Aromatic ring transforms DNA binding modes of an octahedral rhodium complex

Octahedral rhodium complexes serve as a three-dimensional scaffold for small DNA binding moieties. We compare the DNA binding characteristics of two ligands complexed to rhodium, phenanthrene diimine quinone (phi) and 5,6-chrysene quinone diimine (chrysi). These flat aromatic ligands differ only by an additional ring on chrysi absent in the phi complex. Previous work showed that although chrysi is principally bound to mismatched DNA via metalloinsertion, phi acted as a classical intercalator, binding strongly between basepairs of matched DNA. In dual-beam optical tweezers, we force-unfold DNA hairpins containing key mismatches. We confirm that chrysi stabilizes basepair mismatches, even at zero force, supporting the preferential binding to mismatches through minor groove binding observed in previous studies. However, in contrast to prior work, force extension and constant force data on long, fully paired DNA reveal that both compounds intercalate into double-stranded DNA. Interestingly, chrysi exhibits a higher binding affinity, though the binding kinetics for phi are faster, suggesting tighter binding into the major groove.