SCANNING FORCE MICROSCOPY OF SMALL LIGAND NUCLEIC-ACID COMPLEXES - TRIS(O-PHENANTHROLINE)RUTHENIUM(II) AS A TEST FOR A NEW ASSAY

An understanding of DNA-ligand, interactions at the molecular level is important for the design of new drugs and probes that can recognize s pecific DNA sequences and structural motifs. Interestingly, determinin g the mode-of-binding of a DNA ligand is not always straightforward du e to uncertainties inherent in traditional assays. We have recently re ported an exciting new assay utilizing scanning force microscopy (SFM) that can discern whether a ligand binds to DNA by intercalative or no nintercalative modes [Coury et al, Proc. Natl. Acad. Sc; U.S.A. 1996, 93, 12283-12286]. Visualization of individual DNA molecules by SFM and observation of ligand-induced lengthening provides direct evidence fo r intercalation. Metal complexes of polypyridyl ligands have been exte nsively studied as new probes of DNA structure and function because th ey exist tie chiral molecules with the potential of enantioselective r ecognition of DNA, The binding mode of even the most. widely studied o f the members of this group, tris(o-phenanthroline)ruthenium(II) (Ru(p hen)(3)(2+)), remains somewhat controversial due in large part to its low binding affinity. We report here the use of Ru(phen)(3)(2+) as a t est of our new assay toward the studies of weakly-binding ligands and to resolve the ambiguity surrounding the mode-of-binding of Delta and Lambda-Ru(phen)(3)(2+). Experiments reported here reveal that the expe rimental conditions of our assay do not preclude the binding of Ru(phe n)(3)(2+) to DNA and that NO lengthening occurs. Our findings are cons istent with the view that Ru(phen)(3)(2+) binds to duplex nucleic acid s through nonintercalative modes.