Sequence selective binding to the dna major groove

Abstract

Molecular modelling and energy minimisation calculations that incorporate solvent effects have been used to investigate the complexation of Δ and Λ-[Ru(1, 10-phenanthroline]2+to DNA. The most stable binding geometry for both enantiomers is one in which a phenanthroline chelate is positioned in the major groove. The chelate is partially inserted between neighbouring base pairs, but is not intercalated. For Δ, though not for Λ, a geometry with two chelates in the major groove is only slightly less favourable. Minor groove binding is shown to be no more favourable than external electrostatic binding. The optimised geometries of the DNA/[Ru(1, 10-phenanthroline]2+complexes enable published linear dichroism spectra to be used to determine the percentage of each enantiomer in the two most favourable major groove sites. For Δ 57±15% and for Λ 82±7% of bound molecules are in the partially inserted site. Show more