DISCRIMINATION OF 5'-GGGG-3',5'-GCGC-3', AND 5'-GGCC-3' SEQUENCES IN THE MINOR-GROOVE OF DNA BY 8-RING HAIRPIN POLYAMIDES

Eight-ring hairpin polyamides which differ only by the linear arrangem ent of pyrrole (Py) and imidazole (Im) amino acids were designed for r ecognition of six base pair DNA sequences containing four contiguous G ,C base pairs. The respective DNA binding properties of three polyamid es, ImImPyPy-gamma-ImImPyPy-beta-Dp, ImPyImPy-gamma-ImPyImPy-beta-Dp, and ImImImIm-gamma-PyPyPyPy-beta-Dp, were analyzed by footprinting and affinity cleavage on a DNA fragment containing the respective match s ites 5'-TGGCCA-3', 5'-TGCGCA-3', and 5'-TGGGGA-3'. Quantitative footpr int titrations demonstrate that ImImPyPy-gamma-ImImPyPy-beta-Dp binds the designed match site 5'-TGGCCA-3' with an equilibrium association c onstant of K-a = 1 x 10(10) M-1 and >250-fold specificity versus the m ismatch sequences, 5'-TGCGCA-3' and 5'-TGGGGA-3'. The polyamides ImPyI mPy-gamma-ImPyImPy-beta-Dp and ImImImIm-gamma-PyPyPyPy-beta-Dp recogni ze their respective 5'-TGCGCA-3' and 5'-TGGGGA-3' match sites with red uced affinity relative to ImImPyPy-gamma-ImImPyPy-beta-Dp, but again w ith high specificity with regard to mismatch sites. These results expa nd the DNA sequence repertoire targeted by pyrrole-imidazole polyamide s and identify sequence composition effects which will, guide further second-generation polyamide design for DNA recognition.