Recognition of nine base pairs in the minor groove of DNA by a tripyrrole peptide-Hoechst conjugate

A tripyrrole peptide-Hoechst conjugate (FPH-1) has been designed which reco gnizes nine dA/dT base pair A/T rich dsDNA sequences at subnanomolar concen trations and complexes its targets at near diffusion controlled rates to fo rm a fluorescent product. Spectrofluorometric titrations show the stoichiom etry of the complex to be (FPH-1)(2):dsDNA. Spectrofluorometric titrations were also employed to determine the product of the equilibrium constant for complexation (K1K2) of dsDNA by two FPH-1 molecules for 35 different oligo meric duplexes. Single base pair mismatches in the FPH-1 binding site were found to cause significant decreases in K1K2 of 18- to 2300-fold. Thermal d enaturation experiments provided similar results. Arguments are presented w hich favor the structure of the (FPH-1)(2):dsDNA minor groove complex to in volve the two FPH-1 molecules in a slightly staggered, side-by-side, and an tiparallel arrangement such that the bis-benzimidazole moiety of one FPH-1 molecule lies adjacent to the tripyrrole moiety of the second FPH-1 molecul e.