The role of loops and cation on the volume of unfolding of G-quadruplexes related to HTel

In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)₃GGG]), which contains four repeats of the human telomeric sequence. The experiments are conducted in aqueous buffers containing either 100mM NaCl or KCl at pH7.4. The G4s stabilized by Na⁺ are less sensitive to pressure perturbation than those stabilized by K⁺. The overall molar volume changes (ΔV_tot) of the unfolding transition for all of the G4s are large and negative. A large fraction of the measured ΔV_tot value arises from the re-hydration of the cations released from the interior of the folded structure. However, the differences in the measured ΔV_tot values demonstrate that variations in the structure of G4s formed by each ODN, arising from differences in the sequence of the loops, contribute significantly to ΔV_tot and presumably the hydration of the folded structures. Depending on the sequence of the loops, the magnitude of the measured ΔV_tot can be larger or smaller than that of HTel in solutions containing sodium. However, the magnitude of ΔV_tot is smaller than HTel for the unfolding of all G4s that are stabilized by potassium ions.