Cytotoxic binuclear η6-arene-Ru(II) complexes: DNA sequence specific helix unwinding and binding properties

Cytotoxic bifunctional DNA binders of the general formula {[(η⁶-cym)Ru(phe)]₂(μ-BL)}Cl₄, where cym = p-cymene, phe = 1,10-phenanthroline, BL = 4,4′-bipyridine (BL-1), (1), 1,2-bis(4-pyridyl)ethane (BL-2), (2) and 1,3-bis(4-pyridyl)propane (BL-3), (3), were investigated for their binding properties with B-type DNA sequences d(5′-CGCGCG-3′), d(5′-CTTTTGCAAAAG-3′) and CT-DNA using NMR spectroscopy and fluorescence titrations. The results revealed distinct binding modes and affinities, significantly influenced by both the DNA sequence and the length of the BL. The interactions were non-selective and occurred through multiple binding modes. Complex (1) was found to disrupt the W.-C. imino hydrogen bonds at both C·G and A·T base pairs, effectively mimicking the DNA strand separation mechanism by helicase enzymes. In contrast, the binding of (2) does not disrupt the C.-W. GN1-H imino hydrogen bonds in the G·C-only sequence d(5′-CGCGCG-3′)₂ but it selectively disrupts the T2N3H imino hydrogen bond of the T2·A11 base pair in the AT-rich sequence d(5′-CTTTTGCAAAAG-3′). Complex (3) induced localized unwinding of the helix near the center of the d(5′-CGCGCG-3′)₂. The DNA binding affinities of complexes (1)–(3) exhibit strong sequence dependence, with binding constants (K_b) ranging from 1.23 × 10³ M⁻¹ to 6.34 × 10⁵ M⁻¹.