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 recognizes nine dA/dT base pair A/T rich dsDNA sequences at subnanomolar concentrations and complexes its targets at near diffusion controlled rates to form a fluorescent product. Spectrofluorometric titrations show the stoichiometry of the complex to be (FPH-1)(2):dsDNA. Spectrofluorometric titrations were also employed to determine the product of the equilibrium constant for complexation (K(1)K(2)) of dsDNA by two FPH-1 molecules for 35 different oligomeric duplexes. Single base pair mismatches in the FPH-1 binding site were found to cause significant decreases in K(1)K(2) of 18- to 2300-fold. Thermal denaturation experiments provided similar results. Arguments are presented which favor the structure of the (FPH-1)(2):dsDNA minor groove complex to involve the two FPH-1 molecules in a slightly staggered, side-by-side, and antiparallel arrangement such that the bis-benzimidazole moiety of one FPH-1 molecule lies adjacent to the tripyrrole moiety of the second FPH-1 molecule.
Satz
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Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA.
Bruice
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TC
D020029:Base Pairing; D006690:Bisbenzimidazole; D004247:DNA / Q000737:chemistry*; D011758:Pyrroles
D011758:Pyrroles; D004247:DNA; D006690:Bisbenzimidazole