Bimolecular Quadruplexes and Their Transitions to Higher-Order Molecular Structures Detected by ESI-FTICR-MS

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands—d(G4T4G4), d(G3T4G4), d(G3T4G3), and d(G4T4G3)—have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH4+ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d(G3T4G3) and d(G4T4G3) are unstable, being converted into trimolecular and tetramolecular structures with increasing concentrations of NH4+ in the solution. Circular dichroism (CD) spectra reveal structural changes during the process of strand stoichiometric transitions, in which the relative orientation of strands in the quadruplexes changes from an antiparallel to a parallel arrangement. Such changes were observed for the strand d(G4T4G3), but not for the strand d(G3T4G3). The present work provides a significant insight into the formation of various DNA quadruplexes, especially the higher-order species.