Affinity and specificity of multiple hydroxypyrrole/pyrrole ring pairings for coded recognition of DNA

Abstract

Pairings rules have been developed to guide the design of synthetic polyamides for recognition of predetermined sequences in the minor groove of DNA. We recently reported that eight-ring hairpin-polyamides containing 3-hydroxypyrrole (Hp), imidazole (Im), and pyrrole (Py) amino acids form four-ring pairings (Im/Py, Py/Im, Hp/Py, and Py/Hp) which distinguish the four Watson-Crick base pairs in the minor groove of DNA. An Im/ Py pair distinguishes G·C from C·G and both of these from A· T/T·A base pairs. A Hp/Py specifies T·A from A·T, and both of these from G·C/C·G. The T·A selectivity of the Hp/Py pair likely arises from a combination of differential destabilization of polyamide binding via placement of Hp/Py opposite A·T or T·A, and specific hydrogen bonds between the 3-hydroxy and 4-carboxamido groups of Hp with the O2 of T (Figure 1). A general pairing rule would require the same discrimination to be observed for the recognition of multiple T·A base pairs within other sequence contexts, including A·T rich sequences. In the original report, we observed that a single Hp/Py pair replacing a Py/Py pair destabilizes an eight-ring hairpin polyamide by 5-fold for an identical match site. It remains to be determined whether consecutive Hp/Py ring pairings could target binding sites varying in their A·T base pair sequence composition without compromising polyamide affinity and sequence specificity. We report here that three consecutive Hp/Py pairs can be combined within a hairpin template to distinguish core sequence 5'-TTA-3' from 5'-TAT-3' in the DNA minor groove.