Gas-Phase Stability of G-quadruplex DNA Determined by Electrospray Ionization Tandem Mass Spectrometry and Molecular Dynamics Simulations

The relative gas-phase stabilities of seven quadruplex DNA structures, [d(TG₄T)]₄, [d(T₂G₃T)]₄, [d(G₄T₄G₄)]₂, [d(T₂AG₃)₂]₂, d(T₂AG₃)₄, d(T₂G₄)₄, and d(G₂T₄)₄, were investigated using molecular dynamics simulations and electrospray ionization mass spectrometry (ESI-MS). MD simulations revealed that the G-quadruplexes maintained their structures in the gas phase although the G-quartets were distorted to some degree and ammonium ions, retained by [d(TG₄T)]₄ and [d(T₂G₃T)]₄, played a key role in stabilizing the tetrad structure. Energy-variable collisional activated dissociation was used to assess the relative stabilities of each quadruplex based on E_1/2 values, and the resulting order of relative stabilities was found to be [d(TG₄T)]₄ ≫ d(T₂AG₃)₄ ∼ d(T₂G₄)₄ > [d(T₂G₃T)]₄ > [d(T₂AG₃)₂]₂ ∼ d(G₂T₄)₄ ∼ [d(G₄T₄G₄)]_2. The stabilities from the E_1/2 values generally paralleled the RMSD and relative free energies of the quadruplexes based on the MD energy analysis. One exception to the general agreement is [d(G₄T₄G₄)]₂, which had the lowest E_1/2 value, but was determined to be the most stable quadruplex according to the free-energy analysis and ranked fourth based on the RMSD comparison. This discrepancy is attributed to differences in the fragmentation pathway of the quadruplex.