Cation involvement in telomestatin binding to g-quadruplex DNA

Abstract

The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show the incorporation of one extra ammonium ion in the telomestatin complexes. Experiments on telomestatin alone also show that the telomestatin alone is able to coordinate cations in a similar way as a crown ether. Finally, density functional theory calculations suggest that in the G-quadruplex-telomestatin complex, potassium or ammonium cations are located between the telomestatin and a G-quartet. This study underlines that monovalent cation coordination capabilities should be integrated in the rational design of G-quadruplex binding ligands.

Figure 1

Chemical structure of telomestatin and folding pattern of the three G-quadruplexes studied here. [TG₄T]₄ adopts a parallel fold and can incorporate three ammonium ions between its four G-quartets [21], the 4-repeat telomeric sequence (T₂AG₃)₄ adopts an intramolecular antiparallel fold in ammonium acetate and incorporates up to two ammonium ions [22], and the Pu22myc promoter sequence GAG₃TG₄AG₃TG₄A₂G adopts a predominantly parallel fold in ammonium acetate and incorporates two ammonium ions [23].

Figure 2

Negative ion mode electrospray mass spectra of mixtures of 10 μM telomestatin and 5 μM of G-quadruplexes. Zooms on the peaks of free G-quadruplex (a) [TG₄T]₄, (b) telomeric sequence (T₂AG₃)₄, and (c) Pu22myc promoter sequence GAG₃TG₄AG₃TG₄A₂G, and on the complexes between (d) one telomestatin and [TG₄T]₄, (e) one telomestatin and (T₂AG₃)₄, and (f) one telomestatin and GAG₃TG₄AG₃TG₄A₂G. The spectra were recorded from and 80/20 aqueous ammonium acetate (150 mM)/methanol solution, using soft source conditions to preserve the specifically bound ammonium ions.

Figure 3

Positive ion mode electrospray mass spectra of 15 μM telomestatin (a) in 80/20 water/methanol, (b) in 80/20 water methanol and 5 μM ammonium acetate, and (c) in 80/20 water methanol and 5 μM potassium chloride.

Figure 4

Optimized geometries (DFT B3LYP, 6-31G(d,p)) of the telomestatin—cation complexes (side view) for (a) NH₄ ⁺, (b) K⁺, and (c) Na⁺, and optimized geometries of the telomestatin—cation—G-quartet complexes (top view and side view) for (d) NH₄ ⁺, (e) K⁺, and (f) Na⁺. Telomestatin is shown in yellow, the cation is shown in purple, and the G-quartet is colored by elements.