Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection

Abstract

Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation.

Increased Ribozyme Activity in Crowded Solutions

“…Tellingly, hammerhead self-cleavage was not accelerated when using Ficoll as a crowder, and from this, the authors inferred that the excluded volume effects were minimal. PEG was also reported to directly alter DNA quadruplex conformation (22). By contrast, compartmentalization increased selfcleavage of a two-part hammerhead ribozyme, showing that co-localization can increase RNA interactions (23).…”

The Human Telomere Sequence, (TTAGGG)4, in the Absence and Presence of Cosolutes: A Spectroscopic Investigation

“…Thus PEG is driving the equilibrium to the side of Conformer II with increasing concentrations as observed before with different G-rich sequences [22][23][24][25][26][27][28][29]31]. According to Chaires et al, this shift in equilibrium is due to conformational selection rather than excluded volume or crowding effects [31]. None the less, the high concentrations of PEG will slightly influence the activity of water which will contribute to overall conformational stability.…”

“…Thus, PEG 200 falls under the regime of preferential interaction rather than excluded volume. Further, a recent report suggests that PEG preferentially interacts with a particular quadruplex conformation and that excluded volume effects are negligible [31]. Although the presence of PEG in solution clearly influences the conformation and stability of a DNA quadruplex, referring to it as a crowding agent is not recommended [31][32][33][34][35].…”

Pressure Effect on the Folding of G-Quadruplex DNA Modified with Hexaethylene Glycol

“…Recently, it has been shown that the surface of a protein near the site of PEGylation is locally dehydrated [12]. Furthermore, PEG has been shown to interact specifically with the surface of a G-quartet by molecular modeling analysis [13]. Thus, it is possible that PEGylation of that DNA forms a G-quadruplex will cause dehydration during formation of G-quadruplex structure through specific interactions with a G-quartet surface.…”