Effects of the A.T/T.A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA

The affinity and binding orientation of the hairpin polyamide ImPyPy-gamma-PyPyPy-beta-Dp were measured for eight possible five base pair 5'-TG(A,T)(sub 3)-3' match sites to test the A.T/T.A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA. Findings indicated that the Py/Py pair is approximately degenerate for recognition of A,T base pairs, affording generality with regard to targeting sequences of mixed A.T/T.A composition.