Binding of Tetrapentylammonium to a c-MYC G-quadruplex Depicted through NMR and Volumetric Assessment

We recently have demonstrated that, their structural simplicity notwithstanding, tetraalkylammonium (TAA⁺) ions, i.e., [H(CH₂)_n]₄N⁺, strongly stabilize the parallel c-MYC G-quadruplex while not affecting the thermal stabilities of the antiparallel human telomeric G-quadruplex or duplex DNA. In the present work, we expand on our discovered paradigm of topology-selective G-quadruplex recognition by performing NMR spectroscopic and volumetric characterization of the complex between tetrapentylammonium (TPeA⁺) and the c-MYC G-quadruplex. The binding of TAA⁺ to the c-MYC G-quadruplex is optically silent, which necessitates the use of nonoptical observables, such as density and sound velocity. Our NMR results revealed that TPeA⁺ forms a stable complex with the c-MYC G-quadruplex in which the ligand is positioned above the G9-G13-G18-G22 quartet and is surrounded by the 3'-(T23-A24-A25) flanking region. We used our densimetric and ultrasonic velocimetric results to calculate changes in volume, ΔV, and adiabatic compressibility, ΔK_S, accompanying the binding of TPeA⁺ to the c-MYC G-quadruplex. We rationalized these volumetric properties to determine binding-induced changes in hydration of the associating molecules and the internal dynamics of the host G-quadruplex. In general, the structural and physico-chemical insights emerging from this work lay the foundation for further studies of TAA⁺-based compounds as a possible starting point for designing topology-sensitive G-quadruplex-binding agents.