Abstract/Summary

The following cations: rac-[Ru(phen)2phi]2+ , rac-[Ru(bpy)2phi]2+ , rac-[Ru(TMP)2dpq]2+ , rac- [Ru(DIP)2dpq]2+ , rac-[Ru(TMP)2dppz]2+ , rac-[Ru(DIP)2dppz]2+ , rac-[Ru(TMP)2qdppz]2+ , rac- [Ru(TMP)2lin-dppz]2+, and rac-[Ru(DIP)2qdppz]2+ were synthesised and characterised as PF6 - and Cl salts. All the complexes were separated as their enantiomers using a chiral column in 10 to 50 mg quantities. The carefully purified enantiomers of each cation were used in extensive crystallisation trials with ten selected DNA oligomers. From these, diffraction-quality crystals were obtained with the combination Λ-[Ru(phen)2phi]2+ + d(CCGGTACCGG). The oligonucleotides were obtained from commercial sources. This work provides the first structural evidence that a ruthenium polypyridyl complex can bind from the DNA major groove. In particular, Λ-[Ru(phen)2phi]2+ (phi= 9,10- phenanthrenediimine) has been successfully crystallised with the decamer sequence d(CCGGTACCGG). The complex binds DNA with two different orientations: symmetrical intercalation to the central TA/TA step from the DNA major groove and asymmetrical intercalation at the CC/GG step from the DNA minor groove. A particular characteristic of the latter type of bonding is the formation of a hydrogen bond between the -NH proton of the imine group of the complex with the ribose oxygen of the (C8) cytosine below. Subsequently, solution studies demonstrated the higher binding affinity of the lambda enantiomer to DNA compared to the Δ-[Ru(phen)2phi]2+, specifically for the TATA sequence. Furthermore, differential behaviour has also been seen in a topoisomerase I inhibition assay and ethidium bromide displacement assay. Moreover, the same ruthenium metal complex – rac-[Ru(phen)2phi]2+ - has been crystallised at atomic resolution 0.9 Å bound to a consecutive DNA double mismatch, which induces a bulged base formation in the DNA sequence. The overall crystal structure presents three metal complexes: two Λ-[Ru(phen)2phi]2+ binding at the consecutive DNA double mismatch TT: AA from the DNA major groove, causing the ejection of one adenine base and forming specific interactions between its phenanthroline ligands and the adenines. On the other hand, only one Δ-[Ru(phen)2phi]2+ interacts via the minor groove, which shows sandwiching of its phi ligand with the phi ligands of the other two lambda enantiomers. This crystal structure shows for the first time a metallo-insertion from the DNA major groove, different from the previous minor groove metallo-insertion, a type of binding previously demonstrated for DNA single mismatches. Lastly, four ruthenium polypyridyl complexes were characterised as PF6 - or Cl salts by small molecule X-ray crystallography methods. These structures are valuable reference points for model building and comparison with published data.