Aromatic ring transforms DNA binding modes of an octahedral rhodium complex.

Area of Science:

• Coordination chemistry
• Biophysical chemistry
• Molecular biology

Background:

• Octahedral rhodium complexes can scaffold DNA binding ligands.
• Phenanthrene diimine quinone (phi) and 5,6-chrysene quinone diimine (chrysi) are two such ligands with differing structures.
• Previous studies suggested different DNA binding modes for phi and chrysi.

Purpose of the Study:

• To compare the DNA binding characteristics of rhodium complexes with phi and chrysi ligands.
• To investigate the binding mechanisms of these complexes to both matched and mismatched DNA.
• To elucidate the role of ligand structure in DNA interaction.

Main Methods:

• Dual beam optical tweezers to force-unfold DNA hairpins with mismatches.
• Force-extension and constant force measurements on long, fully paired DNA.
• Comparison of binding affinity and kinetics between phi and chrysi complexes.

Main Results:

• chrysi stabilizes base pair mismatches, supporting preferential minor groove binding.
• Both phi and chrysi complexes intercalate into double-stranded DNA.
• chrysi shows higher binding affinity, while phi has faster binding kinetics, suggesting major groove interaction.

Conclusions:

• Rhodium complexes with phi and chrysi ligands exhibit complex DNA binding behaviors.
• chrysi demonstrates a dual binding mode, interacting with mismatches and intercalating into DNA.
• Ligand structure significantly influences DNA binding affinity and kinetics, with implications for drug design.