³Na NMR findings but contrary to the only crystal structure of this quadruplex. For Q3, the MRD data suggest a less symmetric coordination of the two stem ions. In both quadruplexes, the stem ions have residence times of 0.6-1.0 ms at 27°C. The equilibrium constant for Na ⁺ → K⁺ exchange is ∼4 for both loop and stem sites in Q3, in agreement with previous ¹H NMR findings.