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

• Published in: Biophysical chemistry 2017-12, Vol.231, p.55-63
• Main Authors: Li, Yang Yun, Dubins, David N., Le, Dianna My Nhi Thi, Leung, Karen, Macgregor, Robert B.
• Format: Article
• Language: English
• Subjects: Cations - chemistry; Dynamic Light Scattering; G-Quadruplexes; Humans; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleic Acid Denaturation - radiation effects; Oligonucleotides - chemistry; Potassium - chemistry; Pressure; Sodium - chemistry; Telomere - chemistry; Temperature; Ultraviolet Rays
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2016.12.003

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 (ΔVtot) of the unfolding transition for all of the G4s are large and negative. A large fraction of the measured ΔVtot value arises from the re-hydration of the cations released from the interior of the folded structure. However, the differences in the measured ΔVtot 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 ΔVtot and presumably the hydration of the folded structures. Depending on the sequence of the loops, the magnitude of the measured ΔVtot can be larger or smaller than that of HTel in solutions containing sodium. However, the magnitude of ΔVtot is smaller than HTel for the unfolding of all G4s that are stabilized by potassium ions. [Display omitted] •The molar volume change of 10 G4-forming ODNs related to HTel (d[A(GGGTTA)3GGG])•G4 structures stabilized by Na+ and K+ and studied as a function of hydrostatic pressure.•The overall molar volume change of unfolding for all G4s is large and negative.•A large fraction of the volume change arises from the hydration of the coordinated cations.•The loops contribute significantly to ΔVtot and the hydration of the folded structures.