Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

Area of Science:

• Biophysics
• Chemical Biology
• Molecular Biology

Background:

• DNA intercalation is a key mechanism for DNA-binding molecules.
• Threading intercalation is predicted to offer high affinity and slow dissociation.
• These properties are desirable for developing DNA-targeted therapeutics.

Purpose of the Study:

• To quantify the binding affinity and force-dependent threading intercalation kinetics of a binuclear ruthenium complex (Δ,Δ-P).
• To evaluate the potential of Δ,Δ-P as a DNA-targeted therapeutic agent.

Main Methods:

• Single-molecule DNA stretching using optical tweezers.
• Measurement of DNA elongation at various constant stretching forces.
• Direct characterization of intercalation kinetics and equilibrium binding.

Main Results:

• Higher forces facilitate binding, reducing binding site size to nearly one ligand per base stack.
• The zero-force dissociation constant (Kd) for Δ,Δ-P is 44 nM, 25-fold stronger than the mono-nuclear analog.
• Force-dependent kinetics reveal specific DNA elongation requirements for association and dissociation.

Conclusions:

• Δ,Δ-P exhibits strong DNA binding affinity and slow dissociation via threading intercalation.
• This complex may interfere with DNA replication and transcription by remaining bound for extended periods.
• The findings support the potential of Δ,Δ-P and similar molecules as DNA-targeted therapeutics.