A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps

Area of Science:

• Biophysical Chemistry
• Molecular Biology
• Materials Science

Background:

• Ruthenium-based intercalators are explored for therapeutic applications.
• Optimizing DNA binding properties is crucial for drug development.

Purpose of the Study:

• To investigate the DNA binding mechanism of the bis-intercalator [μ-C4(cpdppz)2(phen)4Ru2](4+).
• To quantify ligand binding kinetics and thermodynamics under force.

Main Methods:

• Utilizing optical tweezers to stretch double-stranded DNA.
• Exposing stretched DNA to the ligand under constant applied force.
• Measuring force-dependent binding rates and DNA elongation.

Main Results:

• Ligand association follows a two-step process: fast initial intercalation, followed by a slower second intercalation.
• The second step is rate-limited by DNA-ligand conformational changes.
• Binding involves fast association, slow dissociation, and high affinity (Kd ~10 nM) at zero force.

Conclusions:

• The study elucidates the energy landscape and structural dynamics of multi-step DNA intercalation.
• The developed methodology can be applied to other DNA-binding ligands and proteins.
• Understanding these mechanisms is vital for designing novel DNA-targeting therapeutics.