Conformational Change in a Four-Tetrad DNA G-Quadruplex upon Intercalation of a Small-Molecule Ligand PyDH2

Area of Science:

• Biochemistry
• Structural Biology
• Medicinal Chemistry

Background:

• G-quadruplexes (G4s) are non-canonical DNA structures involved in various biological processes.
• Small-molecule ligands can modulate G4 stability and folding, presenting therapeutic opportunities.

Purpose of the Study:

• To investigate the interaction between the telomeric DNA fragment TET25 and the G4 ligand PyDH2.
• To elucidate the structural and functional consequences of this interaction.

Main Methods:

• X-ray crystallography to determine the complex structure.
• Solution studies to analyze G4 topology, stability, and ligand binding stoichiometry.
• Differential scanning fluorimetry (DSF) to measure G4 stabilization (Tm).

Main Results:

• TET25 alone forms a hybrid G4, but in the presence of PyDH2, it adopts an antiparallel chair G4 conformation.
• PyDH2 was observed intercalated between G-tetrads, providing crystallographic evidence for ligand intercalation into G4s.
• PyDH2 significantly stabilizes TET25 G4 (ΔTm = 12.4 °C) and induces hysteresis, indicating complex binding and folding dynamics.

Conclusions:

• Ligand intercalation into G4 structures is structurally feasible and can dictate G4 topology.
• PyDH2 binding to TET25 G4 leads to significant stabilization and complex solution behavior.
• This interaction highlights the potential of small molecules for G4-based therapeutic strategies.