NMR structral studies on ruthenium complexes binding to DNA

Abstract: The Ru-complex Λ,Λ-[bidppz(bipy)4Ru2]4+ (Λ,Λ-B) exhibits multiple modes of interactions with the palindromic DNA dodecamer [d(CGCGAATTCGCG)]2, however excluding any type of intercalation as shown by both optical spectroscopy and NMR. NMR observation of Λ,Λ-B titration into a DNA solution results in both a transient binding, with observation of fast exchange for protons located near the ends of the DNA duplex, and a more stable interaction in the DNA minor groove indicated by a slow exchange mechanism and binding sites for G2, G4 and A5 of the same DNA strand. The latter binding occurs on one half of the DNA, but prevents symmetric binding on the other half, indicating a longer range DNA distortion. Three DNA strands could be assigned: a complete, symmetric strand for which fast exchange is observed, and two separate strands forming a duplex that contains the slow-exchange binding sites; for this duplex, assignments are missing for the terminal nucleotides. Structural calculations using a (due to extensive resonance overlap) very limited number of NOEs provide a model for the modes of interaction between Λ,Λ-B and the DNA. MD simulations based on this model show that both binding modes are meta-stable and suggest that the fast-exchange interactions may be a first step towards the minor groove binding.