Berenil Binds Tightly to Parallel and Mixed Parallel/Antiparallel G-Quadruplex Motifs with Varied Thermodynamic...

Area of Science:

• Biochemistry
• Molecular Biology
• Medicinal Chemistry

Background:

• G-quadruplexes are nucleic acid structures often found in oncogene promoter regions.
• These structures can regulate gene expression through their folding topology and stability.
• Diminazene (DMZ), also known as berenil, is a known G-quadruplex binder.

Purpose of the Study:

• To characterize the binding specificity of Diminazene (DMZ) to various G-quadruplex topologies.
• To investigate the thermodynamic profiles of DMZ and its analogs binding to oncogene and telomere G-quadruplexes.
• To elucidate the binding modes and affinities of DMZ with different G-quadruplex structures.

Main Methods:

• Design and synthesis of mutant G-quadruplex sequences with restricted loop lengths and topologies.
• Circular dichroism spectroscopy to confirm G-quadruplex structures and DMZ complexation.
• Isothermal titration calorimetry to determine the thermodynamic parameters (ΔG, ΔH, -TΔS) of binding.

Main Results:

• DMZ binds to parallel and mixed parallel/antiparallel G-quadruplex DNA motifs with varying stoichiometries (up to 8:1) and affinities.
• Binding thermodynamics differ based on G-quadruplex topology: enthalpy-driven for parallel and mixed motifs (except long-looped c-MYC mutant), and entropy-driven for intermediate and weak binding modes.
• The long-looped c-MYC mutant showed a favorable entropy change alongside a moderate enthalpy change for high-affinity binding.

Conclusions:

• DMZ exhibits distinct binding modes and thermodynamic signatures with different G-quadruplex topologies.
• Understanding these interactions is crucial for developing G-quadruplex-targeting therapeutics.
• The study provides a detailed thermodynamic characterization of DMZ binding to biologically relevant G-quadruplex structures.