Complex DNA binding kinetics resolved by combined circular dichroism and luminescence analysis.

We recently reported that ruthenium complexes, with general structure [mu-bidppz(bipy)4Ru2](4+) (B) or [mu-bidppz(phen)4Ru2](4+) (P) (bidppz=11,11'-bi(dipyrido[3,2- a:2',3'-c]phenazinyl)), show extreme kinetic selectivity for long AT tracts over mixed-sequence calf thymus DNA (ct-DNA), a selectivity that also varies markedly with the size (between B and P) and sense of chirality of the complex. Earlier studies, exploiting the great increase in luminescence intensity when the compound intercalates, have yielded complex kinetics indicating the presence of both first- and second-order processes. Even with a homogeneous DNA sequence, such as poly(dAdT)2, the luminescence kinetics generally requires more than a single exponential for a satisfactory fit. We here reveal that at least part of the complexity is a result of the extreme sensitivity of the effective quantum yield of the complexes, so that the luminescence trajectories also reflect subtle variations in the environment and binding geometry that the complex is sampling on its path to its final binding site. By monitoring the rearrangement process using circular dichroism (CD), we show that threading of both enantiomers of B and P into poly(dAdT)2 is effectively a monoexponential process, as expected if the compounds are not affecting each other during the intercalation process. Thus, the complex luminescence trajectories may be explained by slow relaxations in the binding geometry (DNA conformation) and associated changes in the environment of the entering complexes. To further disentangle the intriguing features of the threading intercalation kinetics, and how they may depend on the flexibility and size of the ruthenium complexes, we have also designed and studied two new ruthenium complexes, [mu-dtpf(phen)4Ru2](4+) (F) (dtpf=4,5,9,12,16,17,21,25-octaaza-23 H-ditriphenyleno[2,3-b:2,3-h]fluorene), in which the bridging ligand is made totally rigid, and [mu-bidppz([12]aneS4) 2Ru2](4+) (S), which has less bulky, nonaromatic ancillary ligands. The threading of F into poly(dAdT)2, also found to be a monoexponential process, is about 3 times slower than for P, indicating that the flexibility of the bridging ligand is an important factor for the intercalation rate. Surprisingly, in contrast to all other compounds, S requires two exponentials to fit its binding kinetics as monitored by CD. Also surprisingly, in view of the smaller steric bulk, even the fastest phase is roughly 2 times slower for S than for B and P. Thus, not only the size of the ancillary ligand but also other properties that can influence the energy landscape of the threading path are rate-determining factors. With mixed-sequence ct-DNA, threading of B and that of P are both multiphasic processes when monitored with CD as well as with luminescence. The rate constants for threading into ct-DNA show much larger variations between complexes than for poly(dAdT)2, confirming earlier results based on luminescence data.