Extension of Sequence-Specific Recognition in the Minor Groove of DNA by Pyrrole-Imidazole Polyamides to 9-13 Base Pairs

The sequence-specific recognition of the minor groove of DNA by pyrrole-imidazole polyamides has been extended to 9-13 base pairs (bp). Four polyamides, ImPyPy-Py-PyPyPy-Dp, ImPyPy-G-PyPyPy-Dp, ImPyPyâ-PyPyPy-Dp, and ImPyPy-γ-PyPyPy-Dp (Im ) N-methylimidazole, Py ) N-methylpyrrole, Dp ) N,Ndimethylaminopropylamide, G ) glycine, â ) â-alanine, and γ ) γ-aminobutyric acid), were synthesized and characterized with respect to their DNA-binding affinities and specificities at sequences of composition 5′-(A,T)G(A,T)5C(A,T)-3′ (9 bp) and 5′-(A,T)5G(A,T)C(A,T)5-3′ (13 bp). In both sequence contexts, the â-alanine-linked compound ImPyPy-â-PyPyPy-Dp has the highest binding affinity of the four polyamides, binding the 9 bp site 5′-TGTTAAACA-3′ (Ka ) 8 × 108 M-1) and the 13 bp site 5′-AAAAAGACAAAAA-3′ (Ka ) 5 × 109 M-1) with affinities higher than the formally N-methylpyrrole-linked polyamide ImPyPy-Py-PyPyPy-Dp by factors of ∼8 and ∼85, respectively (10 mM Tris‚HCl, 10 mM KCl, 10 mM MgCl2, and 5 mM CaCl2, pH 7.0). The binding data for ImPyPy-γ-PyPyPy-Dp, which has been shown previously to bind DNA in a “hairpin” conformation, indicates that γ-aminobutyric acid does not effectively link polyamide subunits in an extended conformation. These results expand the binding site size targetable with pyrrole-imidazole polyamides and provide structural elements that will facilitate the design of new polyamides targeted to other DNA sequences.