Alternative heterocycles for DNA recognition: an N-methylpyrazole/N-methylpyrrole pair specifies for Aradical dotT/Tradical dotA base pairs Original Research Article

Side-by-side pairs of three five-membered rings, N-methylpyrrole (Py), N-methylimidazole (Im), and N-methylhydroxypyrrole (Hp), have been demonstrated to distinguish each of the four Watson–Crick base pairs in the minor groove of DNA. However, not all DNA sequences targeted by these pairing rules achieve affinities and specificities comparable to DNA binding proteins. We have initiated a search for new heterocycles which can expand the sequence repetoire currently available. Two heterocyclic aromatic amino acids, N-methylpyrazole (Pz) and 4-methylthiazole (Th), were incorporated into a single position of an eight-ring polyamide of sequence ImImXPy-γ-ImPyPyPy-β-Dp to examine the modulation of affinity and specificity for DNA binding by a Pz/Py pair and/or a Th/Py pair. The X/Py pairings Pz/Py and Th/Py were evaluated by quantitative DNase I footprint titrations on a DNA fragment with the four sites 5′-TGGNCA-3′ (NT, A, G, C). The Pz/Py pair binds Tradical dotA and Aradical dotT with similar affinity to a Py/Py pair but with improved specificity, disfavoring both Gradical dotC and Cradical dotG by about 100-fold. The Th/Py pair binds poorly to all four Watson–Crick base pairs. These results demonstrate that in some instances new heterocyclic aromatic amino acid pairs can be incorporated into imidazole–pyrrole polyamides to mimic the DNA specificity of Py/Py pairs which may be relevant as biological criteria in animal studies become important.