Investigating a quadruplex-ligand interaction by unfolding kinetics.

Area of Science:

• Biochemistry
• Molecular Biology
• Chemical Biology

Background:

• Intramolecular human telomeric DNA G-quadruplexes are crucial structures in telomere maintenance.
• Understanding ligand interactions with G-quadruplexes is vital for developing novel therapeutics.

Purpose of the Study:

• To investigate the kinetic interaction between a hemicyanine-peptide ligand and human telomeric DNA G-quadruplex.
• To determine the thermodynamic and kinetic parameters of this interaction.

Main Methods:

• Studied G-quadruplex opening rates using a complementary DNA oligonucleotide.
• Employed a minimal kinetic model to analyze ligand concentration effects.
• Utilized van't Hoff and Arrhenius analyses for thermodynamic and activation energy determination.

Main Results:

• Estimated the dissociation constant for the ligand-G-quadruplex complex.
• Determined binding enthalpy (-77 ± 22 kJ mol⁻¹) and entropy (-163 ± 75 J mol⁻¹ K⁻¹).
• Observed a small change in activation energy upon ligand binding (118 ± 2 vs. 98 ± 10 kJ mol⁻¹).

Conclusions:

• The hemicyanine-peptide ligand binds to the human telomeric G-quadruplex.
• Ligand unbinding likely occurs after the transition state of G-quadruplex unfolding.
• These findings contribute to understanding G-quadruplex ligand dynamics for potential therapeutic applications.