Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs

Abstract

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, ImPyPy-β-PyPyPy-Dp, and ImPyPy-γ-PyPyPy-Dp (Im = N-methylimidazole, Py = N-methylpyrrole, Dp = N,N-dimethylaminopropylamide, G = glycine, β = β-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 β-alanine-linked compound ImPyPy-β-PyPyPy-Dp has the highest binding affinity of the four polyamides, binding the 9 bp site 5‘-TGTTAAACA-3‘ (K_a = 8 × 10^8 M^(-1)) and the 13 bp site 5‘-AAAAAGACAAAAA-3‘ (K_a = 5 × 10^9 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 MgCl_2, and 5 mM CaCl_2, 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.