DNA Interactions with Chiral Polyaza-aromatic Ruthenium(II) Complexes

Doctoral thesis, 1998

The binding to DNA of a series of chiral ruthenium complexes is studied with optical spectroscopy techniques, including isotropic absorption, linear dichroism (LD) and emission anisotropy as well as steady-state and time-resolved luminescence. The thesis focuses on the ìlight-switchî complex [Ru(phen)2dppz]2+ which binds to DNA by intercalation and luminesces when bound to DNA but not in pure buffer solution (phen=1,10-phenanthroline; dppz=dipyrido[3,2-a:2',3'-c]phenazine). A general method for the synthesis of pure .DELTA.- and .LAMBDA.-enantiomers of this complex and its analogues is described. We find both enantiomers to have similar, high binding constants, but unexpectedly that the quantum yield of luminescence for the DNA-bound .DELTA.-enantiomer of [Ru(phen)2dppz]2+ is more than five times higher than for .LAMBDA.. The isotropic absorption spectrum of the DNA-adduct of this complex is decomposed into four component spectra of different polarisation directions by use of LD and emission anisotropy, whereby the LD spectra of the enantiomers could be quantitatively analysed in terms of angular binding geometry. We conclude that both enantiomers have a very similar binding geometry, characterised by a small (5-15°) clock-wise rotation (roll) around the complex 2-fold axis from an idealised intercalated geometry with the dppz ligand coplanar with the DNA base-pairs. A very similar angular geometry is found when the dppz ligand is replaced by phen. From LD spectra of complexes with phen and/or bpy (bpy=2,2'-bipyridine), we conclude that one phen in [Ru(phen)3]2+ has a limited stacking interaction with the base-pairs. Direct linkage of two [Ru(phen)2dppz]2+ moieties at the 11-dppz position gave dimers, which were found to bind very strongly to DNA with the long-axis of the 11,11'-bidppz ligand at angles, relative to the DNA helix axis, of 49° and 64° for the .DELTA., .DELTA..- and .LAMBDA.,.LAMBDA.-enantiomer, respectively. By contrast, angles close to the latter value were found for both enantiomers when phen was replaced by bpy. Since the DNA forms a linear lattice of adjacent binding sites, direct or allosteric interactions between adjacently bound complexes may be of importance. In a system consisting of DNA and the two intercalating complexes .DELTA.-[Ru(phen)2dppz]2+ and .DELTA.-[Rh(phi)2bpy]3+ (phi=9,10-phenanthrenediimine), the luminescence of the ruthenium complex is very efficiently quenched by excited-state electron transfer to the rhodium complex. We find that a simple cooperative binding model can quantitatively explain this extraordinary quenching without invoking long-range electron-transfer. The mathematical relation between the statistical thermodynamic and probabilistic approach to the problem of cooperative, multi-component DNA-binding is studied. Two algorithms for efficient calculation of theoretical binding isotherms in such systems are derived.