DNA binding of ruthenium tris(1,10-phenanthroline): Evidence for the dependence of binding mode on metal complex concentration

The interaction with calf thymus DNA, poly(dA-dT)₂ and poly(dG-dC)₂ of the two enantiomers (Λ and Δ) of [Ru(1,10-phenanthroline)₃]₂₊, denoted PHEN, and of [Ru(4,7-dimethyl-1,10-phenanthroline)₃]²⁺, denoted [4,7], [Ru(5,6-dimethyl-1,10-phenanthroline)₃]²⁺, denoted [5,6], and [Ru(3,4,7,8-tetramethyl-1,10-phenanthroline)₃]²⁺, denoted [3,4,7,8], has been investigated by normal absorption, linear dichroism (LD), circular dichroism (CD), and computer modeling. These studies have been performed at the saturated binding limit and the "isolated" limit where the DNA is in excess. The binding mode is dependent upon the enantiomer (Λ or Δ), the DNA base sequence, the ring substituent pattern, and, for the Δ enantiomer, the relative concentrations of DNA and metal complex. Both the Λ and Δ enantiomers of PHEN and [4,7] show at least two binding regimes. One binding regime operates below a metal complex:DNA phosphate mixing ratio, R, of 1:4-6. The average site size (number of DNA bases per bound metal complex) also decreases from 8-12 bases per metal complex at low R to 3 bases at high R. The average angle (α_eff) between the metal complex 3-fold axis and the DNA helical axis was derived from the LD. At high R (saturated metal complex binding) for both enantiomers of both compounds, this angle is 55° ± 3°. For low R (isolated metal complex binding), the average binding orientations for the enantiomers are different for PHEN (Λ, α_eff = 59°; Δ, α_eff = 38°) and for [4,7] (Λ, α_eff = 84°; Δ, α_eff = 42°). Under the low-R conditions the Δ enantiomer of both compounds binds to calf thymus DNA more strongly than the Λ enantiomer. [3,4,7,8] binds to DNA but is not oriented in the LD experiment. There is no evidence that [5,6] binds to DNA. To explain the LD results for PHEN several possible binding orientations were considered in computer modeling studies. These have the metal complex located with (i) a single phenanthroline chelate approximately parallel to the base pair planes in the major groove (referred to as partially inserted); (ii) a single chelate along the minor groove (referred to as slotted); (iii) two chelates in the minor groove (referred to as minor facial). Using orientations adopted in energy-minimized complexes it was possible to deduce the approximate relative occupancy of the different modes. For Λ-PHEN the partially inserted mode is favored at all mixing ratios. For Δ-PHEN at low-R minor groove binding is preferred for most sequences with most metal complexes adopting a minor facial orientation. However, at high R (close packed metal complexes) the slotted mode becomes more favorable and some major groove partial insertion also occurs. For both Δ- and Λ-[4,7] the minor facial mode is favored at low R. As R increases, the slotted mode becomes more favorable for both enantiomers of [4,7].