Recognition of a 5‘-(A,T)GGG(A,T)2-3‘ Sequence in the Minor Groove of DNA by an Eight-Ring Hairpin Polyamide

Abstract

The use of pyrrole−imidazole polyamides for the recognition of core 5‘-GGG-3‘ sequences in the minor groove of double stranded DNA is described. Two hairpin pyrrole−imidazole polyamides, ImImIm-γ-PyPyPy-β-Dp and ImImImPy-γ-PyPyPyPy-β-Dp (Im = N-methylimidazole-2-carboxamide, Py = N-methylpyrrole-2-carboxamide, β = β-alanine, γ = γ-aminobutyric acid, and Dp = ((dimethylamino)propyl)amide), as well as the corresponding EDTA affinity cleaving derivatives, were synthesized and their DNA binding properties analyzed. Quantitative DNase I footprint titrations demonstrate that ImImIm-γ-PyPyPy-β-Dp binds the formal match sequence 5‘-AGGGA-3‘ with an equilibrium association constant of K_a = 5 × 10^6 M^(-1) (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl_2, and 5 mM CaCl_2, pH 7.0 and 22 °C). ImImImPy-γ-PyPyPyPy-β-Dp binds the same site, 5‘-AGGGAA-3‘, approximately two orders of magnitude more tightly than the six ring polyamide, with an equilibrium association constant of K_a = 4 × 10^8 M^(-1). The eight-ring hairpin polyamide demonstrates greater specifity for single base pair mismatches than does the six ring hairpin. Polyamides with an EDTA·Fe(II) moiety at the carboxy terminus confirm that each hairpin binds in a single orientation. The high affinity recognition of a 5‘-GGG-3‘ core sequence by an eight ring polyamide containing three contiguous imidazole amino acids demonstrates the versatility of pyrrole−imidazole polyamides and broadens the sequence repertoire for DNA recognition.