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 (ΔVtot) of the unfolding transition for all of the G4s are large and negative. A large fraction of the measured ΔVtotvalue arises from the re-hydration of the cations released from the interior of the folded structure. However, the differences in the measured ΔVtotvalues demonstrate that variations in the structure of G4s formed by each ODN, arising from differences in the sequence of the loops, contribute significantly to ΔVtotand presumably the hydration of the folded structures. Depending on the sequence of the loops, the magnitude of the measured ΔVtotcan be larger or smaller than that of HTel in solutions containing sodium. However, the magnitude of ΔVtotis smaller than HTel for the unfolding of all G4s that are stabilized by potassium ions.
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
Yang Yun
YY
Li
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
David N
DN
Dubins
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
Dianna My Nhi Thi
DMNT
Le
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
Karen
K
Leung
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada. Electronic address: rob.macgregor@utoronto.ca.
Robert B
RB
Macgregor
D002412:Cations / Q000737:chemistry; D000067493:Dynamic Light Scattering; D054856:G-Quadruplexes; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation / Q000528:radiation effects; D009841:Oligonucleotides / Q000737:chemistry; D011188:Potassium / Q000737:chemistry; D011312:Pressure; D012964:Sodium / Q000737:chemistry; D016615:Telomere / Q000737:chemistry; D013696:Temperature; D014466:Ultraviolet Rays
D002412:Cations; D009841:Oligonucleotides; D012964:Sodium; D011188:Potassium